diff --git a/Lectures/Deadlines.tex b/Lectures/Deadlines.tex
index b2d3f0909bd14518562f1e35ce560a2cf8563eb5..0292422e9acd1a6b69f3ae48e251c058e8c43f27 100644
--- a/Lectures/Deadlines.tex
+++ b/Lectures/Deadlines.tex
@@ -82,7 +82,7 @@ Unit VnV/Implement & Week 12 & Week of Apr 3\\
% \ei
\item Drasil Project Present (25 min each)
\bi
-\item Mar 30: Karen, Sam, Jason
+\item \textbf{Mar 30: Karen, Sam, Jason}
\ei
\ei
diff --git a/Lectures/Figures/CodeCircleGlassBR.png b/Lectures/Figures/CodeCircleGlassBR.png
new file mode 100644
index 0000000000000000000000000000000000000000..ab9b792db0554c6edd24ea1fdde99bca4d679f96
Binary files /dev/null and b/Lectures/Figures/CodeCircleGlassBR.png differ
diff --git a/Lectures/Figures/DrasilInputs.pdf b/Lectures/Figures/DrasilInputs.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..8b5e34c9b5a3da39b4f4757d92b41ddcd9466752
Binary files /dev/null and b/Lectures/Figures/DrasilInputs.pdf differ
diff --git a/Lectures/Figures/DrasilSupportsChange.png b/Lectures/Figures/DrasilSupportsChange.png
new file mode 100644
index 0000000000000000000000000000000000000000..e485a86b0dc504bfbd6502a4e5e39cac334eb7af
Binary files /dev/null and b/Lectures/Figures/DrasilSupportsChange.png differ
diff --git a/Lectures/Figures/FoldersFiles.pdf b/Lectures/Figures/FoldersFiles.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..6d28857bd015ac3b969fb48395ab8c0277ebdf36
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diff --git a/Lectures/Figures/FoldersFilesCircleGlassBR.pdf b/Lectures/Figures/FoldersFilesCircleGlassBR.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..b41c334ff7e25ee8827bed034f217868fb56cd68
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diff --git a/Lectures/Figures/FrigFamily.pdf b/Lectures/Figures/FrigFamily.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..87a77278831787d3e7ede2f266905d7e76cf983d
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diff --git a/Lectures/Figures/GenAllThings.png b/Lectures/Figures/GenAllThings.png
new file mode 100644
index 0000000000000000000000000000000000000000..1244d10da588ad1a32793cb860ad070cf8336b9a
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diff --git a/Lectures/Figures/InputsCircleGlassBR.pdf b/Lectures/Figures/InputsCircleGlassBR.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..ba6b6f9759d74a3debb49916b9197749b5d3b69b
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diff --git a/Lectures/Figures/Launch.jpg b/Lectures/Figures/Launch.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..ed79e94ad67a88f3a8822808eabd7ae21fea0155
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diff --git a/Lectures/Figures/MakefileCircleGlassBR.pdf b/Lectures/Figures/MakefileCircleGlassBR.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..e283101d3abc856465f922327356941a1705af69
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diff --git a/Lectures/Figures/MobileAppFeatureModel.pdf b/Lectures/Figures/MobileAppFeatureModel.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..d1a203fb3dcd0d252a6cb2720e85bebbd7394162
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diff --git a/Lectures/Figures/READMECircleGlassBR.pdf b/Lectures/Figures/READMECircleGlassBR.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..4ec14989b577e516cbd17aecd7f8edf0617fbb4f
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diff --git a/Lectures/Figures/SRSCircleGlassBR.pdf b/Lectures/Figures/SRSCircleGlassBR.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..e6a4776c01c515e72238234968d5c3226b5e61f3
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diff --git a/Lectures/Figures/SackExample.png b/Lectures/Figures/SackExample.png
new file mode 100644
index 0000000000000000000000000000000000000000..667957cc45aa1d02fb1fa5abe485e5454cb9ffe4
Binary files /dev/null and b/Lectures/Figures/SackExample.png differ
diff --git a/Lectures/Figures/dblpendulum.png b/Lectures/Figures/dblpendulum.png
new file mode 100644
index 0000000000000000000000000000000000000000..d41868fe38fce6a16aa12d8f58a120c66c576e69
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diff --git a/Lectures/Figures/physicalsystimage.png b/Lectures/Figures/physicalsystimage.png
new file mode 100644
index 0000000000000000000000000000000000000000..736376bf7000da84c2be0ee1fda4c265ec3aff04
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diff --git a/Lectures/L16_MISContinued/MISContinued.tex b/Lectures/L16_MISContinued/MISContinued.tex
index 7f5bf035ce8f3b81f6769c46659c86d5ef34a5d4..929e6fb248494806bbda3c7d3d1a8660fb70eac4 100755
--- a/Lectures/L16_MISContinued/MISContinued.tex
+++ b/Lectures/L16_MISContinued/MISContinued.tex
@@ -1024,6 +1024,27 @@ where $a$, $b$ and $c$ are suitable constants
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}
+\frametitle{Implementing Your MIS}
+\begin{itemize}
+\item The mapping between the MIS and the code is generally not ``term'' by
+ ``term''
+\item You do not need to use the mathematical type listed in the spec
+\item Consider A2 (Allocation to Engineering Programs) for set types
+\begin{itemize}
+\item
+ \href{https://gitlab.cas.mcmaster.ca/smiths/se2aa4_cs2me3/-/blob/master/Assignments/PreviousYears/2019/A2/A2.pdf}
+ {Problem Description}
+\item
+ \href{https://gitlab.cas.mcmaster.ca/smiths/se2aa4_cs2me3/-/tree/master/Assignments/PreviousYears/2019/A2/A2Soln/src}
+ {Source Code}
+\end{itemize}
+
+\end{itemize}
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
\begin{frame}[allowframebreaks]
\frametitle{References}
diff --git a/Lectures/L20_ArtifactGen/ArtifactGen.pdf b/Lectures/L20_ArtifactGen/ArtifactGen.pdf
index 058a65088dbd37f5b6ceb3e908637c7eb7c5eaa8..5211638fd43d92284f587ce1018d4d8e7366f12d 100644
Binary files a/Lectures/L20_ArtifactGen/ArtifactGen.pdf and b/Lectures/L20_ArtifactGen/ArtifactGen.pdf differ
diff --git a/Lectures/L20_ArtifactGen/ArtifactGen.tex b/Lectures/L20_ArtifactGen/ArtifactGen.tex
index 93da7ca59e633a48eb496a6b8527a25af5447517..da0b6889d63078a1a9f29884d3c8a423b14f327a 100755
--- a/Lectures/L20_ArtifactGen/ArtifactGen.tex
+++ b/Lectures/L20_ArtifactGen/ArtifactGen.tex
@@ -1,5 +1,6 @@
%\documentclass[handout]{beamer}
-\documentclass[t,12pt,numbers,fleqn]{beamer}
+%\documentclass[t,12pt,numbers,fleqn]{beamer}
+\documentclass{beamer}
%\documentclass[ignorenonframetext]{beamer}
\newif\ifquestions
@@ -59,8 +60,8 @@
\frametitle{Artifact Generation}
\bi
-\item Start recording
\item Administrative details
+\item Finish Assurance Case review
%\item Next week's presentations
%\item Feedback on VnV
%\item Questions about MG/MIS?
@@ -71,128 +72,16 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\begin{frame}
-\frametitle{Administrative Details}
-
-\bi
-\item Upcoming classes
-\bi
-\item L20 - Artifact Generation (Today)
-\item L21 - Drasil Demos
-\item L22 -- L24 - Implementation and testing presentations
-\ei
-\ei
-
-\end{frame}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\begin{frame}
-\frametitle{Administrative Details}
-
-\bi
-\item For final documentation, make sure you have \textbf{addressed and closed}
- all open issues
-\item MIS marking scheme on Avenue
-% \bi
-% \item On Avenue
-% \item Not all of the spec has to be formal
-% \item First steps
-% \bi
-% \item Syntax of access programs
-% \item State variables?
-% \item Environment variables?
-% \ei
-% \ei
-\item Course evaluation
-\bi
-\item Wed, Nov 25, 10:00 am to Wed, Dec 9, 11:59 pm
-\item \url{https://evals.mcmaster.ca}
-\ei
-\item MG/MIS Reviews
-\bi
-\item Assign issues to your domain expert and secondary reviewer
-\item Due two days after assignment (but we can be flexible on this)
-\ei
-\item Further Deliverable Reviews
-\bi
-\item Not part of marking scheme for course
-\item Encouraged to do anyway, maybe as a quid pro quo?
-\ei
-
-\ei
-
-\end{frame}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\begin{frame}
-\frametitle{Administrative Details: Report Deadlines}
-~\newline
-\begin{tabular}{l l}
-%\textbf{SRS} & Oct 8\\
-\textbf{MG + MIS (Traditional)} & Nov 23\\
-\textbf{Drasil Code and Report (Drasil)} & Nov 23\\
-Final Documentation & Dec 9\\
-\end {tabular}
-
-\bi
-\item The written deliverables will be graded based on the repo contents as of
-11:59 pm of the due date
-\item If you need an extension for a written deliverable, please ask
-\item You should inform your primary and secondary reviewers of the extension
-\item Two days after each major deliverable, your GitHub issues will be due
-%\item Domain expert code due 1 week after MIS deadline
-\ei
-
-\end{frame}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\begin{frame}
-\frametitle{Admin Details: Presentation Schedule}
-
-\bi
-\item Drasil Project Present (20 min each)
-\bi
-\item Thurs, Nov 26: Andrea, Naveen, Ting-Yu
-\ei
-\item Test or Impl.\ Present (15 min each)
-\bi
-\item Mon, Nov 30: John, Salah, Liz, Xingzhi, Leila
-\item Thurs, Dec 3: Shayan, Naveen, Sid, Gaby, Seyed
-\item Mon, Dec 7: Ting-Yu, Xuanming, Mohamed, Andrea, Tiago
-\ei
-\item 4 presentations each
-\item If you will miss a presentation, please trade with someone else
-\ei
-
-\end{frame}
+\input{../Deadlines.tex}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}
-\frametitle{Implementation and Testing Presentations}
-
-You can present anything related to implementation or testing
-\bi
-\item Show off your code, or as much of it as you have completed
-\item Unit VnV Plan
-\item Test case report
-\item Verification/validation activities
-\item Demonstrate technology
-\bi
-\item Continuous integration
-\item Valgrind
-\item Doxygen for API documentation
-\item Etc.
-\ei
-\item Drasil presentations - emphasize testing
-\item Fine to show work in progress
-\item Good to ask the audience for advice, feedback
-\item Other ideas are likely fine
-\ei
-
+\frametitle{Course Evaluations}
+\begin{itemize}
+\item Course experience surveys will close on Wednesday, April 12, 2023 11:59 PM
+\item \url{https://mcmaster.bluera.com/mcmaster/}
+\end{itemize}
\end{frame}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -201,9 +90,10 @@ You can present anything related to implementation or testing
\frametitle{Questions?}
\begin{itemize}
\item Questions on administrative details?
-\item Questions about Module Guide?
-\item Questions about upcoming presentation?
-\item Questions about MIS?
+\item Questions on final documentation?
+\item Questions on reflection document?
+\item Questions on final implementation?
+\item Questions on VnV report?
\item Other questions?
\end{itemize}
\end{frame}
@@ -249,25 +139,200 @@ You can present anything related to implementation or testing
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}
-\frametitle{Implementing Your MIS}
-\begin{itemize}
-\item The mapping between the MIS and the code is generally not ``term'' by
- ``term''
-\item You do not need to use the mathematical type listed in the spec
-\item Consider A2 (Allocation to Engineering Programs) for set types
-\begin{itemize}
-\item
- \href{https://gitlab.cas.mcmaster.ca/smiths/se2aa4_cs2me3/-/blob/master/Assignments/PreviousYears/2019/A2/A2.pdf}
- {Problem Description}
-\item
- \href{https://gitlab.cas.mcmaster.ca/smiths/se2aa4_cs2me3/-/tree/master/Assignments/PreviousYears/2019/A2/A2Soln/src}
- {Source Code}
-\end{itemize}
+\frametitle{Assurance Cases in Scientific Computing \cite{SmithEtAl2020,SmithEtAl2018_ICSEPoster}}
+
+\bi
+\item Assurance cases
+\bi
+\item Organized and explicit argument for correctness
+\item Successfully used for safety critical systems
+\ei
+\item Advantages for SC
+\bi
+\item Engaging domain experts
+\item Producing necessary and relevant documentation
+\item Evidence that can be verified/replicated by a third party
+\ei
+\item Example of 3dfim+
+\bi
+\item No errors found
+\item However
+\bi
+\item Documentation ambiguities
+\item No warning about parametric statistical model
+\ei
+\ei
+\ei
-\end{itemize}
\end{frame}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{frame}
+\frametitle{Assurance Cases in SC Motivation}
+
+\bi
+\item Do we put too much trust in the quality of SCS?
+\item Are enough checks and balances in place, especially for safety related
+ software?
+\item Problems with imposing external requirements for certification
+\bi
+\item External body does not have expertise
+\item SCS developers dislike documentation
+\ei
+\item Solution -- Assurance Cases by experts
+\bi
+\item Experts engaged
+\item Relevant documentation
+\ei
+\item Current techniques of development and testing still used, but arguments
+ will no longer be ad hoc and incompletely documented
+\ei
+
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.45in
+\begin{frame}[plain]
+%\frametitle{Goal Structuring Notation}
+
+\includegraphics[width=1.19\textwidth]{../Figures/assuranceBasic.pdf}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.2in
+\begin{frame}[plain]
+%\frametitle{3dfim+ Software}
+
+\includegraphics[width=0.8\textwidth]{../Figures/AFNI_screenshot.PNG}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.2in
+\begin{frame}[plain]
+%\frametitle{Correlation of One Voxel}
+
+\includegraphics[width=1.\textwidth]{../Figures/scaledvoxelANDIdealsignalVStime_least.png}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.2in
+\begin{frame}[plain]
+%\frametitle{Context and Assumption in Top Goal}
+
+\includegraphics[width=0.95\textwidth]{../Figures/TopAC.pdf}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.27in
+\begin{frame}[plain]
+%\frametitle{Top Goal}
+
+\includegraphics[width=1.15\textwidth]{../Figures/TopGoal.pdf}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.2in
+\begin{frame}[plain]
+%\frametitle{GR Decomposition}
+
+\includegraphics[width=0.95\textwidth]{../Figures/GRTop.pdf}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.21in
+\begin{frame}[plain]
+%\frametitle{Modifiability of Documentation Requirements}
+
+\includegraphics[width=1.14\textwidth]{../Figures/Modifiable.pdf}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.3in
+\begin{frame}[plain]
+%\frametitle{Generic Evidence}
+
+\includegraphics[width=1.15\textwidth]{../Figures/Generic.pdf}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hoffset=-.2in
+\begin{frame}[plain]
+%\frametitle{Defined Operational Assumptions}
+
+\includegraphics[width=0.75\textwidth]{../Figures/GSN_GA.pdf}
+
+\end{frame}
+\hoffset=0in
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{frame}
+\frametitle{Proposed Changes to 3dfim+}
+
+\bi
+\item No mistakes found in calculations
+\item Goal of original software was not certification
+\item Problems found
+\bi
+\item GR goal not satisfied
+\bi
+\item Not complete, verifiable, modifiable or traceable
+\item Coordinate system information missing
+\item Ambiguous rank function
+\ei
+\item Inputs not checked in code
+\item User not informed of their responsibility to use tool with correct
+ statistical model
+\ei
+\ei
+
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{frame}
+\frametitle{Concluding Remarks}
+
+\bi
+\item Hopefully motivated assurance cases for SC
+\item Quality is improved by looking at a problem from different perspectives,
+ assurance cases provide a systematic and rigorous way to introduce a new
+ perspective
+\item An assurance cases will likely use the same documentation and ideas used
+ in CAS 741
+\item However, an assurance case can focus and direct efforts right from the
+ start of the project
+\ei
+
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}
@@ -346,6 +411,35 @@ You can present anything related to implementation or testing
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}[plain, fragile]
+
+\frametitle{Product Lines in User Manual}
+
+\includegraphics[width=0.95\textwidth]{../figures/FrigFamily.pdf}
+
+% common to see all products in the same manual
+% online version for different languages, but not for different products
+% may vary due to product improvements (not integrated)
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{frame}[plain, fragile]
+
+%\frametitle{Model-Based Product Line}
+
+\includegraphics[width=0.8\textwidth]{../figures/MobileAppFeatureModel.pdf}
+
+\cite{UsmanEtAl2017}
+
+% how program family concept is realized
+% tools to support product line approach
+% systematic way to handle variabilities
+% generate code for family members
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
%\hoffset=-.8in
\begin{frame}[plain, fragile]
@@ -414,6 +508,159 @@ You can present anything related to implementation or testing
\end{frame}
\hoffset=0in
+\begin{frame}
+
+\frametitle{Build on Success of MDSE}
+
+\begin{itemize}
+ \item Codify (capture) code and non-code info together
+ \begin{itemize}
+ \item Natural language (text)
+ \item Definitions
+ \item Assumptions
+ \item Rationale, Derivations
+ \item Abstract theory
+ %\item User characteristics
+ %\item Nonfunctional Requirements
+ \item Etc.
+ \end{itemize}
+\item Generate all artifacts from one framework
+\begin{itemize}
+ \item Requirements
+ \item User manuals
+ %\item README
+ \item Build scripts, dev environment (CI etc)
+ \item Assurance case
+ \item Code (in different languages)
+ \item Test cases
+ \item etc.
+\end{itemize}
+\end{itemize}
+
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\hoffset=-.4in
+\begin{frame}[plain, fragile]
+
+%\frametitle{Generate All Things}
+
+\includegraphics[width=1.0\textwidth]{../figures/GenAllThings.png}
+
+\end{frame}
+%\hoffset=0in
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\hoffset=-.4in
+\begin{frame}[plain, fragile]
+
+%\frametitle{Family of Mechanics Programs - why gen all things?} % physics shows
+%different assumptions, different information, diff coord syst., diff symbols,
+%leads to a family of different physical models
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=4cm,yshift=2.5cm] at (current page.center)
+{
+\includegraphics[width=.5\textwidth]{../figures/dblpendulum.png}
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=4.5cm,yshift=-0.2cm] at (current page.center)
+{
+\includegraphics[width=.45\textwidth]{../figures/Launch.jpg}
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=2.5cm,yshift=2cm] at (current page.center)
+{
+\includegraphics[width=.3\textwidth]{../figures/SackExample.png}
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=4cm,yshift=-2.5cm] at (current page.center)
+{
+\includegraphics[width=.4\textwidth]{../figures/ForceDiagram.png}
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=-3.0cm,yshift=3.5cm] at (current page.center)
+{
+$\mathbf{a} = \frac{d\mathbf{v}}{dt}$ and $\mathbf{v} = \frac{d\mathbf{p}}{dt}$
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=-3.0cm,yshift=2.7cm] at (current page.center)
+{
+$\mathbf{F} = m \mathbf{a}$
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=-3.0cm,yshift=1.9cm] at (current page.center)
+{
+$m \frac{d\mathbf{v}}{dt} = m \mathbf{g} - c\mathbf{v}$
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=-2.5cm,yshift=1.1cm] at (current page.center)
+{
+$g = 9.8 m/s^2$ or $g = 32.2 ft/s^2$
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=-2.0cm,yshift=0.3cm] at (current page.center)
+{
+$y_{n+1} = y_n + \frac{1}{6} ( k_1 + 2 k_2 + 2 k_3 + k_4) h$
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=-3.0cm,yshift=-0.5cm] at (current page.center)
+{
+$\sigma_{ij} = D_{ijkl} \epsilon_{kl}$
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=-3.0cm,yshift=-1.3cm] at (current page.center)
+{
+coordinate system
+};
+\end{tikzpicture}
+
+\begin{tikzpicture}[remember picture,overlay]
+\node [xshift=1.0cm,yshift=-0.8cm] at (current page.center)
+{
+\Huge $\Longrightarrow$
+};
+\end{tikzpicture}
+
+% knowns and unknowns?
+% beam equation
+% well understood
+% practical approach - can build incrementally, don't need all theory to start
+% - can assume knowledge (theories) from the consumer of the documentation, like addition, % differentiation etc.
+% hit on these points while presenting pictures
+% \begin{itemize}
+% \item Different views of the same knowledge
+% \item Generate the view needed by the audience
+% \item Change to different natural languages
+% \item Stay abstract longer
+% \item Certification
+% \item Documentation improve productivity, sustainability
+% \item Reusability
+% \item Modifiability
+% \item One source helps synchronization
+% \end{itemize}
+
+\end{frame}
+\hoffset=0in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\section[Motivation]{Motivation}
@@ -740,160 +987,254 @@ You can present anything related to implementation or testing
\begin{frame}
+\frametitle{GlassBR}
+
+\begin{columns}
+\begin{column}{0.5\textwidth}
+\includegraphics[width=1.0\textwidth]{../figures/physicalsystimage.png}
+\end{column}
+\begin{column}{0.4\textwidth}
+Given
+
+\begin{itemize}
+\item dimensions of glass plane
+\item glass type
+\item explosion characteristics
+\item tolerable breakage probability
+\end{itemize}
+
+Predict whether the glass will withstand the explosion
+
+\end{column}
+\end{columns}
+
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{frame}
+
+%\frametitle{Input Knowledge}
+
+\includegraphics[width=0.95\textwidth]{../figures/DrasilInputs.pdf}
+
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{frame}
+
+%\frametitle{Input Knowledge}
+
+\includegraphics[width=0.95\textwidth]{../figures/InputsCircleGlassBR.pdf}
+
+\end{frame}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\hoffset=-.4in
+\begin{frame}[plain, fragile]
+
+%\frametitle{Input Knowledge}
+
+\includegraphics[width=1.05\textwidth]{../figures/FoldersFiles.pdf}
+
+\end{frame}
+%\hoffset=0in
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\hoffset=-.4in
+\begin{frame}[plain, fragile]
+
+%\frametitle{Input Knowledge}
+
+\includegraphics[width=1.05\textwidth]{../figures/FoldersFilesCircleGlassBR.pdf}
+
+\end{frame}
+%\hoffset=0in
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\hoffset=-.4in
+\begin{frame}[plain, fragile]
+
+%\frametitle{Input Knowledge}
+
+\includegraphics[width=1.02\textwidth]{../figures/SRSCircleGlassBR.pdf}
+
+\end{frame}
+%\hoffset=0in
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\hoffset=-.4in
+\begin{frame}[plain, fragile]
+
+%\frametitle{Input Knowledge}
+
+\includegraphics[width=1.05\textwidth]{../figures/READMECircleGlassBR.pdf}
+
+\end{frame}
+%\hoffset=0in
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\hoffset=-.4in
+\begin{frame}[plain, fragile]
+
+%\frametitle{Input Knowledge}
+
+\includegraphics[width=1.05\textwidth]{../figures/MakefileCircleGlassBR.pdf}
+
+\end{frame}
+%\hoffset=0in
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\hoffset=-.4in
+\begin{frame}[plain, fragile]
+
+%\frametitle{Input Knowledge}
+
+\includegraphics[width=1.05\textwidth]{../figures/CodeCircleGlassBR.png}
+
+\end{frame}
+%\hoffset=0in
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{frame}
+
\frametitle{$J_{\mbox{tol}}$ in SRS.pdf}
\begin{center}
-\includegraphics[width=1.0\textwidth]{../Figures/Jtol_pdf.pdf}
+\includegraphics[width=0.9\textwidth]{../figures/Jtol_pdf.pdf}
\end{center}
\end{frame}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+%\hoffset=-.3in
\begin{frame}[plain, fragile]
\frametitle{$J_{\mbox{tol}}$ in SRS.tex}
~\\
\begin{lstlisting}
-\noindent \begin{minipage}{\textwidth}
-\begin{tabular}{p{0.2\textwidth} p{0.73\textwidth}}
-\toprule \textbf{Refname} & \textbf{DD:sdf.tol}
-\phantomsection
-\label{DD:sdf.tol}
+...
+Label & Stress distribution factor (Function) based on Pbtol
+
\\ \midrule \\
-Label & $J_{tol}$
+Symbol & ${J_{\text{tol}}}$
+
\\ \midrule \\
-Units &
+Units & Unitless
+
\\ \midrule \\
-Equation & $J_{tol}$ =
- $\log\left(\log\left(\frac{1}{1-P_{btol}}\right)\frac{\left(\frac{a}{1000}\frac{b}{1000}\right)^{m-1}}{k\left(\left(E*1000\right)\left(\frac{h}{1000}\right)^{2}\right)^{m}*LDF}\right)$
+Equation & \begin{displaymath}
+ {J_{\text{tol}}}=\ln\left(\ln\left(\frac{1}{1-{P_{\text{b}\text{tol}}}}\right) \frac{\left(\frac{a}{1000} \frac{b}{1000}\right)^{m-1}}{k \left(E\cdot{}1000 \left(\frac{h}{1000}\right)^{2}\right)^{m} LDF}\right)
+ \end{displaymath}
\\ \midrule \\
-Description & $J_{tol}$ is the stress distribution factor (Function) based on
- Pbtol\newline$P_{btol}$ is the tolerable probability of breakage ...
-\end{minipage}\\
+Description & ...
\end{lstlisting}
\end{frame}
-
+%\hoffset=0in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+%\hoffset=-.3in
\begin{frame}[plain, fragile]
\frametitle{$J_{\mbox{tol}}$ in SRS.html}
\begin{lstlisting}
-<a id="">
-<div class="equation">
-<em>J<sub>tol</sub></em> = log(log(<div class="fraction">
-<span class="fup">
-1
-</span>
-<span class="fdn">
-1 − <em>P<sub>btol</sub></em>
-</span>
-</div>)<div class="fraction">
-<span class="fup">
-(<div class="fraction">
-<span class="fup">
-<em>a</em>
-</span>
-<span class="fdn">
-1000
-</span>
-</div><div class="fraction">
+...
+<th>Equation</th>
+<td>
+\[{J_{\text{tol}}}=\ln\left(\ln\left(\frac{1}{1-{P_{\text{b}\text{tol}}}}\right) \frac{\left(\frac{a}{1000} \frac{b}{1000}\right)^{m-1}}{k \left(E\cdot{}1000 \left(\frac{h}{1000}\right)^{2}\right)^{m} LDF}\right)\]
+</td>
...
\end{lstlisting}
\end{frame}
+%\hoffset=0in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+%\hoffset=-.3in
\begin{frame}[plain, fragile]
\frametitle{$J_{\mbox{tol}}$ in Python}
\begin{lstlisting}
-def calc_j_tol(inparams):
- j_tol = math.log((math.log(1.0 / (1.0 - inparams.pbtol))) * ((((inparams.a / 1000.0) * (inparams.b / 1000.0)) ** (inparams.m - 1.0)) / ((inparams.k * (((inparams.E * 1000.0) * ((inparams.h / 1000.0) ** 2.0)) ** inparams.m)) * inparams.ldf)))
- return j_tol
+## \brief Calculates stress distribution factor (Function) based on Pbtol
+# \param inParams structure holding the input values
+# \return stress distribution factor (Function) based on Pbtol
+def func_J_tol(inParams):
+ outfile = open("log.txt", "a")
+ print("function func_J_tol called with inputs: {", file=outfile)
+ print(" inParams = ", end="", file=outfile)
+ print("Instance of InputParameters object", file=outfile)
+ print(" }", file=outfile)
+ outfile.close()
+
+ return math.log(math.log(1.0 / (1.0 - inParams.P_btol)) * ((inParams.a / 1000.0 * (inParams.b / 1000.0)) ** (7.0 - 1.0) / (2.86e-53 * (7.17e10 * 1000.0 * (inParams.h / 1000.0) ** 2.0) ** 7.0 * inParams.LDF)))
\end{lstlisting}
\end{frame}
-
+%\hoffset=0in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+%\hoffset=-.3in
\begin{frame}[plain, fragile]
\frametitle{$J_{\mbox{tol}}$ in Java}
\begin{lstlisting}
-public static double calc_j_tol(InputParameters inparams) {
- double j_tol = Math.log((Math.log(1.0 / (1.0 - inparams.pbtol))) * ((Math.pow((inparams.a / 1000.0) * (inparams.b / 1000.0), inparams.m - 1.0)) / ((inparams.k * (Math.pow((inparams.E * 1000.0) * (Math.pow(inparams.h / 1000.0, 2.0)), inparams.m))) * inparams.ldf)));
- return j_tol;
+ /** \brief Calculates stress distribution factor (Function) based on Pbtol
+ \param inParams structure holding the input values
+ \return stress distribution factor (Function) based on Pbtol
+ */
+ public static double func_J_tol(InputParameters inParams) throws IOException {
+ PrintWriter outfile;
+ outfile = new PrintWriter(new FileWriter(new File("log.txt"), true));
+ ...
+ return Math.log(Math.log(1.0 / (1.0 - inParams.P_btol)) * (Math.pow(inParams.a / 1000.0 * (inParams.b / 1000.0), 7.0 - 1.0) / (2.86e-53 * Math.pow(7.17e10 * 1000.0 * Math.pow(inParams.h / 1000.0, 2.0), 7.0) * inParams.LDF)));
}
\end{lstlisting}
\end{frame}
-
+%\hoffset=0in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+%\hoffset=-.3in
\begin{frame}[plain, fragile]
\frametitle{$J_{\mbox{tol}}$ in Drasil (Haskell)}
\begin{lstlisting}
-stressDistFac = makeVC "stressDistFac" (nounPhraseSP
- $ "stress distribution" ++ " factor (Function)") cJ
-sdf_tol = makeVC "sdf_tol" (nounPhraseSP $
- "stress distribution" ++
- " factor (Function) based on Pbtol")
- (sub (eqSymb stressDistFac) (Atomic "tol"))
-
-tolStrDisFac_eq :: Expr
-tolStrDisFac_eq = log (log ((1)/((1) - (C pb_tol)))
- * ((Grouping (((C plate_len) / (1000)) * ((C
- plate_width) / (1000))) :^
- ((C sflawParamM) - (1)) / ((C sflawParamK) *
- (Grouping (Grouping ((C mod_elas * 1000) *
- (square (Grouping ((C act_thick) / (1000)))))) :^
- (C sflawParamM) * (C lDurFac))))))
-tolStrDisFac :: QDefinition
-tolStrDisFac = mkDataDef' sdf_tol tolStrDisFac_eq
- (aGrtrThanB +:+ hRef +:+ ldfRef +:+ pbTolUsr)
+
+tolStrDisFacEq :: Expr
+tolStrDisFacEq = ln (ln (recip_ (exactDbl 1 $- sy pbTol))
+ `mulRe` (((sy plateLen $/ exactDbl 1000) `mulRe` (sy plateWidth $/ exactDbl 1000)) $^ (sy sflawParamM $- exactDbl 1) $/
+ (sy sflawParamK `mulRe` ((sy modElas `mulRe` exactDbl 1000 `mulRe`
+ square (sy minThick $/ exactDbl 1000)) $^ sy sflawParamM) `mulRe` sy lDurFac)))
+
\end{lstlisting}
\end{frame}
-
+%\hoffset=0in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+%\hoffset=-.3in
\begin{frame}[plain, fragile]
\frametitle{$J_{\mbox{tol}}$ without Unit Conversion}
\begin{lstlisting}
-tolStrDisFac_eq :: Expr
-tolStrDisFac_eq = log (log ((1)/((1) - (C pb_tol)))
- * ((Grouping ((C plate_len) * (C plate_width)) :^
- ((C sflawParamM) - (1)) / ((C sflawParamK) *
- (Grouping (Grouping ((C mod_elas * 1000) *
- (square (Grouping (C act_thick))))) :^
- (C sflawParamM) * (C lDurFac))))))
+tolStrDisFacEq :: Expr
+tolStrDisFacEq = ln (ln (recip_ (exactDbl 1 $- sy pbTol))
+ `mulRe` ((sy plateLen `mulRe` sy plateWidth) $^ (sy sflawParamM $- exactDbl 1) $/
+ (sy sflawParamK `mulRe` ((sy modElas `mulRe`
+ square (sy minThick)) $^ sy sflawParamM) `mulRe` sy lDurFac)))
\end{lstlisting}
\end{frame}
-
+%\hoffset=0in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\subsection[SRS]{SRS}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{frame}
-% \hoffset=-.4in %removing side bar for these frames
+%\frametitle{Input Knowledge}
-% \begin{frame}[plain, fragile]
+\includegraphics[width=0.95\textwidth]{../figures/DrasilInputs.pdf}
-% %\frametitle{SRS for SWHS}
+\end{frame}
-% \begin{center}
-% \includegraphics[scale=0.45]{../Figures/TofC.pdf}
-% \end{center}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\hoffset=-0.4in
+\begin{frame}[plain, fragile]
-% \end{frame}
-% \hoffset=0in
+\includegraphics[width=1.08\textwidth]{../figures/DrasilSupportsChange.png}
+\end{frame}
+\hoffset=0in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\hoffset=-.7in %removing side bar for these frames
@@ -1100,13 +1441,13 @@ R_1^{\mathrm{code}} &= \frac{f}{8\pi k_{\mathrm{AV}}} + \frac{1}{2\pi r_f h_g} \
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\hoffset=-.7in %removing side bar for these frames
-\begin{frame}[plain]
+% \begin{frame}[plain]
-\frametitle{Future Work}
+% \frametitle{Future Work}
-\includegraphics[width=1.\textwidth]{../Figures/ASTM_F2248-09.png}
+% \includegraphics[width=1.\textwidth]{../Figures/ASTM_F2248-09.png}
-\end{frame}
+% \end{frame}
%\hoffset=0in %reset side bar for these frames
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/ReferenceMaterial/References.bib b/ReferenceMaterial/References.bib
index 097cfc1b82bc6d4f1e47d904ccdc298adefbdf07..088ce514e3b689209919c2f5357e05fa9bd0094a 100644
--- a/ReferenceMaterial/References.bib
+++ b/ReferenceMaterial/References.bib
@@ -1,13 +1,26 @@
%% This BibTeX bibliography file was created using BibDesk.
%% https://bibdesk.sourceforge.io/
-%% Created for Spencer Smith at 2022-11-04 16:21:56 -0400
+%% Created for Spencer Smith at 2023-03-23 10:22:24 -0400
%% Saved with string encoding Unicode (UTF-8)
+@article{UsmanEtAl2017,
+ author = {Usman, Muhammad and Iqbal, Muhammad Zohaib and Khan, Muhammad Uzair},
+ date-added = {2023-03-23 10:22:22 -0400},
+ date-modified = {2023-03-23 10:22:22 -0400},
+ doi = {10.1016/j.jss.2016.09.049},
+ journal = {Journal of Systems and Software},
+ month = {01},
+ pages = {1-32},
+ title = {A Product-line Model-driven Engineering Approach for Generating Feature-based Mobile Applications},
+ volume = {123},
+ year = {2017},
+ bdsk-url-1 = {https://doi.org/10.1016/j.jss.2016.09.049}}
+
@inproceedings{Robillard2021,
abstract = {When contributors to a software project leave, the knowledge they hold may become lost, thus impacting code quality and team productivity. Although well-known strategies can be used to mitigate knowledge loss, these strategies have to be tailored to their target context to be effective. To help software development organizations mitigate turnover-induced knowledge loss, we sought to better understand the different contexts in which developers experience this knowledge loss, and the resulting implications. We conducted qualitative interviews with 27 professional developers and managers from three different companies that provide software products and services. Leveraging the experience of these practitioners, we contribute a framework for characterizing turnover-induced knowledge loss and descriptions of the implications of knowledge loss, synthesized into 20 observations. These observations about knowledge loss in practice are organized into four themes, validated by the participants, and discussed within the context of the research literature in software engineering.},
address = {New York, NY, USA},
@@ -35,7 +48,7 @@
pages = {1--8},
title = {Generating Software for Well-Understood Domains},
year = {Submitted 2022},
- bdsk-file-1 = {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}}
+ bdsk-file-1 = {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}}
@inproceedings{CaretteEtAl2022,
author = {Jacques Carette and Spencer Smith and Jason Balaci},
@@ -66,7 +79,7 @@
title = {Program 3dfim+},
url = {https://afni.nimh.nih.gov/afni/doc/manual/3dfim+.pdf},
year = {2000},
- bdsk-file-1 = {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},
+ bdsk-file-1 = {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},
bdsk-url-1 = {https://afni.nimh.nih.gov/afni/doc/manual/3dfim+.pdf}}
@article{Fagan1976,
@@ -80,7 +93,7 @@
title = {Design and code inspections to reduce errors in program development},
volume = {15},
year = {1976},
- bdsk-file-1 = {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},
+ bdsk-file-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxAXLi4vLi4vcHViL0ZhZ2FuMTk3Ni5wZGZPEQE+AAAAAAE+AAIAAAxNYWNpbnRvc2ggSEQAAAAAAAAAAAAAAAAAAAAAAAAAQkQAAf////8NRmFnYW4xOTc2LnBkZgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/////wAAAAAAAAAAAAAAAAACAAIAAAogY3UAAAAAAAAAAAAAAAAAA3B1YgAAAgAmLzpVc2VyczpzbWl0aHM6UmVwb3M6cHViOkZhZ2FuMTk3Ni5wZGYADgAcAA0ARgBhAGcAYQBuADEAOQA3ADYALgBwAGQAZgAPABoADABNAGEAYwBpAG4AdABvAHMAaAAgAEgARAASACRVc2Vycy9zbWl0aHMvUmVwb3MvcHViL0ZhZ2FuMTk3Ni5wZGYAEwABLwAAFQACAA3//wAAAAgADQAaACQAPgAAAAAAAAIBAAAAAAAAAAUAAAAAAAAAAAAAAAAAAAGA},
bdsk-url-1 = {https://doi.org/10.1147/sj.153.0182}}
@inproceedings{RigbyAndBird2013,
@@ -173,7 +186,7 @@
title = {Paradigms of Concurrency: Observations, Behaviours, and Systems -- a Petri Net View},
volume = {1020},
year = {2022},
- bdsk-file-1 = {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}}
+ bdsk-file-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxAkLi4vLi4vcHViL1BhcmFkaWdtc09mQ29uY3VycmVuY3kucGRmTxEBdAAAAAABdAACAAAMTWFjaW50b3NoIEhEAAAAAAAAAAAAAAAAAAAAAAAAAEJEAAH/////GlBhcmFkaWdtc09mQ29uY3VycmVuY3kucGRmAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAP////8AAAAAAAAAAAAAAAAAAgACAAAKIGN1AAAAAAAAAAAAAAAAAANwdWIAAAIAMy86VXNlcnM6c21pdGhzOlJlcG9zOnB1YjpQYXJhZGlnbXNPZkNvbmN1cnJlbmN5LnBkZgAADgA2ABoAUABhAHIAYQBkAGkAZwBtAHMATwBmAEMAbwBuAGMAdQByAHIAZQBuAGMAeQAuAHAAZABmAA8AGgAMAE0AYQBjAGkAbgB0AG8AcwBoACAASABEABIAMVVzZXJzL3NtaXRocy9SZXBvcy9wdWIvUGFyYWRpZ21zT2ZDb25jdXJyZW5jeS5wZGYAABMAAS8AABUAAgAN//8AAAAIAA0AGgAkAEsAAAAAAAACAQAAAAAAAAAFAAAAAAAAAAAAAAAAAAABww==}}
@inproceedings{SmithAndCarette2022_Grenoble,
address = {Hamilton, Ontario, Canada},
@@ -183,7 +196,7 @@
date-modified = {2022-07-19 16:37:53 -0400},
title = {Combining Literate Programming and Code Generation to Improve the Reproducibility and Sustainability of Scientific Computing Software},
year = {June 2022},
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@inproceedings{SmithAndCarette2022_CRSC,
address = {Montr\'eal},
@@ -193,7 +206,7 @@
date-modified = {2022-07-19 16:37:53 -0400},
title = {A Holistic Approach to Pain Relief for Research Software Developers},
year = {May 2022},
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@article{SmithEtAl2022,
author = {Spencer Smith and Peter Michalski and Jacques Carette and Zahra Keshavarz-Motamed},
@@ -289,7 +302,7 @@
date-modified = {2022-06-14 22:39:10 -0400},
title = {Referential Semantics: Briding Between Representations of Mathematical/Technical Documents and Knowledge},
year = {2021},
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@misc{BernholdtEtAl2022,
annote = {- notes on the draft brochure for the SSSDU workshop summary, to help with adding my notes to the PRDs (Priority Research Directions) and Theme documents.
@@ -629,7 +642,7 @@ deployment pipelines.},
pages = {1--14},
title = {Digging Deeper Into the State of the Practice for Domain Specific Research Software},
year = {2022},
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@inproceedings{KumarEtAl2022,
@@ -1311,7 +1324,7 @@ Tip 12: Design for contribution.
volume = {15},
year = {2022},
year1 = {2022},
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bdsk-url-1 = {https://doi.org/10.1016/j.jcmg.2021.09.023}}
@inproceedings{UditAndKatz2017,
@@ -1783,7 +1796,7 @@ non-trivial scientific applications.''},
title = {A Survey of the State of the Practice for Research Software in the United States},
year = {2022},
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bdsk-url-1 = {https://peerj.com/articles/cs-963/},
bdsk-url-2 = {https://doi.org/10.7717/peerj-cs.963}}
@@ -2052,7 +2065,7 @@ Results Discussion
note = {35 pp},
title = {Methodology for Assessing the State of the Practice for Domain {X}},
year = {2021},
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bdsk-url-1 = {https://arxiv.org/abs/2110.11575}}
@article{SadeghiEtAl2020,
@@ -2083,7 +2096,7 @@ Results Discussion
organization = {In conjunction with ICSE 2022},
title = {When Capturing Knowledge Improves Productivity},
year = {Rejected 2021},
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@mastersthesis{Michalski2021,
address = {Hamilton, Ontario, Canada},
@@ -2094,7 +2107,7 @@ Results Discussion
school = {McMaster University},
title = {State of The Practice for Lattice Boltzmann Method Software},
year = {2021},
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@mastersthesis{Dong2021,
address = {Hamilton, ON, Canada},
@@ -2105,7 +2118,7 @@ Results Discussion
school = {McMaster University},
title = {Assessing the State of the Practice for Medical Imaging Software},
year = {2021},
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@article{DouviEtAl2021,
abstract = {In this work, technologies related to the storage of solar energy, utilizing the latent heat content of phase change materials for the production of domestic hot water are reviewed. Many researchers have been involved in this field in order to accomplish the targets of environmentally friendly solutions and higher efficiency. For domestic use, materials with melting temperature between 40 and 80 $\,^{\circ}$C are commonly studied, with paraffins, fatty acids, salt hydrates and alcohols being the most popular. For harvesting the solar radiation, usually flat plate or evacuated tubes solar collectors are used, either commercial ones or modified. The storage unit may include only phase change material or it can have a hybrid form combined with water. The outcome of the most studies, is that the addition of phase change materials in comparison to systems without latent storage, increases the duration of heat release towards the domestic water at the end of the day and also increases the solar collector's efficiency because it does not experience large temperature fluctuations. However, difficulties emerge during the selection of the appropriate storage material as this must have a high melting temperature in order to provide hot enough domestic water, but not higher than the temperature that the solar collector can produce, in order to fully melt the material. Moreover, investigation is necessary for the selection of the optimum water flow rate that minimizes the charging duration and maximizes the system efficiency and hot water amount. Another challenge that researchers face is the low thermal conductivity of many phase change materials. For this purpose, methods for improving the performance of the systems have been examined and they are also reported.},
@@ -2175,7 +2188,7 @@ been added; and the references and glossary have been updated and expanded. },
date-modified = {2021-09-08 13:21:23 -0400},
title = {Software sustainability -- lessons learned from different disciplines},
year = {2018},
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@inbook{AbranAndAl-Qutaish2010,
abstract = {Summary This chapter contains sections titled: Introduction to ISO 9126 Analysis Models of ISO 9126: The (Quantitative) Models The Metrology-Related Part of ISO 9126: Base and Derived Measures Analysis of Derived Measures The Missing Links: From Metrology to Quantitative Analysis Outstanding Measurement Design Issues: Improvement Strategy Advanced Readings 1: Analysis of the Design of the Productivity Measure in ISO 9126 Advanced Readings 2: Attributes and Related Base Measures within ISO 9126},
@@ -2193,7 +2206,7 @@ been added; and the references and glossary have been updated and expanded. },
title = {ISO 9126: Analysis of Quality Models and Measures},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470606834.ch10},
year = {2010},
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bdsk-url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470606834.ch10},
bdsk-url-2 = {https://doi.org/10.1002/9780470606834.ch10}}
@@ -2207,7 +2220,7 @@ been added; and the references and glossary have been updated and expanded. },
title = {Transport Phenomena},
url = {https://books.google.ca/books?id=wYnRQwAACAAJ},
year = {2002},
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bdsk-url-1 = {https://books.google.ca/books?id=wYnRQwAACAAJ}}
@techreport{WeinstockAndGoodenough2009,
@@ -2220,7 +2233,7 @@ been added; and the references and glossary have been updated and expanded. },
title = {Towards an Assurance Case Practice for Medical Devices},
url = {http://resources.sei.cmu.edu/library/asset-view.cfm?AssetID=8999},
year = {2009},
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bdsk-url-1 = {http://resources.sei.cmu.edu/library/asset-view.cfm?AssetID=8999}}
@article{Schwer2007,
@@ -2241,7 +2254,7 @@ been added; and the references and glossary have been updated and expanded. },
url = {http://dblp.uni-trier.de/db/journals/ewc/ewc23.html#Schwer07},
volume = 23,
year = 2007,
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bdsk-url-1 = {http://dblp.uni-trier.de/db/journals/ewc/ewc23.html#Schwer07}}
@inproceedings{ChowduryEtAl2017,
@@ -2364,7 +2377,7 @@ Transcatheter intervention that successfully relieves mild COA pressure gradient
pages = {21},
title = {Sustainable Software via Generation},
year = {2021},
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bdsk-url-1 = {https://www.eng.mcmaster.ca/sept/practice/booth-resource-and-innovation-cluster#Proceedings}}
@incollection{Newman2016,
@@ -2424,7 +2437,7 @@ the end of the rainbow''.},
month = {June},
title = {Physics, Part 4: The Third Dimension},
year = {1997},
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@article{Hecker1997Mar,
author = {Chris Hecker},
@@ -2434,7 +2447,7 @@ the end of the rainbow''.},
month = {March},
title = {Physics, Part 3: Collision Response},
year = {1997},
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@article{Hecker1997Jan,
author = {Chris Hecker},
@@ -2444,7 +2457,7 @@ the end of the rainbow''.},
month = {January},
title = {Physics, Part 2: Angular Effects},
year = {1997},
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@article{Hecker1996,
author = {Chris Hecker},
@@ -2454,7 +2467,7 @@ the end of the rainbow''.},
month = {October/November},
title = {Physics, The Next Frontier},
year = {1997},
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@misc{ZabardastEtAl2021,
abstract = {When developing and maintaining software-intensive products or services, we often depend on various "assets", denoting the inherent value to selected artefacts when carrying out development and maintenance activities. When exploring various areas in Software Engineering, such as Technical Debt and our work with industry partners, we soon realised that many terms and concepts are frequently intermixed and used inconsistently. Despite the central role of assets to software engineering, management, and evolution, little thoughts are yet invested into what assets eventually are. A clear terminology of "assets" and related concepts, such as "value" or "value degradation", just to name two, are crucial for setting up effective software engineering practices. As a starting point for our own work, we had to define the terminology and concepts, and extend the reasoning around the concepts. In this position paper, we critically reflect upon the resulting notion of Assets in Software Engineering. We explore various types of assets, their main characteristics, such as providing inherent value. We discuss various types of value degradation and the possible implications of this on the planning, realisation, and evolution of software-intensive products and services over time. With our work, we aspire to contribute to a more standardised definition of Asset Management in Software Engineering and foster research endeavours and their practical dissemination in a common, more unified direction.},
@@ -2479,7 +2492,7 @@ the end of the rainbow''.},
school = {McMaster University},
title = {Automated Knowledge Extraction Based on a Scientific Computing Software Dcomentation Generation Framework},
year = {2018},
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@article{RaminEtAl2020,
abstract = {Motivated and competent team members are a vital part of Agile Software development and make or break any project's success. Motivation is fostered by continuous progress and recognition of efforts. These concepts are founding pillars of the Scrum methodology, which focuses on self-organizing teams. The types of contributions Scrum development team members make to a project's progress are not only technical. However, a comprehensive model comprising the varied contributions in modern software engineering teams is not yet established. We propose a model that incorporates contributions of all Scrum roles, explicitly including those which are not directly related to project artifacts. It improves the visibility of performed tasks, acts as a starting point for team retrospection, and serves as a foundation for discussion in the research community.},
@@ -2745,7 +2758,7 @@ We will conduct some case studies on specific domains (such as medical imaging s
pages = {43--47},
title = {Improving Software Productivity},
year = {1987},
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bdsk-url-1 = {http://citeseerx.ist.psu.edu/viewdoc/summary;jsessionid=8A5967CE077ECB46DE9EBFC12F443C68?doi=10.1.1.365.9038}}
@article{Drucker1999,
@@ -2764,7 +2777,7 @@ We will conduct some case studies on specific domains (such as medical imaging s
title = {{Knowledge-Worker Productivity: The Biggest Challenge}},
volume = 41,
year = 1999,
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@misc{Sundheim2020,
author = {Doug Sundheim},
@@ -2950,7 +2963,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
title = {IEEE Standard Glossary of Software Engineering Terminology},
type = {Standard},
year = {1991},
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@book{MacKenzie2013,
address = {San Francisco, CA, USA},
@@ -2962,7 +2975,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
publisher = {Morgan Kaufmann Publishers Inc.},
title = {Human-Computer Interaction: An Empirical Research Perspective},
year = {2013},
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@misc{MolnarandMotogna2020,
archiveprefix = {arXiv},
@@ -3051,7 +3064,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
publisher = {Springer Publishing Company, Incorporated},
title = {Guide to Advanced Empirical Software Engineering},
year = {2010},
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@phdthesis{Remmel2014,
annote = {- says Smith and Yu are the first to do SPLE for scientific software
@@ -3106,7 +3119,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
title = {On Formalism in Specifications},
volume = {2},
year = {1985},
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@misc{Baber2002,
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month = {October},
title = {Translating English to Mathematics},
year = {2002},
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@misc{YeEtAl2019,
archiveprefix = {arXiv},
@@ -3163,7 +3176,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
title = {Raising the Bar: Assurance Cases for Scientific Computing Software},
volume = {23},
year = {2020},
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bdsk-url-1 = {https://ieeexplore.ieee.org/document/9178774}}
@misc{DiskinEtAl2019,
@@ -3192,7 +3205,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
title = {The Software Sustainability Institute: Changing Research Software Attitudes and Practices},
volume = {15},
year = {2013},
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bdsk-url-1 = {https://doi.org/10.1109/MCSE.2013.133}}
@inproceedings{SehestedtEtAl2014,
@@ -3214,7 +3227,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
title = {Towards Quantitative Metrics for Architecture Models},
url = {http://doi.acm.org/10.1145/2578128.2578226},
year = {2014},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2578128.2578226},
bdsk-url-2 = {https://doi.org/10.1145/2578128.2578226}}
@@ -3286,7 +3299,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
timestamp = {2014-07-08T11:07:50.000+0200},
title = {{ISO/IEC} 9126. Software engineering -- Product quality},
year = 2001,
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@misc{CaretteEtAl2019,
author = {Jacques Carette and Brooks MacLachlan and W. Spencer Smith},
@@ -3309,7 +3322,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
pages = {1--6},
title = {{GOOL}: A Generic Object-Oriented Language},
year = {2020},
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bdsk-url-1 = {https://github.com/JacquesCarette/Drasil/tree/master/Papers/GOOL}}
@misc{Prechelt2019,
@@ -3353,7 +3366,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
publisher = {McGraw-Hill},
title = {Software Engineering, A Practitioner's Approach},
year = {1999},
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@misc{GallardEtAl2019,
archiveprefix = {arXiv},
@@ -3436,7 +3449,7 @@ it sustainable, and evaluating both the obtained results and the achieved perfor
school = {McMaster University},
title = {Towards Automating Code Reviews},
year = {2019},
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@book{Sommerville2010,
address = {USA},
@@ -3997,7 +4010,7 @@ Legal, Environmental)''},
primaryclass = {cs.GL},
title = {Sustainable Research Software Hand-Over},
year = {2019},
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bdsk-url-1 = {https://arxiv.org/abs/1909.09469#}}
@book{Anton1987,
@@ -4023,7 +4036,7 @@ Legal, Environmental)''},
month = {September},
title = {Talk to Me: A Case Study on Coordinating Expertise in Large-Scale Scientific Software Projects},
year = {2018},
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@misc{PHA2009,
author = {PHA, Public Health Agency of Canada},
@@ -4094,7 +4107,7 @@ Legal, Environmental)''},
title = {Fusing Modeling and Programming into Language-Oriented Programming - Our Experiences with {MPS}},
url = {https://doi.org/10.1007/978-3-030-03418-4\_19},
year = {2018},
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@article{RunesonAndHost2009,
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url = {https://doi.org/10.1007/s10664-008-9102-8},
volume = {14},
year = {2009},
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@article{EbertAndJones2009,
@@ -4193,7 +4206,7 @@ A plan for a case study should at least contain the following elements (Robson 2
title = {Embedded Software: Facts, Figures, and Future},
volume = {42},
year = {2009},
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@article{KitchenhamEtAl2002,
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url = {https://doi.org/10.1109/TSE.2002.1027796},
volume = {28},
year = {2002},
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@misc{Drasil2019,
@@ -4292,7 +4305,7 @@ Sections 4, 5, 6 and 7 - more detail on statistical measures, quality control, p
month = {June},
title = {Debunking the Myth that Upfront Requirements are Infeasible for Scientific Computing Software Debunking the Myth that Upfront Requirements are Infeasible for Scientific Computing Software},
year = {2019},
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@inproceedings{MilewiczAndRodeghero2019,
author = {Reed Milewicz and Paige Rodeghero},
@@ -4302,7 +4315,7 @@ Sections 4, 5, 6 and 7 - more detail on statistical measures, quality control, p
pages = {1--2},
title = {Position Paper: Towards Usability as a First-Class Quality of HPC Scientific Software},
year = {2019},
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@inproceedings{BadreddinEtAl2019,
author = {Omar Badreddin and Wahab Hamou-Lhadj and Swapnil Chauhan},
@@ -4312,7 +4325,7 @@ Sections 4, 5, 6 and 7 - more detail on statistical measures, quality control, p
pages = {1--4},
title = {Susereum: Towards a Reward Structure for Sustainable Scientific Research Software},
year = {2019},
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@inproceedings{DanishEtAl2019,
author = {Matthew Danish and Miltiadis Allamanis and Marc Brockschmidt and Andrew Rice and Dominic Orchard},
@@ -4322,7 +4335,7 @@ Sections 4, 5, 6 and 7 - more detail on statistical measures, quality control, p
pages = {1--4},
title = {Learning units-of-measure from scientific code},
year = {2019},
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@inproceedings{VogelEtAl2019,
author = {Thomas Vogel and Stephan Druskat and Markus Scheidgen and Claudia Draxl and Lars Grunske},
@@ -4332,7 +4345,7 @@ Sections 4, 5, 6 and 7 - more detail on statistical measures, quality control, p
number = {1--8},
title = {Challenges for Verifying and Validating Scientific Software in Computational Materials Science},
year = {2019},
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@inproceedings{KempfAndBastian2019,
author = {Dominic Kempf and Peter Bastian},
@@ -4342,7 +4355,7 @@ Sections 4, 5, 6 and 7 - more detail on statistical measures, quality control, p
pages = {1--8},
title = {An {HPC} Perspective on Generative Programming},
year = {2019},
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@inproceedings{SmithEtAl2019,
author = {Spencer Smith and Malavika Srinivasan and Sumanth Shankar},
@@ -4352,7 +4365,7 @@ Sections 4, 5, 6 and 7 - more detail on statistical measures, quality control, p
pages = {1--8},
title = {Debunking the Myth that Upfront Requirements are Infeasible for Scientific Computing Software},
year = {2019},
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@article{DioszegiAndHattel2004,
author = {Di{\'o}szegi, Attila and Hattel, Jesper},
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title = {Software System Design based on Patterns for Newton-Type Methods},
volume = {arXiv:1905.04642},
year = {2019},
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@article{Morales-TrujilloEtAl2018,
author = {Miguel Morales Trujillo and Hanna Oktaba and Francisco Hern{\'{a}}ndez Quiroz and Boris Escalante{-}Ram{\'{\i}}rez},
@@ -4405,7 +4418,7 @@ reusable},
url = {http://www.cai.sk/ojs/index.php/cai/article/view/2018\_1\_109},
volume = {37},
year = {2018},
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@inproceedings{DubeyEtAl2019,
@@ -4437,7 +4450,7 @@ reusable},
pages = {1-1},
title = {Naming the Pain in Developing Scientific Software},
year = {2019},
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bdsk-url-1 = {https://doi.org/10.1109/MS.2019.2899838}}
@article{deSouzaEtAl2019,
@@ -4456,7 +4469,7 @@ reusable},
url = {http://arxiv.org/abs/1903.06039},
volume = {abs/1903.06039},
year = {2019},
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bdsk-url-1 = {http://arxiv.org/abs/1903.06039}}
@article{Bjorner2019,
@@ -4471,7 +4484,7 @@ reusable},
title = {Domain Analysis and Description Principles, Techniques, and Modelling Languages},
volume = {28},
year = {2019},
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@inproceedings{Farmer2004,
abstract = {Undefined terms are commonplace in mathematics, particularly in calculus. The traditional approach to undefinedness in mathematical practice is to treat undefined terms as legitimate, nondenoting terms that can be components of meaningful statements. The traditional approach enables statements about partial functions and undefined terms to be stated very concisely. Unfortunately, the traditional approach cannot be easily employed in a standard logic in which all functions are total and all terms are defined, but it can be directly formalized in a standard logic if the logic is modified slightly to admit undefined terms and statements about definedness. This paper demonstrates this by defining a version of simple type theory called Simple Type Theory with Undefinedness (sttwu) and then formalizing in sttwu examples of undefinedness arising in calculus. The examples are taken from M. Spivak's well-known textbook Calculus.},
@@ -4486,7 +4499,7 @@ reusable},
publisher = {Springer Berlin Heidelberg},
title = {Formalizing Undefinedness Arising in Calculus},
year = {2004},
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@incollection{Patrick2016,
address = {Boca Raton, FL},
@@ -4501,7 +4514,7 @@ reusable},
series = {Chapman \& Hall/{CRC} Computational Science},
title = {Making Scientific Software Easier to Understand, Test, and Communicate through Software Engineering},
year = {2016},
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@inproceedings{Smith2019_CSE,
author = {W. Spencer Smith},
@@ -4511,7 +4524,7 @@ reusable},
month = {Feb},
title = {Toward Automatic Generation of Scientific Software Artifacts},
year = {2019},
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bdsk-url-1 = {https://figshare.com/articles/Toward_Automatic_Generation_of_Scientific_Software_Artifacts_SIAM_CS19_MS2_Scientific_Software_Practices_Concerns_and_Solution_Strategies_February_25_2019/7771061}}
@inproceedings{SmithEtAl2019_CSE,
@@ -4523,9 +4536,9 @@ reusable},
month = {Feb},
title = {No Need for Excuses: Applying Software Engineering Principles to Facilitate Scientific Software Documentation},
year = {2019},
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@article{SahinEtAl2005,
@@ -4539,7 +4552,7 @@ reusable},
title = {Determination of unidirectional heat transfer coefficient during unsteady-state solidification at metal casting--chill interface},
volume = {47},
year = {2006},
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@mastersthesis{Srinivasan2018,
author = {Malavika Srinivasan},
@@ -4548,7 +4561,7 @@ reusable},
school = {McMaster University, Hamilton, Ontario, Canada},
title = {Investigating Common Perceptions of Software Engineering Methods Applied to Scientific Computing Software},
year = {2018},
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@article{Lange2013,
acmid = {2590217},
@@ -4569,7 +4582,7 @@ reusable},
url = {http://dl.acm.org/citation.cfm?id=2590215.2590217},
volume = {4},
year = {2013},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2590215.2590217}}
@inproceedings{SouagEtAl2015,
@@ -4585,7 +4598,7 @@ reusable},
publisher = {Springer International Publishing},
title = {A Security Ontology for Security Requirements Elicitation},
year = {2015},
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@inproceedings{OfenbeckEtAl2017,
annote = {- space is referring to design space - list of design choices and specialization
@@ -4598,7 +4611,7 @@ reusable},
publisher = {{ACM}},
title = {Staging for generic programming in space and time},
year = {2017},
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@inproceedings{ButlerEtAl2017,
acmid = {3102076},
@@ -4619,7 +4632,7 @@ reusable},
title = {Program Synthesis As a Generative Method},
url = {http://doi.acm.org/10.1145/3102071.3102076},
year = {2017},
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bdsk-url-1 = {http://doi.acm.org/10.1145/3102071.3102076},
bdsk-url-2 = {https://doi.org/10.1145/3102071.3102076}}
@@ -4632,7 +4645,7 @@ reusable},
publisher = {{ACM}},
title = {Parsing and reflective printing, bidirectionally},
year = {2016},
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@article{KanewalaAndChen2018,
author = {Upulee Kanewala and Tsong Yueh Chen},
@@ -4641,7 +4654,7 @@ reusable},
journal = {Computing in Science \& Engineering},
title = {Metamorphic Testing: A Simple yet Effective Approach for Testing Scientific Software},
year = {2018},
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@inproceedings{ReisAndJarvi2005,
author = {Gabriel Dos Reis and Jaakko Jarvi},
@@ -4650,7 +4663,7 @@ reusable},
date-modified = {2018-11-09 12:59:26 -0500},
title = {What is generic programming?},
year = {2005},
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@inproceedings{MayerhoferEtAl2016,
abstract = {Although several software modeling languages permit the representation of key aspects of physical entities, such as units, precision or measurement uncertainty, these aspects are not typically incorporated into their type systems. Therefore, operating with such properties is normally cumbersome and contrived. This paper shows how both data uncertainty and units can be captured in software models and naturally incorporated into their type systems. In particular, we present extensions of the UML/OCL type Real and define a set of operations on values of these new types. Furthermore, we show how they can be used in software models to carry out computations that consider measurement uncertainty and permit the detection of unit mismatches when trying to operate with their values.},
@@ -4672,7 +4685,7 @@ reusable},
title = {Adding Uncertainty and Units to Quantity Types in Software Models},
url = {http://doi.acm.org/10.1145/2997364.2997376},
year = {2016},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2997364.2997376},
bdsk-url-2 = {https://doi.org/10.1145/2997364.2997376}}
@@ -4693,7 +4706,7 @@ reusable},
title = {A Comprehensive Study of Real-world Numerical Bug Characteristics},
url = {http://dl.acm.org/citation.cfm?id=3155562.3155627},
year = {2017},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=3155562.3155627}}
@inproceedings{Gibbons2006,
@@ -4716,7 +4729,7 @@ reusable},
title = {Design Patterns As Higher-order Datatype-generic Programs},
url = {http://doi.acm.org/10.1145/1159861.1159863},
year = {2006},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1159861.1159863},
bdsk-url-2 = {https://doi.org/10.1145/1159861.1159863}}
@@ -4728,7 +4741,7 @@ reusable},
pages = {302--307},
title = {Mechanizing the Development of Software},
year = {1999},
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@article{CaretteEtAl2009,
acmid = {1630626},
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url = {http://dx.doi.org/10.1017/S0956796809007205},
volume = {19},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1017/S0956796809007205}}
@article{HemelAndVisser2011,
@@ -4772,7 +4785,7 @@ reusable},
url = {http://doi.acm.org/10.1145/2076021.2048121},
volume = {46},
year = {2011},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2076021.2048121},
bdsk-url-2 = {https://doi.org/10.1145/2076021.2048121}}
@@ -4794,7 +4807,7 @@ reusable},
title = {Rhythm-based Level Generation for 2D Platformers},
url = {http://doi.acm.org/10.1145/1536513.1536548},
year = {2009},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1536513.1536548},
bdsk-url-2 = {https://doi.org/10.1145/1536513.1536548}}
@@ -4817,7 +4830,7 @@ reusable},
title = {Automatic Level Generation for Platform Videogames Using Genetic Algorithms},
url = {http://doi.acm.org/10.1145/2071423.2071433},
year = {2011},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2071423.2071433},
bdsk-url-2 = {https://doi.org/10.1145/2071423.2071433}}
@@ -4829,7 +4842,7 @@ reusable},
school = {Civil Engineering Department, McMaster University},
title = {Flexible Pavement Response Modelling Using the Indirect Boundary Element Method},
year = {2009},
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@mastersthesis{El-Sewify2012,
address = {Hamilton, ON, Canada},
@@ -4840,7 +4853,7 @@ reusable},
school = {School of Computational Science and Engineering, McMaster University},
title = {Multi-particle Collision Dynamics},
year = {2012},
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@article{RudeEtAl2018,
author = {R{\"u}de, U. and Willcox, K. and McInnes, L. and Sterck, H.},
@@ -4855,7 +4868,7 @@ reusable},
url = {https://doi.org/10.1137/16M1096840},
volume = {60},
year = {2018},
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bdsk-url-1 = {https://doi.org/10.1137/16M1096840}}
@misc{HettrickEtAl2014,
@@ -4900,7 +4913,7 @@ This survey data is licensed under a Creative Commons by Attribution licence. Co
date-modified = {2018-10-05 14:09:44 -0400},
title = {Tecton: A Framework for Specifying and Verifying Generic System Components},
year = {1992},
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@inproceedings{KatsAndVisser2010,
annote = {- students say that the paper is repetitive
@@ -4933,7 +4946,7 @@ Spoofax also has a meta description of ``editing'' features of PLs
tags = {Spoofax, language workbench},
title = {The {Spoofax} Language Workbench. {Rules} for Declarative Specification of Languages and {IDEs}},
year = {2010},
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@article{LucivEtAl2018,
abstract = {Contemporary software documentation is as complicated as the software itself. During its lifecycle, the documentation accumulates a lot of ``near duplicate'' fragments, i.e. chunks of text that were copied from a single source and were later modified in different ways. Such near duplicates decrease documentation quality and thus hamper its further utilization. At the same time, they are hard to detect manually due to their fuzzy nature. In this paper we give a formal definition of near duplicates and present an algorithm for their detection in software documents. This algorithm is based on the exact software clone detection approach: the software clone detection tool Clone Miner was adapted to detect exact duplicates in documents. Then, our algorithm uses these exact duplicates to construct near ones. We evaluate the proposed algorithm using the documentation of 19 open source and commercial projects. Our evaluation is very comprehensive -- it covers various documentation types: design and requirement specifications, programming guides and API documentation, user manuals. Overall, the evaluation shows that all kinds of software documentation contain a significant number of both exact and near duplicates. Next, we report on the performed manual analysis of the detected near duplicates for the Linux Kernel Documentation. We present both quantative and qualitative results of this analysis, demonstrate algorithm strengths and weaknesses, and discuss the benefits of duplicate management in software documents.},
@@ -4951,7 +4964,7 @@ Spoofax also has a meta description of ``editing'' features of PLs
url = {https://doi.org/10.1134/S0361768818050079},
volume = {44},
year = {2018},
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bdsk-url-1 = {https://doi.org/10.1134/S0361768818050079}}
@article{Zwart2018,
@@ -4965,7 +4978,7 @@ Spoofax also has a meta description of ``editing'' features of PLs
title = {Computational Astrophysics for the Future},
volume = {361},
year = {2018},
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@article{Keshavarz-MotamedEtAl2014,
annote = {{the derivation of the ODEs is unclear.}
@@ -4980,7 +4993,7 @@ Spoofax also has a meta description of ``editing'' features of PLs
title = {Non-Invasive Determination of Left Ventricular Workload in Patients with Aortic Stenosis Using Magnetic Resonance Imaging and Doppler Echocardiography},
volume = {9},
year = {2014},
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bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0086793}}
@article{Keshavarz-MotamedEtAl2011,
@@ -4992,7 +5005,7 @@ Spoofax also has a meta description of ``editing'' features of PLs
title = {Modeling the impact of concomitant aortic stenosis and coarctation of the aorta on left ventricular workload},
volume = {44},
year = {2011},
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@article{MilewiczAndRayborn2018,
abstract = {Large-scale collaborative scientific software projects require more knowledge than any one person typically possesses. This makes coordination and communication of knowledge and expertise a key factor in creating and safeguarding software quality, without which we cannot have sustainable software. However, as researchers attempt to scale up the production of software, they are confronted by problems of awareness and understanding. This presents an opportunity to develop better practices and tools that directly address these challenges. To that end, we conducted a case study of developers of the Trilinos project. We surveyed the software development challenges addressed and show how those problems are connected with what they know and how they communicate. Based on these data, we provide a series of practicable recommendations, and outline a path forward for future research.},
@@ -5010,7 +5023,7 @@ Spoofax also has a meta description of ``editing'' features of PLs
title = {Talk to Me: A Case Study on Coordinating Expertise in Large-Scale Scientific Software Projects},
volume = {arXiv:1905.04642},
year = {2018},
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@article{RompfAndOdersky2010,
abstract = {Software engineering demands generality and abstraction, performance demands specialization and concretization. Generative programming can provide both, but the effort required to develop high-quality program generators likely offsets their benefits, even if a multi-stage programming language is used. We present lightweight modular staging, a library-based multi-stage programming approach that breaks with the tradition of syntactic quasi-quotation and instead uses only types to distinguish between binding times. Through extensive use of component technology, lightweight modular staging makes an optimizing compiler framework available at the library level, allowing programmers to tightly integrate domain-specific abstractions and optimizations into the generation process. We argue that lightweight modular staging enables a form of language virtualization, i.e. allows to go from a pure-library embedded language to one that is practically equivalent to a stand-alone implementation with only modest effort.},
@@ -5022,8 +5035,8 @@ Spoofax also has a meta description of ``editing'' features of PLs
title = {Lightweight Modular Staging: A Pragmatic Approach to Runtime Code Generation and Compiled DSLs},
volume = {46},
year = {2010},
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@inbook{PueschelEtAl2011,
abstract = {Spiral is a program generation system (software that generates other software) for linear transforms and
@@ -5043,7 +5056,7 @@ intrinsics and threading instructions.},
publisher = {Springer},
title = {Encyclopedia of Parallel Computing},
year = {2011},
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@misc{MernikEtAl2003,
abstract = {Domain-specific languages (DSLs) are languages tailored to a specific application domain. They offer substantial gains in expressiveness and ease of use compared with general purpose programming languages in their domain of application. DSL development is hard, requiring both domain knowledge and language development expertise. Few people have both. Not surprisingly, the decision to develop a DSL is often postponed indefinitely, if considered at all, and most DSLs never get beyond the application library stage. While many articles have been written on the development of particular DSLs, there is very limited literature on DSL development methodologies and many questions remain regarding when and how to develop a DSL. To aid the DSL developer, we identify patterns in the decision, analysis, design, and implementation phases of DSL development. Our patterns try to improve on and extend earlier work on DSL design patterns, in particular by Spinellis (2001). We also discuss domain analysis tools and language development systems that may help to speed up DSL development. Finally, we state a number of open problems.},
@@ -5061,7 +5074,7 @@ intrinsics and threading instructions.},
date-modified = {2018-09-17 14:22:59 -0400},
title = {When And How To Develop Domain-Specific Languages},
year = {2003},
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@misc{Soergel2014,
author = {David Soergel},
@@ -5081,7 +5094,7 @@ intrinsics and threading instructions.},
month = {June},
title = {A tutorial introduction to the minimum description length principle},
year = {2004},
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@article{PostAndVotta2005,
adsnote = {Provided by the SAO/NASA Astrophysics Data System},
@@ -5103,7 +5116,7 @@ intrinsics and threading instructions.},
title = {{Computational Science Demands a New Paradigm}},
volume = 58,
year = 2005,
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bdsk-url-1 = {https://doi.org/10.1063/1.1881898}}
@article{FaulkEtAl2009,
@@ -5130,7 +5143,7 @@ intrinsics and threading instructions.},
title = {Scientific Computing's Productivity Gridlock: How Software Engineering Can Help},
volume = {11},
year = {2009},
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bdsk-url-1 = {https://doi.org/10.1109/MCSE.2009.205}}
@article{HealyAndCaudell2006,
@@ -5149,7 +5162,7 @@ intrinsics and threading instructions.},
url = {https://doi.org/10.1007/s10516-005-5474-1},
volume = {16},
year = {2006},
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bdsk-url-1 = {https://doi.org/10.1007/s10516-005-5474-1}}
@article{KatzEtAl2018,
@@ -5160,7 +5173,7 @@ intrinsics and threading instructions.},
pages = {1--19},
title = {The State of Sustainable Research Software: Results from the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1)},
year = {2018},
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@article{MillsEtAl2018,
annote = {- has good references on traceability},
@@ -5171,7 +5184,7 @@ intrinsics and threading instructions.},
pages = {1--12},
title = {Automatic Traceability Maintenance via Machine Learning Classification},
year = {2018},
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@inproceedings{BezzecchiEtAl2018,
address = {Toulouse, France},
@@ -5187,7 +5200,7 @@ intrinsics and threading instructions.},
title = {{Making Agile Development Processes fit for V-style Certification Procedures}},
url = {https://hal.archives-ouvertes.fr/hal-01702815},
year = {2018},
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bdsk-url-1 = {https://hal.archives-ouvertes.fr/hal-01702815}}
@phdthesis{Bagge2009,
@@ -5203,7 +5216,7 @@ intrinsics and threading instructions.},
title = {Constructs \& {C}oncepts: Language Design for Flexibility and Reliability},
url = {http://www.ii.uib.no/~anya/phd/},
year = 2009,
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bdsk-url-1 = {http://www.ii.uib.no/~anya/phd/}}
@article{JinAndParnas2010,
@@ -5226,7 +5239,7 @@ intrinsics and threading instructions.},
url = {http://dx.doi.org/10.1016/j.scico.2009.12.009},
volume = {75},
year = {2010},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.scico.2009.12.009}}
@article{JohansonAndHasselbring2018,
@@ -5238,7 +5251,7 @@ intrinsics and threading instructions.},
title = {Software Engineering for Computational Science: Past, Present, Future},
volume = {Accepted},
year = {2018},
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@inproceedings{SimmEtAl2018,
author = {W. A. Simm and F. Samreen and R. Bassett and M. A. Ferrario and G. Blair and J. Whittle and P. J. Young},
@@ -5248,7 +5261,7 @@ intrinsics and threading instructions.},
pages = {1--10},
title = {SE in ES: Opportunities for Software Engineering and Cloud Computing in Environmental Science},
year = {2018},
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@inproceedings{LinEtAl2018,
author = {Xuanyi Lin and Michelle Simon and Nan Niu},
@@ -5258,7 +5271,7 @@ intrinsics and threading instructions.},
pages = {1--8},
title = {Hierarchical Metamorphic Relations for Testing Scientific Software},
year = {2018},
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@inproceedings{HauptEtAl2018,
abstract = {Software is a vital part of modern research. The competence to develop sustainable software becomes increasingly important for research organizations. The DLR - a large research organization in Germany - has set up a software engineering initiative to address typical obstacles in this regard such as missing long-term funding, lack of incentives, or missing knowledge about essential software development practices. In this paper, we describe the concept and activities of the initiative as well as discuss the impact of these activities on the identified obstacles.},
@@ -5274,7 +5287,7 @@ https://elib.dlr.de/114050/
pages = {1--4},
title = {The Software Engineering Initiative of DLR},
year = {2018},
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@inproceedings{DubeyAndWan2018,
abstract = {Computational science and engineering communities develop com- plex application software with multiple mathematical models that need to interact with one another. Partly due to complexity of veri- fying scientific software, and partly because of the way incentives work in science, there has been insufficient testing of these codes. With a spotlight on the results produced with scientific software, and increasing awareness of software testing and verification as a critical contributor to the reliability of these results, testing is gaining more attention by the developing teams. However, many science teams struggle to find a good solution for themselves due either to lack of training or lack of resources within the team. In this experience paper we describe test development methodologies utilized in two different scenarios: one explains a methodology for building granular tests where none existed before, while the second demonstrates a methodology for selecting test cases that build con- fidence in the software through a process similar to scaffolding. The common insight from both the experiences is that testing should be a part of software design from the beginning for better software and scientific productivity.},
@@ -5288,7 +5301,7 @@ https://elib.dlr.de/114050/
pages = {1--7},
title = {Methodology for Building Granular Testing in Multicomponent Scientific Software},
year = {2018},
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@inproceedings{BicketEtAl2018,
author = {Isobel C. Bicket and Alexandre Pofelski and Spencer Smith and Gianluigi A. Botton},
@@ -5298,8 +5311,8 @@ https://elib.dlr.de/114050/
organization = {Canadian Centre for Electron Microscopy (CCEM)},
title = {Enhancing Trust in Electron Microscopy Data Analysis Software Through Software Engineering Principles, Tools and Techniques (Poster)},
year = {2018},
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@inproceedings{Smith2018,
author = {W. Spencer Smith},
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pages = {1--8},
title = {Beyond Software Carpentry},
year = {2018},
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@article{ShackleyEtAl1998,
author = {Shackley, S. and Young, P. and Parkinson, S. and Wynne, B.},
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pages = {582-591},
title = {How Do Scientists Develop and Use Scientific Software? An External Replication},
year = {2018},
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bdsk-url-1 = {https://doi.org/10.1109/SANER.2018.8330263}}
@techreport{ChenEtAl1998,
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title = {Metamorphic testing: a new approach for generating next test cases},
type = {Technical Report},
year = {1998},
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@article{BenureauAndRougier2017,
abstract = {- there isn't one},
@@ -5727,7 +5740,7 @@ side and outside your lab.''
primaryclass = {cs.GL},
title = {{Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions}},
year = 2017,
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@article{DaviesEtAl2014,
author = {Jim Davies and Jeremy Gibbons and Steve Harris and Charles Crichton},
@@ -5741,7 +5754,7 @@ side and outside your lab.''
url = {http://www.comlab.ox.ac.uk/people/jeremy.gibbons/publications/cancergrid.pdf},
volume = {89B},
year = {2014},
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bdsk-url-1 = {http://www.comlab.ox.ac.uk/people/jeremy.gibbons/publications/cancergrid.pdf},
bdsk-url-2 = {https://doi.org/10.1016/j.scico.2013.02.010}}
@@ -5753,7 +5766,7 @@ side and outside your lab.''
month = feb,
title = {State of the Practice for {GIS} Software},
year = {2018},
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@inproceedings{Bartlett2009,
author = {Roscoe A. Bartlett},
@@ -5960,7 +5973,7 @@ side and outside your lab.''
title = {Self-Perceptions about Software Engineering: A Survey of Scientists and Engineers},
volume = {15},
year = {2013},
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bdsk-url-1 = {https://doi.org/10.1109/MCSE.2013.12}}
@article{CastelliEtAl2013,
@@ -6075,7 +6088,7 @@ side and outside your lab.''
month = may,
title = {Grounded Theory in Software Engineering Research: A Critical Review and Guidelines},
year = {2016},
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@inproceedings{deOliveiraEtAl2013,
author = {Diego Caminha B. de Oliveira and Alan Humphrey and Zvonimir Rakamari and Qingyu Meng and Martin Berzins and Ganesh Gopalakrishnan},
@@ -6140,7 +6153,7 @@ side and outside your lab.''
publisher = {Springer Berlin Heidelberg},
title = {Software engineering or methods for the multi-person construction of multi-version programs},
year = {1975},
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@misc{Wilson2009,
author = {Greg Wilson},
@@ -6169,7 +6182,7 @@ side and outside your lab.''
slaccitation = {%%CITATION = ARXIV:1712.06982;%%},
title = {{A Roadmap for HEP Software and Computing R\&D for the 2020s}},
year = {2017},
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@article{Obreshkov2011,
abstract = {ATLAS is one of the largest collaborations in the physical sciences and involves 3000 scientists and engineers from 174 institutions in 38 countries. The geographically dispersed developer community has produced a large amount of software which is organized in 10 projects. In this presentation we discuss how the software is built on a variety of compiler and operating system combinations every night. File level and package level parallelism together with multi-core build servers are used to perform fast builds of the different platforms in several branches. We discuss the different tools involved during the software release build process and also the various mechanisms implemented to provide performance gains and error detection and retry mechanisms in order to counteract network and other instabilities that would otherwise degrade the robustness of the system. The goal is to provide high quality software built as fast as possible ready for final validation and deployment.},
@@ -6183,7 +6196,7 @@ side and outside your lab.''
url = {http://stacks.iop.org/1742-6596/331/i=4/a=042017},
volume = {331},
year = {2011},
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bdsk-url-1 = {http://stacks.iop.org/1742-6596/331/i=4/a=042017}}
@book{CarverEtAl2016,
@@ -6204,7 +6217,7 @@ side and outside your lab.''
title = {Analysis of Software Carpentry's Post-Workshop Surveys},
url = {https://doi.org/10.5281/zenodo.1043533},
year = 2017,
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bdsk-url-1 = {https://doi.org/10.5281/zenodo.1043533}}
@article{SimperlerAndWilson2015,
@@ -6221,7 +6234,7 @@ side and outside your lab.''
url = {http://arxiv.org/abs/1506.02575},
volume = {abs/1506.02575},
year = {2015},
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bdsk-url-1 = {http://arxiv.org/abs/1506.02575}}
@misc{Libarkin2012,
@@ -6232,7 +6245,7 @@ side and outside your lab.''
month = jun,
title = {Software Carpentry Workshop Evaluation},
year = {2012},
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@misc{Aranda2012,
author = {Jorge Aranda},
@@ -6242,7 +6255,7 @@ side and outside your lab.''
month = jul,
title = {Software Carpentry Assessment Report},
year = {2012},
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@inproceedings{SmithEtAl2018_ICSEPoster,
author = {W. Spencer Smith and Mojdeh Sayari Nejad and Alan Wassyng},
@@ -6253,8 +6266,8 @@ side and outside your lab.''
note = {2 pp},
title = {Assurance Cases for Scientific Computing Software (poster)},
year = {2018},
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@article{SamoulyEtAl2018,
author = {Aly Al Samouly and Chanh Nien Luong and Zhong Li and Spencer Smith and Brian Baetz and Maysara Ghaith},
@@ -6267,7 +6280,7 @@ side and outside your lab.''
title = {Performance of a Multi-Model Ensemble for the Simulation of Temperature Variability Over {O}ntario, {C}anada},
volume = {77},
year = {2018},
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bdsk-url-1 = {https://link.springer.com/epdf/10.1007/s12665-018-7701-2?author_access_token=76ouzh_jvD5JNOMyAzT6I_e4RwlQNchNByi7wbcMAY6Am9ftz0eCKyzCBckTeCc3hS5JsDRfK9Mv0NATwZXN5vAT9TO2sltKf3G7m4MVWqz3Zzdq_MXEhVuAiIrTzuth3VXSZmuvoTTwyGq-AahPtQ%3D%3D},
bdsk-url-2 = {https://doi.org/10.1007/s12665-018-7701-2}}
@@ -6302,7 +6315,7 @@ shows running example of summation at various levels of abstraction - uses count
url = {http://arxiv.org/abs/0707.4166},
volume = {abs/0707.4166},
year = {2007},
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bdsk-url-1 = {http://arxiv.org/abs/0707.4166}}
@article{ShampineAndThompson2000,
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title = {Event Location for Ordinary Differential Equations},
volume = {39},
year = {2000},
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@techreport{Jackson2013,
@@ -6333,7 +6346,7 @@ shows running example of summation at various levels of abstraction - uses count
title = {Conceptual Design of Software: A Research Agenda},
url_paper = {pubs/2013/conceptual-research-agenda-2013.pdf},
year = {2013},
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@misc{CummaudoEtAl2019,
abstract = {Background: Good API documentation facilities the development process, improving productivity and quality. While the topic of API documentation quality has been of interest for the last two decades, there have been few studies to map the specific constructs needed to create a good document. In effect, we still need a structured taxonomy against which to capture knowledge. Aims: This study reports emerging results of a systematic mapping study. We capture key conclusions from previous studies that assess API documentation quality, and synthesise the results into a single framework. Method: By conducting a systematic review of 21 key works, we have developed a five dimensional taxonomy based on 34 categorised weighted recommendations. Results: All studies utilise field study techniques to arrive at their recommendations, with seven studies employing some form of interview and questionnaire, and four conducting documentation analysis. The taxonomy we synthesise reinforces that usage description details (code snippets, tutorials, and reference documents) are generally highly weighted as helpful in API documentation, in addition to design rationale and presentation. Conclusions: We propose extensions to this study aligned to developer's utility for each of the taxonomy's categories.},
@@ -6369,7 +6382,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
url = {http://dx.doi.org/10.1109/MC.1987.1663532},
volume = {20},
year = {1987},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MC.1987.1663532}}
@inproceedings{MeshAndHawker2013,
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title = {Scientific Software Process Improvement Decisions: A Proposed Research Strategy},
url = {http://dl.acm.org/citation.cfm?id=2663370.2663376},
year = {2013},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2663370.2663376}}
@incollection{CrookEtAl2013,
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title = {Reproducible and User-Controlled Software Environments in HPC with Guix},
url = {https://doi.org/10.1007/978-3-319-27308-2_47},
year = {2015},
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bdsk-url-1 = {https://doi.org/10.1007/978-3-319-27308-2_47},
bdsk-url-2 = {http://dx.doi.org/10.1007/978-3-319-27308-2_47}}
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url = {http://libaccess.mcmaster.ca/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=bth&AN=113448638&site=ehost-live&scope=site},
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@article{Wilson1996,
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url = {http://www.computer.org/cse/cs1998/c2046abs.htm},
volume = {3},
year = {1996},
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bdsk-url-1 = {http://dx.doi.org/10.1109/99.503313},
bdsk-url-2 = {http://www.computer.org/cse/cs1998/c2046abs.htm}}
@@ -6477,7 +6490,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
title = {Software Carpentry: lessons learned [version 2; referees: 3 approved]},
volume = {3},
year = {2016},
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bdsk-url-1 = {http://dx.doi.org/10.12688/f1000research.3-62.v2}}
@article{LandwehrEtAl2017,
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url = {https://doi.org/10.1016/j.jss.2016.12.016},
volume = {125},
year = {2017},
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bdsk-url-2 = {http://dx.doi.org/10.1016/j.jss.2016.12.016}}
@@ -6511,7 +6524,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
date-modified = {2017-09-28 16:07:13 +0000},
title = {Software Engineering, Why And What},
urldate = {2013},
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@electronic{Parnas2009_Slides,
author = {David Lorge Parnas},
@@ -6520,7 +6533,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
title = {How Precise Documentation allows Information Hiding to Reduce Software Complexity and Increase its Agility},
url = {http://www.comp.hkbu.edu.hk/%7Epgday/2009/10th_PPT/HOSEI%20Making%20Information%20Hiding%20Work%20slides.pdf},
urldate = {2009},
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@electronic{Parnas2012_Slides,
@@ -6530,7 +6543,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
title = {Software Development: What is Still Missing?},
url = {https://www.research.ibm.com/haifa/Workshops/plse2012/papers/thumbs.pdf},
urldate = {2012},
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@article{DeissenboeckEtAl2017,
@@ -6546,7 +6559,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
url = {http://arxiv.org/abs/1707.08341},
volume = {abs/1707.08341},
year = {2017},
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bdsk-url-1 = {http://arxiv.org/abs/1707.08341}}
@misc{FDA2014,
@@ -6557,7 +6570,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
month = dec,
title = {Infusion Pumps Total Product Life Cycle: Guidance for Industry and FDA Staff},
year = {2014},
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@mastersthesis{Nejad2017,
address = {Hamilton, ON, Canada},
@@ -6569,7 +6582,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
school = {McMaster University},
title = {A Case Study in Assurance Case Development for Scientific Software},
year = {2017},
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@article{Wassyng2015,
author = {Alan Wassyng and Neeraj Kumar Singh and Mischa Geven and Nicholas Proscia and Hao Wang and Mark Lawford and Tom Maibaum},
@@ -6586,7 +6599,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
url = {https://doi.org/10.1109/MDAT.2015.2462720},
volume = {32},
year = {2015},
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bdsk-url-1 = {https://doi.org/10.1109/MDAT.2015.2462720},
bdsk-url-2 = {http://dx.doi.org/10.1109/MDAT.2015.2462720}}
@@ -6600,7 +6613,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
number = {CR-2014-218678},
title = {Current Practices in Constructing and Evaluating Assurance Cases with Applications to Aviation},
year = {2015},
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bdsk-url-1 = {https://books.google.ca/books?id=7BaDrgEACAAJ}}
@article{Smith2017_CISE,
@@ -6647,7 +6660,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
month = jan,
title = {General Principles of Software Validation; Final Guidance for Industry and {FDA} Staff},
year = {2002},
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@incollection{KanewalaAndLundgren2016,
author = {Upulee Kanewala and Anders Lundgren},
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series = {Chapman \& Hall/{CRC} Computational Science},
title = {Automated Metamorphic Testing of Scientific Software},
year = {2016},
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@book{Knuth1992,
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publisher = {IEEE Press},
title = {Designing Software for Ease of Extension and Contraction},
year = {1978},
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@book{Spriggs2012,
address = {London},
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publisher = {Springer-Verlag},
title = {{GSN} - The Goal Structuring Notation},
year = {2012},
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@techreport{CollbergEtAl2015,
address = {Tucson, AZ},
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title = {Repeatability and Benefaction in Computer Systems Research},
url = {http://repeatability.cs.arizona.edu/v2/RepeatabilityTR.pdf},
year = {2015},
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@inproceedings{HaveraaenEtAl1992,
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url = {http://doi.acm.org/10.1145/1055531.1055533},
volume = {31},
year = {2005},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1055531.1055533},
bdsk-url-2 = {http://dx.doi.org/10.1145/1055531.105553},
bdsk-url-3 = {http://dx.doi.org/10.1145/1055531.1055533}}
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month = nov,
title = {The {Drasil} Framework for Literate Scientific Software},
year = {2016},
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@inproceedings{Wilson2013,
acmid = {2508189},
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title = {Two Solitudes},
url = {http://doi.acm.org/10.1145/2508075.2508189},
year = {2013},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2508075.2508189},
bdsk-url-2 = {http://dx.doi.org/10.1145/2508075.2508189},
bdsk-url-3 = {http://www.slideshare.net/gvwilson/splash-2013}}
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school = {McMaster University},
title = {Case Studies in Document Driven Design of Scientific Computing Software},
year = {2016},
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bdsk-url-1 = {https://macsphere.mcmaster.ca/handle/11375/20454}}
@article{LeVequeEtAl2012,
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url = {http://dx.doi.org/10.1109/mcse.2012.38},
volume = {14},
year = {2012},
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@article{Palinscar1998,
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url = {http://arxiv.org/abs/1407.5981},
volume = {abs/1407.5981},
year = {2014},
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@book{Pilato2004,
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pages = {1-40},
title = {Recommended Practice for Software Requirements Specifications},
year = {1998},
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bdsk-url-1 = {http://dx.doi.org/10.1109/IEEESTD.1998.88286}}
@article{JohnsonAndJohnson1997,
@@ -7100,7 +7113,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
series = {Chapman \& Hall/{CRC} Computational Science},
title = {A Rational Document Driven Design Process for Scientific Computing Software},
year = {2016},
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@mastersthesis{Sarafraz2014,
address = {Hamilton, ON, Canada},
@@ -7255,7 +7268,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
url = {http://dx.doi.org/10.1016/j.infsof.2014.05.006},
volume = {56},
year = {2014},
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@article{HeatonAndCarver2015,
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url = {http://dx.doi.org/10.1016/j.infsof.2015.07.011},
volume = {67},
year = {2015},
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@inproceedings{Pueschel2001,
@@ -7292,7 +7305,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
title = {Fast Automatic Generation of {DSP} Algorithms},
volume = {2073},
year = {2001},
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@techreport{ISO2010,
author = {{ISO/IEC}},
@@ -7305,7 +7318,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
title = {{ISO/IEC 25010 - Systems and software engineering - Systems and software Quality Requirements and Evaluation (SQuaRE) - System and software quality models}},
type = {Standard},
year = {2010},
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@techreport{ISO2007,
author = {{ISO/IEC}},
@@ -7317,7 +7330,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
publisher = {ISO/IEC},
title = {{ISO/IEC 25021:2007 - Software engineering - Software product Quality Requirements and Evaluation (SQuaRE) - Quality measure elements}},
year = {2007},
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@book{Adams2013,
address = {Thousand Oaks, CA, USA},
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url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2548561/},
volume = {310},
year = {1995},
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@inproceedings{BarnesEtAl2008,
@@ -7735,7 +7748,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
pages = {203--212},
title = {An Evolvable Meshing Tool Through a Flexible Object-Oriented Design.},
year = {2004},
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@article{deLeeuwAndMair2007,
accepted = {2007-05-01},
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url = {http://www.jstatsoft.org/v20/i01},
volume = {20},
year = {2007},
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@article{Rosseel2012,
@@ -7776,7 +7789,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
url = {http://www.jstatsoft.org/v48/i02},
volume = {48},
year = {2012},
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bdsk-url-1 = {http://www.jstatsoft.org/v48/i02}}
@techreport{DOE2003,
@@ -7788,7 +7801,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
number = {CRAD - 4.2.4.1},
title = {Assessment Criteria and Guidelines for Determining the Adequacy of Software Used in the Safety Analysis and Design of Defense Nuclear Facilities},
year = {2003},
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@techreport{CNSC2000,
author = {{Canadian Nuclear Safety Commission (CNSC)}},
@@ -7799,7 +7812,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
number = {G-149},
title = {Computer Programs Used in Design and Safety Analyses of Nuclear Power Plants and Research Reactors},
year = {2000},
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@article{AntoniolEtAl2002,
acmid = {631291},
@@ -7821,7 +7834,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
url = {http://dx.doi.org/10.1109/TSE.2002.1041053},
volume = {28},
year = {2002},
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bdsk-url-1 = {http://dx.doi.org/10.1109/TSE.2002.1041053}}
@incollection{Nedialkov2011,
@@ -7841,7 +7854,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
howpublished = {\url{http://www.ata.org/sites/ata.org/files/pdf/Most_common_ServiceConnectedDisabilities_FY2012.pdf}},
title = {Actual and Projected Cost to Compensate Veterans for Tinnitus, Analysis of Department of Veterans Affairds Data by ATA},
year = {2013},
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@article{ShargorodskyEtAl2010,
author = {Josef Shargorodsky and Gary C. Curhan and Wildon R. Farwell},
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title = {Prevalence and Characteristics of Tinnitus among {US} Adults},
volume = {123},
year = {2010},
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@article{Corliss1987,
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url = {http://search.proquest.com/docview/920880417?accountid=12347},
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@inproceedings{PryceEtAl2008,
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title = {Second Note on Basic Interval Arithmetic for IEEE754R},
url = {http://drops.dagstuhl.de/opus/volltexte/2008/1451},
year = {2008},
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@misc{Lipovaca2015,
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url = {http://doi.acm.org/10.1145/502102.502106},
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url = {http://dx.doi.org/10.1002/nme.1620030407},
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@book{Thompson1997,
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title = {A Methodology for Generating Verified Combinatorial Circuits},
url = {http://doi.acm.org/10.1145/1017753.1017794},
year = {2004},
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title = {How Can a Social Debugging Game Effectively Teach Computer Programming Concepts?},
url = {http://doi.acm.org.libaccess.lib.mcmaster.ca/10.1145/2493394.2493424},
year = {2013},
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title = {A Multiplayer Online Game for Teaching Software Engineering Practices},
url = {http://doi.acm.org.libaccess.lib.mcmaster.ca/10.1145/2556325.2567858},
year = {2014},
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school = {Oregon Graduate Institute of Science and Technology},
title = {Multi-stage programming: its theory and applications.},
year = 1999,
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@inproceedings{ThulasiEtAl2015,
author = {Thulasi Jegatheesan and W. Spencer Smith and Ned Nedialkov},
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title = {Application of the PSUADE Tool for Sensitivity Analysis of an Engineering Simulation},
type = {Technical report},
year = {2007},
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@techreport{SmithEtAl2015-MG-TR,
author = {W. Spencer Smith and Adam Lazzarato and Jacques Carette},
@@ -8097,7 +8110,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
title = {State of the Practice for Developing Oceanographic Software},
type = {Technical Report},
year = {2015},
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@techreport{SmithEtAl2015-SS-TR,
author = {W. Spencer Smith and Yue Sun and Jacques Carette},
@@ -8126,7 +8139,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
url = {http://dx.doi.org/10.1080/08993408.2011.579808},
volume = {21},
year = {2011},
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bdsk-url-1 = {http://dx.doi.org/10.1080/08993408.2011.579808}}
@mastersthesis{Chan2014,
@@ -8150,7 +8163,7 @@ into the system [1] - reference 1 is McLeodAndMacDonell2011 - {following up on t
title = {DSL implementation in MetaOCaml, Template Haskell, and C},
volume = {3016},
year = {2004},
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@inproceedings{Czarnecki2004,
abstract = {System family engineering seeks to exploit the commonalities among systems from a given problem domain while managing the variabilities among them in a systematic way. In system family engineering, new system variants can be rapidly created based on a set of reusable assets (such as a common architecture, components, models, etc.). Generative software development aims at modeling and implementing system families in such a way that a given system can be automatically generated from a specification written in one or more textual or graphical domain-specific languages. This paper gives an overview of the basic concepts and ideas of generative software development including DSLs, domain and application engineering, generative domain models, networks of domains, and technology projections. The paper also discusses the relationship of generative software development to other emerging areas such as Model Driven Development and Aspect-Oriented Software Development.},
@@ -8189,7 +8202,7 @@ NOTES FROM CAS 761 DISCUSSION
publisher = {Springer-Verlag},
title = {Overview of generative software development},
year = {2004},
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@misc{SageDevTeam2014,
author = {{Sage Development Team}},
@@ -8247,7 +8260,7 @@ NOTES FROM CAS 761 DISCUSSION
school = {School of Computational Science and Engineering, McMaster University},
title = {Virtual Material Testing Laboratory (Version 1.1)},
year = {2010},
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@book{Bird98:Introduction,
author = {Richard S. Bird},
@@ -8258,7 +8271,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Introduction to Functional Programming Using {H}askell},
url = {http://www.cs.ox.ac.uk/publications/books/functional/},
year = {1998},
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bdsk-url-1 = {http://www.cs.ox.ac.uk/publications/books/functional/}}
@book{Millington2007,
@@ -8272,7 +8285,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Game Physics Engine Development},
url = {http://books.google.ca/books?id=OsJ-8IRkRWgC},
year = {2007},
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bdsk-url-1 = {http://books.google.ca/books?id=OsJ-8IRkRWgC}}
@inproceedings{Owen1998,
@@ -8283,7 +8296,7 @@ NOTES FROM CAS 761 DISCUSSION
pages = {239--267},
title = {A Survey of Unstructured Mesh Generation Technology},
year = {1998},
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@article{saaty-ahp,
author = {Thomas L. Saaty},
@@ -8296,7 +8309,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {How to make a decision: The Analytic Hierarchy Process},
volume = {48},
year = {1990},
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@book{PharrAndHumphreys2004,
address = {San Francisco, CA, USA},
@@ -8314,7 +8327,7 @@ NOTES FROM CAS 761 DISCUSSION
note = {Part of MEng Report},
title = {Radio Astronomy Software: State of Practice},
year = {2014},
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@article{SmithEtAl2018,
author = {W. Spencer Smith and Zheng Zeng and Jacques Carette},
@@ -8328,7 +8341,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Seismology Software: State of the Practice},
volume = {22},
year = {2018},
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@article{KapilEtAl2014SA,
author = {Vasudha Kapil and W. Spencer Smith and Jacques Carette},
@@ -8337,7 +8350,7 @@ NOTES FROM CAS 761 DISCUSSION
journal = {Applied Spatial Analysis and Policy},
title = {State of the Practice for Software Tools in Spatial Analysis},
year = {Submitted 2014?},
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@article{KapilEtAl2014MI,
author = {Vasudha Kapil and W. Spencer Smith and Jacques Carette},
@@ -8346,7 +8359,7 @@ NOTES FROM CAS 761 DISCUSSION
journal = {Journal of Digital Imaging},
title = {State of the Practice for Software Tools in Medical Imaging},
year = {Submitted 2014?},
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@article{LazzaratoEtAl2017GIS,
author = {Adam Lazzarato and W. Spencer Smith and Jacques Carette},
@@ -8366,7 +8379,7 @@ NOTES FROM CAS 761 DISCUSSION
date-modified = {2017-09-28 14:24:37 +0000},
title = {Verifiable, Maintainable and Understandable Scientific Computing Code},
year = {2014},
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@article{SmithEtAl2014JOS,
author = {W. Spencer Smith and Yue Sun and Jacques Carette},
@@ -8386,7 +8399,7 @@ NOTES FROM CAS 761 DISCUSSION
note = {33 pp.},
title = {Statistical Software for Psychology: Comparing Development Practices Between {CRAN} and Other Communities},
year = {2018},
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@article{Wickham2011,
author = {Hadley Wickham},
@@ -8446,7 +8459,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis},
url = {http://www.stat.uni-muenchen.de/~leisch/Sweave},
year = 2002,
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bdsk-url-1 = {http://www.stat.uni-muenchen.de/~leisch/Sweave}}
@article{NorrisEtAl2014,
@@ -8461,7 +8474,7 @@ NOTES FROM CAS 761 DISCUSSION
url = {http://arxiv.org/abs/1408.1363},
volume = {abs/1408.1363},
year = {2014},
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@article{SarrabAndRehman2014,
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url = {http://dx.doi.org/10.1016/j.advengsoft.2013.12.001},
volume = {69},
year = {2014},
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@article{Barnes2010,
@@ -8487,7 +8500,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Publish your computer code: it is good enough},
volume = {467},
year = {2010},
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bdsk-url-1 = {doi:10.1038/467753a}}
@techreport{Nedialkov2006,
@@ -8508,7 +8521,7 @@ NOTES FROM CAS 761 DISCUSSION
number = {{CAS-10-02-NN}},
title = {{Implementing a Rigorous {ODE} Solver through Literate Programming}},
year = {2010},
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@inproceedings{GuanaAndStroulia2014,
author = {Victor Guana and Eleni Stroulia},
@@ -8534,7 +8547,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Notes on Structured Programming},
url = {http://dl.acm.org/citation.cfm?id=1243380.1243381},
year = {1972},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=1243380.1243381}}
@book{DahlEtAl1972,
@@ -8547,7 +8560,7 @@ NOTES FROM CAS 761 DISCUSSION
source = {Library of Congress Catalog Card Number: 72-84452},
title = {Structured Programming},
year = {1972},
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@article{SchulteEtAl2012,
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url = {http://www.jstatsoft.org/v46/i03},
volume = {46},
year = {2012},
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bdsk-url-1 = {http://www.jstatsoft.org/v46/i03}}
@article{HatcliffEtAl2009,
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url = {http://linkinghub.elsevier.com/retrieve/pii/S1571066109003570},
volume = {238},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.entcs.2009.09.002},
bdsk-url-2 = {http://linkinghub.elsevier.com/retrieve/pii/S1571066109003570}}
@@ -8632,7 +8645,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Collaborative and Competitive Video Games for Teaching Computing in Higher Education},
volume = {26},
year = {2017},
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bdsk-url-1 = {https://doi.org/10.1007/s10956-017-9690-4}}
@@ -8660,7 +8673,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Teaching Assistant Scheduling with Binary Integer Programming},
type = {Technical Report},
year = {2014?},
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@techreport{SmithMcCutchanAndCarette2017,
author = {W. Spencer Smith and John McCutchan and Jacques Carette},
@@ -8671,7 +8684,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Commonality Analysis for a Family of Material Models},
type = {Technical Report},
year = {2017},
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@inproceedings{ChanAndSmith2014,
author = {Samantha Chan and W. Spencer Smith},
@@ -8738,7 +8751,7 @@ NOTES FROM CAS 761 DISCUSSION
url = {http://dblp.uni-trier.de/db/conf/padl/padl2008.html#KellerCCSB08},
volume = 4902,
year = 2008,
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bdsk-url-1 = {http://dblp.uni-trier.de/db/conf/padl/padl2008.html#KellerCCSB08}}
@inproceedings{Korelc2001,
@@ -8759,7 +8772,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Hybrid System for Multi-language and Multi-environment Generation of Numerical Codes},
url = {http://doi.acm.org/10.1145/384101.384130},
year = {2001},
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bdsk-url-1 = {http://doi.acm.org/10.1145/384101.384130},
bdsk-url-2 = {http://dx.doi.org/10.1145/384101.384130}}
@@ -8774,7 +8787,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Should Code by Released?},
volume = {53},
year = {2010},
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@book{Wriggers2008,
annote = {- has information on automatic code generation for FEM},
@@ -8787,7 +8800,7 @@ NOTES FROM CAS 761 DISCUSSION
title = {Nonlinear Finite Element Methods},
url = {http://books.google.ca/books?id=IaV0wgG2jacC},
year = {2008},
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bdsk-url-1 = {http://books.google.ca/books?id=IaV0wgG2jacC}}
@inproceedings{Taha2004,
@@ -8801,7 +8814,7 @@ This hands-on tutorial is aimed at the reader interested in learning the basics
publisher = {Springer-Verlag},
title = {A gentle introduction to multi-stage programming},
year = {2004},
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@article{GabardoEtAl2015,
annote = {- originally submitted to ASEE Advances in Engineering Education - rejected
@@ -8814,7 +8827,7 @@ This hands-on tutorial is aimed at the reader interested in learning the basics
title = {Intelligent Prediction Modelling for Determining Students at Risk of Failure},
volume = {Submitted},
year = {2015},
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@book{Voelter2013,
author = {Markus Voelter},
@@ -8858,7 +8871,7 @@ This hands-on tutorial is aimed at the reader interested in learning the basics
title = {Multi-stage programming with {F}unctors and {M}onads: {E}liminating abstraction overhead from generic code},
volume = {76},
year = {2011},
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@inproceedings{Smith2013,
author = {W. Spencer Smith},
@@ -8909,7 +8922,7 @@ This hands-on tutorial is aimed at the reader interested in learning the basics
month = apr,
title = {An Elliptical Shaped Classroom: A Room with a View},
year = {2012},
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@article{Merali2010,
annote = {doi:10.1038/467775a
@@ -8948,7 +8961,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {{C}ertification of {S}cientific {C}omputing {S}oftware},
type = {Technical Report},
year = {2011},
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@article{Prince2004,
author = {Michael Prince},
@@ -8998,7 +9011,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
month = nov,
title = {Analysis of Critical Scientific Software},
year = {2011},
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@inproceedings{SmithAndYu2011,
author = {W. Spencer Smith and Wen Yu},
@@ -9008,7 +9021,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
month = jul,
title = {A Family Approach for Scientific Computing Software},
year = {2011},
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@inproceedings{Smith2011,
author = {W. Spencer Smith},
@@ -9019,7 +9032,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
note = {6 pp},
title = {Strategic Planning in an Academic Context},
year = {2011},
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@inproceedings{CurwinEtAl2011,
author = {Michael D. Curwin and Thomas E. Doyle and W. Spencer Smith},
@@ -9041,7 +9054,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
organization = {American Society for Engineering Education},
title = {Closing the Design Loop in Freshman Engineering},
year = {2011},
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@techreport{ElSheikhEtAl2011,
author = {Ahmed H. ElSheikh and W. Spencer Smith and Samir E. Chidiac},
@@ -9054,9 +9067,9 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Assessment of two a posteriori error estimators for steady-state flow problems},
type = {Technical Report},
year = {2011},
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@article{IEEE2003,
author = {IEEE},
@@ -9067,7 +9080,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
pages = {54},
title = {{IEEE} Standard on Transitions, Pulses, and Related Waveforms},
year = {2003},
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bdsk-url-1 = {http://dx.doi.org/10.1109/IEEESTD.2003.94394}}
@book{Zelle2004,
@@ -9113,7 +9126,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
number = {CMU/SEI-2010-TR-037},
title = {Strategic Planning with Critical Success Factors and Future Scenarios: An Integrated Strategic Planning Framework},
year = {2010},
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@article{Lorenzen2006,
author = {Michael Lorenzen},
@@ -9288,7 +9301,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {{GrAL}-the grid algorithms library},
volume = {22},
year = {2006},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.future.2003.09.002}}
@misc{Indiana2010,
@@ -9529,7 +9542,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Engineering the Software for Understanding Climate Change},
volume = {11},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.193}}
@article{DiFelice1993,
@@ -9587,7 +9600,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
url = {http://www.sciencemag.org},
volume = {314},
year = {2006},
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bdsk-url-1 = {http://www.sciencemag.org},
bdsk-url-2 = {http://dx.doi.org/10.1126/science.314.5807.1856}}
@@ -9600,7 +9613,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
note = {5 pp},
title = {Undergraduate Engineering Computing Virtualisation},
year = {2010},
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@article{TverskyandKahneman1974,
author = {Amos Tversky and Daniel Kahneman},
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month = aug,
title = {Combining Software Engineering and Scientific Computing: Some Potential Research Directions},
year = {2008},
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@techreport{WorthAndGreenough2007,
author = {D. J. Worth and C. Greenough},
@@ -9854,7 +9867,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {A Software Chasm: Software Engineering and Scientific Computing},
volume = {24},
year = {2007},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MS.2007.155}}
@inbook{BoisvertEtAl2005,
@@ -9883,7 +9896,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
publisher = {IEEE Computer Society},
title = {Software Development Environments for Scientific and Engineering Software: A Series of Case Studies},
year = {2007},
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bdsk-url-1 = {http://dx.doi.org/10.1109/ICSE.2007.77}}
@article{Glass2004,
@@ -9941,7 +9954,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
publisher = {IEEE, Piscataway, NJ},
title = {Teaching and Using Service-Oriented Architecture ({SOA}) in an Academic Environment},
year = {2008},
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@article{SquiresEtAl2006,
author = {S. Squires and M. L. Van de Vanter and L. G. Votta},
@@ -9980,7 +9993,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
pages = {1--15},
title = {The Danger of Hidden Assumptions and the Need for Requirements in Scientific Computing},
year = {Submitted January 2008},
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@book{VanVliet2000,
address = {New York, NY, USA},
@@ -9991,7 +10004,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
publisher = {John Wiley \& Sons, Inc.},
title = {Software Engineering (2nd ed.): Principles and Practice},
year = {2000},
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@book{Kreyszig1988,
author = {Erwin Kreyszig},
@@ -10104,7 +10117,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
url = {doi:10.1139/L08-063},
volume = {35},
year = {2008},
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local-url = {file://localhost/Users/smiths/Work/Research/Papers/ElSheikhEtAl_Submit2008_CNM_Rejected/ElSheikhEtAl_Submitted2008_CNM.pdf},
title = {Assessment of Two A Posteriori Error Estimators for Steady-State Flow Problems},
year = {Sumbitted 2008 Rejected 2009},
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@mastersthesis{McCutchan2007,
address = {Hamilton, ON, Canada},
@@ -10144,8 +10157,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {A posteriori error estimation based on numerical realization of the variational multiscale method},
volume = {197},
year = {2008},
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@inproceedings{CohenEtAl2006,
address = {New York, NY, USA},
@@ -10195,7 +10208,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Intelligent Computer Mathematics, 9th International Conference, AISC 2008},
url = {{http://dx.doi.org/10.1007/978-3-540-85110-3_4}},
year = {2008},
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bdsk-url-1 = {%7Bhttp://dx.doi.org/10.1007/978-3-540-85110-3_4%7D}}
@inproceedings{ChinEtAl2002,
@@ -10278,7 +10291,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Gaussian Elimination: A case study in efficient genericity with {M}eta{OC}aml},
volume = {62},
year = {2006},
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@book{Long1961,
address = {Englewood Cliffs, New Jersey},
@@ -10395,7 +10408,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
publisher = {% IEEE %Computer %Society %Conference %Publishing %Services %(CPS)},
title = {Report from the 3rd International Symposium on Software Engineering Course Projects ({SWECP} 2006)},
year = {2007},
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@article{Perzyna1966,
author = {P. Perzyna},
@@ -10415,8 +10428,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
local-url = {file://localhost/Users/smiths/Work/Research/Papers/SNC2007/Version3/snc/McCutchanAndSmith_AsSubmitted.pdf},
title = {A Virtual Material Testing Laboratory Using Symbolic Processing and Code Generation},
year = {rejected},
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@article{HullEtAl1972,
author = {T.E. Hull and W.H. Enright and B.M. Fellen and A. E. Seddwick},
@@ -10581,7 +10594,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Numerical investigation of the reliability of a posteriori error estimation for advection-diffusion equations},
volume = {24},
year = {2008},
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@article{Wilkinson1971,
author = {J. H. Wilkinson},
@@ -10655,8 +10668,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
local-url = {file://localhost/Users/smiths/Work/Research/Papers/LimerickPresent2006/LimerickPresent2006.pdf},
title = {Is Computer Science to Software Engineering as Physics is to Civil Engineering?},
year = {2006},
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@book{Saaty1980,
address = {New York, New York},
@@ -10676,8 +10689,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
local-url = {file://localhost/Users/smiths/Work/Research/Papers/AIMS2006/SmithAbstract.txt},
title = {Improving the Quality of Scientific Computing Software Through Requirements Analysis},
year = {2006},
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@article{Parnas1997,
address = {New York, NY, USA},
@@ -10706,8 +10719,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Quality Assurance in Developing an Interval Subroutine Library},
url = {http://www.dagstuhl.de/06021/index.en.phtml},
year = {2006},
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@techreport{Pryce2005,
@@ -11028,8 +11041,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
pages = {492--493},
title = {A comparative analysis of two posteriori error estimators for the finite element method},
year = {2005},
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@book{Mase1970,
author = {George E. Mase},
@@ -11087,7 +11100,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {An Algorithm Oriented Mesh Database},
volume = {58},
year = {2003},
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@inproceedings{ErwigAndFu2004,
author = {Martin Erwig and Zhe Fu},
@@ -11193,8 +11206,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
local-url = {file://localhost/Users/smiths/Work/Research/Papers/USNCCM8/abstract_v2.pdf},
title = {On the Choice of An Error Norm for Advection Diffusion Equations},
year = {2005},
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@misc{BruasetAndLangtangen1996,
author = {A. Bruaset and H. Langtangen},
@@ -11394,8 +11407,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
pages = {273--278},
title = {A Virtual Laboratory for Material Testing},
year = {2005},
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@article{PetersAndParnas2002,
author = {Dennis K.~Peters and David Lorge Parnas},
@@ -11427,7 +11440,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {The {Draw-Bot}: A Project for Teaching Software Engineering},
volume = {3},
year = {1998},
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bdsk-url-1 = {https://doi.org/10.1109/FIE.1998.738548}}
@article{CraigenEtAl1995,
@@ -11513,8 +11526,8 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Numerical Simulation of Film Casting Using an Updated {L}agrangian Finite Element Algorithm},
volume = {43},
year = {2003},
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@inproceedings{SmithAndStolle1999,
address = {Hamilton, Ontario},
@@ -11556,7 +11569,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {A Comparison of Updated {L}agrangian and {E}ulerian Finite Element Algorithms for the Simulation of Film Casting},
volume = {38},
year = {2002},
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@inproceedings{SmithEtAl1998,
address = {Toronto, Ontario},
@@ -12066,7 +12079,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
school = {McMaster University, Hamilton, Ontario, Canada},
title = {Requirements Documentation for Engineering Mechanics Software: Guidelines, Template and a Case Study},
year = {2004},
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@misc{Fujio2000,
author = {Hidehiro Fujio},
@@ -12106,7 +12119,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
school = {Von der Fakult\"{a}t IV - Elektrotechnik und Informatik der Technischen Universit\"{a}t Berlin},
title = {Domain Engineering and Generic Programming for Parallel Scientific Computing},
year = {2002},
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@book{IEEE2000,
date-added = {2017-09-28 14:24:37 +0000},
@@ -12163,7 +12176,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Semi-formal design of reliable mesh generation systems},
volume = {35},
year = {2004},
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@article{Parnas1984,
@@ -12183,7 +12196,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
publisher = {PhD Dissertation, TU Cottbus},
title = {Generic Software Components for Scientific Computing},
year = {2000},
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@techreport{Parnas1992,
author = {D. L. Parnas},
@@ -12205,7 +12218,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {A Rational Design Process: How and Why to Fake it},
volume = {12},
year = {1986},
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@article{ParnasEtAl1981,
author = {David L. Parnas and S. Hester and D. Utter},
@@ -12355,7 +12368,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Designing Software for Ease of Extension and Contraction},
volume = {SE-5},
year = {1979},
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@book{BernAndPlassmann2000,
author = {Marshall Bern and Paul Plassmann},
@@ -12418,7 +12431,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Generic Components for Grid Data Structures and Algorithms with C++},
url = {http://www.math.tu-cottbus.de/INSTITUT/lsnmwr/papers/},
year = {2000},
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@article{BertiAndBader1998,
@@ -12641,7 +12654,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
title = {Specifying Executable Commands: An example of {FAST} domain engineering},
url = {http://www.research.avayalabs.com/user/weiss/Publications.html},
year = {Submitted 1997},
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bdsk-url-1 = {http://www.research.avayalabs.com/user/weiss/Publications.html}}
@book{WeissAndLai1999,
@@ -12681,7 +12694,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
publisher = {IEEE Computer Society},
title = {Engineering Domains: Executable Commands as an Example},
year = {1998},
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bdsk-url-1 = {http://doi.ieeecomputersociety.org/10.1109/ICSR.1998.685727}}
@article{ParnasAndWeiss2001,
@@ -12691,7 +12704,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
journal = {technical report ALR-2001-023},
title = {Definition and Documentation of Software Architectures},
year = {October 2001},
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@inproceedings{ArdisAndWeiss1997,
author = {Mark Ardis and David M. Weiss},
@@ -12704,7 +12717,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
publisher = {ACM, Inc.},
title = {Defining families: The commonality analysis},
year = {1997},
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@article{Weiss1998,
author = {David M. Weiss},
@@ -12718,7 +12731,7 @@ and uncertainty quantification. The product-based approach for certifying softwa
url = {citeseer.ist.psu.edu/13585.html},
volume = {1429},
year = {1998},
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@article{FQS607,
@@ -12736,7 +12749,7 @@ URN: urn:nbn:de:0114-fqs040245},
url = {http://www.qualitative-research.net/index.php/fqs/article/view/607},
volume = {5},
year = {2004},
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bdsk-url-2 = {http://dx.doi.org/10.17169/fqs-5.2.607}}
@@ -12761,7 +12774,7 @@ URN: urn:nbn:de:0114-fqs040245},
url = {http://doi.acm.org/10.1145/1525880.1525883},
volume = {18},
year = {2009},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1525880.1525883},
bdsk-url-2 = {http://dx.doi.org/10.1145/1525880.1525883}}
@@ -12788,7 +12801,7 @@ URN: urn:nbn:de:0114-fqs040245},
primaryclass = {cs.SE},
title = {Experience Report: Formal Methods in Material Science},
year = 2018,
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@article{WilsonEtAl2016,
author = {Greg Wilson and Jennifer Bryan and Karen Cranston and Justin Kitzes and Lex Nederbragt and Tracy K. Teal},
@@ -12802,7 +12815,7 @@ URN: urn:nbn:de:0114-fqs040245},
url = {http://arxiv.org/abs/1609.00037},
volume = {abs/1609.00037},
year = {2016},
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bdsk-url-1 = {http://arxiv.org/abs/1609.00037}}
@article{TaschukAndWilson2017,
@@ -12862,7 +12875,7 @@ Best practices in software engineering specifically aim to increase software rob
url = {http://mfkp.org/INRMM/article/14337051},
volume = {13},
year = {2017},
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bdsk-url-2 = {http://dx.doi.org/10.1371/journal.pcbi.1005412}}
@@ -12879,7 +12892,7 @@ Best practices in software engineering specifically aim to increase software rob
series = {Haskell '12},
title = {Template Your Boilerplate: Using {T}emplate {H}askell for Efficient Generic Programming},
year = {2012},
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bdsk-url-1 = {http://dx.doi.org/10.1145/2364506.2364509}}
@article{WagnerAndDeissenboeck2017,
@@ -12896,7 +12909,7 @@ Best practices in software engineering specifically aim to increase software rob
primaryclass = {cs.SE},
title = {{Abstractness, specificity, and complexity in software design}},
year = 2017,
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@techreport{KreymanAndParnas2002,
author = {K. Kreyman and D. L. Parnas},
@@ -12909,7 +12922,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {On Documenting the Requirements for Computer Programs Based on Models of Physical Phenomena},
type = {SQRL Report},
year = {2002},
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@article{Storer2017,
abstract = {The use of software is pervasive in all fields of science. Associated software development efforts may be very large, long lived, and complex, requiring the commitment of significant resources. However, several authors have argued that the ``gap'' or ``chasm'' between software engineering and scientific programming is a serious risk to the production of reliable scientific results, as demonstrated in a number of case studies. This article reviews the research that addresses the gap, exploring how both software engineering and research practice may need to evolve to accommodate the use of software in science.},
@@ -12936,7 +12949,7 @@ Best practices in software engineering specifically aim to increase software rob
url = {http://doi.acm.org/10.1145/3084225},
volume = {50},
year = {2017},
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bdsk-url-1 = {http://doi.acm.org/10.1145/3084225},
bdsk-url-2 = {http://dx.doi.org/10.1145/3084225}}
@@ -12955,7 +12968,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Designing Linear Algebra Algorithms by Transformation: Mechanizing the Expert Developer},
url = {https://doi.org/10.1007/978-3-642-38718-0_34},
year = {2013},
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bdsk-url-2 = {http://dx.doi.org/10.1007/978-3-642-38718-0_34}}
@@ -12972,7 +12985,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Evaluating replicability of laboratory experiments in economics},
url = {http://science.sciencemag.org/content/early/2016/03/02/science.aaf0918},
year = {2016},
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bdsk-url-2 = {http://dx.doi.org/10.1126/science.aaf0918}}
@@ -12987,7 +13000,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Development of scientific software and practices for software development: A systematic literature review.},
volume = {12},
year = {2017},
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@article{KuksenokEtAl2017,
abstract = {Computing affects how scientific knowledge is constructed, verified, and validated. Rapid changes in hardware capability, and software flexibility, are coupled with a volatile tool and skill set, particularly in the interdisciplinary scientific contexts of oceanography. Existing research considers the role of scientists as both users and producers of code. We focus on how an intentional, individually-initiated but socially-situated, process of uptake influences code written by scientists. We present an 18-month interview and observation study of four oceanography teams, with a focus on ethnographic shadowing of individuals undertaking code work. Through qualitative analysis, we developed a framework of deliberate individual change, which builds upon prior work on programming practices in science through the lens of sociotechnical infrastructures. We use qualitative vignettes to illustrate how our theoretical framework helps to understand changing programming practices. Our findings suggest that scientists use and produce software in a way that deliberately mitigates the potential pitfalls of their programming practice. In particular, the object and method of visualization is subject to restraint intended to prevent accidental misuse.},
@@ -13002,7 +13015,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Deliberate Individual Change Framework for Understanding Programming Practices in four Oceanography Groups},
url = {http://dx.doi.org/10.1007/s10606-017-9285-x},
year = {2017},
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bdsk-url-1 = {http://dx.doi.org/10.1007/s10606-017-9285-x}}
@article{WilsonAndLumsdaine2006,
@@ -13020,7 +13033,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Software Carpentry: Getting Scientists to Write Better Code by Making Them More Productive},
volume = {8},
year = {2006},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2006.122}}
@article{CarverEtAl2017,
@@ -13038,7 +13051,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {The 4th International Workshop on Software Engineering for HPC in Computational Science and Engineering},
volume = {19},
year = {2017},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2017.28}}
@article{KatzEtAl2017,
@@ -13056,7 +13069,7 @@ Best practices in software engineering specifically aim to increase software rob
primaryclass = {cs.SE},
title = {{Report on the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4)}},
year = 2017,
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@article{GrebhahnEtAl2017,
author = {Grebhahn, Alexander and Engwer, Christian and Bolten, Matthias and Apel, Sven},
@@ -13071,7 +13084,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Variability of stencil computations for porous media},
url = {http://dx.doi.org/10.1002/cpe.4119},
year = {2017},
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bdsk-url-1 = {http://dx.doi.org/10.1002/cpe.4119}}
@article{DonohoEtAl2009,
@@ -13088,7 +13101,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Reproducible Research in Computational Harmonic Analysis},
volume = {11},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.15}}
@article{HattonAndRoberts1994,
@@ -13121,7 +13134,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {The chimera of software quality},
volume = {40},
year = {2007},
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@article{IoannidisEtAl2009,
author = {Ioannidis, John PA and Allison, David B and Ball, Catherine A and Coulibaly, Issa and Cui, Xiangqin and Culhane, Aed{\'\i}n C and Falchi, Mario and Furlanello, Cesare and Game, Laurence and Jurman, Giuseppe and others},
@@ -13134,7 +13147,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Repeatability of published microarray gene expression analyses},
volume = {41},
year = {2009},
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@article{QueirozAndSpitz2016,
author = {Francisco Queiroz and Rejane Spitz},
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title = {The Lens of the Lab: Design Challenges in Scientific Software},
volume = {10},
year = {2016},
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@inbook{BaileyEtAl2016,
address = {New York},
@@ -13159,7 +13172,7 @@ Best practices in software engineering specifically aim to increase software rob
publisher = {John Wiley and Sons},
title = {Reproducibility: Principles, Problems, Practices},
year = {2016},
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@article{GentlemanAndTempleLang2007,
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url = {http://dx.doi.org/10.1198/106186007X178663},
volume = {16},
year = {2007},
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@mastersthesis{Tang2008,
@@ -13188,7 +13201,7 @@ Best practices in software engineering specifically aim to increase software rob
school = {McMaster University},
title = {Developing Scientific Computing Software: Current Processes and Future Directions},
year = {2008},
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@article{Parnas1972MIS,
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title = {A Technique for the Specification of Software Modules with Examples},
volume = {15},
year = {1972},
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@inproceedings{BrittonEtAl1981,
author = {Britton, Kathryn Heninger and Parker, R Alan and Parnas, David L},
@@ -13213,7 +13226,7 @@ Best practices in software engineering specifically aim to increase software rob
pages = {195--204},
title = {A procedure for designing abstract interfaces for device interface modules},
year = {1981},
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@article{PflugerEtAl2016,
author = {Dirk Pfl{\"{u}}ger and Miriam Mehl and Julian Valentin and Florian Lindner and Stefan Wagner and Daniel Graziotin and Yang Wang},
@@ -13227,7 +13240,7 @@ Best practices in software engineering specifically aim to increase software rob
url = {http://arxiv.org/abs/1608.04336},
volume = {abs/1608.04336},
year = {2016},
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bdsk-url-1 = {http://arxiv.org/abs/1608.04336}}
@article{Parnas1985,
@@ -13249,7 +13262,7 @@ Best practices in software engineering specifically aim to increase software rob
url = {http://doi.acm.org/10.1145/214956.214961},
volume = {28},
year = {1985},
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bdsk-url-1 = {http://doi.acm.org/10.1145/214956.214961},
bdsk-url-2 = {http://dx.doi.org/10.1145/214956.214961}}
@@ -13263,7 +13276,7 @@ Best practices in software engineering specifically aim to increase software rob
organization = {In conjunction with SC16: The International Conference for High Performance Computing, Networking, Storage and Analysis},
title = {Advantages, Disadvantages and Misunderstandings About Document Driven Design for Scientific Software},
year = {2016},
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@inbook{Wassyng2016,
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publisher = {CRC},
title = {New Standards for Trustworthy Cyber-Physical Systems},
year = {2016},
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@book{HaveraaenEtAl1999,
author = {Haveraaen, M. and Friis, H.A. and Johansen, T.A. and Universitetet i Bergen. Department of Informatics},
@@ -13284,7 +13297,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Formal Software Engineering for Computational Modeling},
url = {https://books.google.ca/books?id=pzI0HQAACAAJ},
year = {1999},
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@incollection{PawlikEtAl2012,
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publisher = {D{\"u}sseldorf University Press},
title = {Developing Scientific Software: The Role of the Internet},
year = {2012},
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@article{ParnasEtAl1991,
author = {Parnas, D. L. and Asmis, G. J. K. and Madey, J.},
@@ -13316,7 +13329,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {{Assessment of Safety-Critical Software in Nuclear Power Plants}},
volume = {32},
year = {1991},
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@inproceedings{SzymczakEtAl2016,
address = {Austin, Texas, United States},
@@ -13328,7 +13341,7 @@ Best practices in software engineering specifically aim to increase software rob
note = {4 pp.},
title = {Position Paper: A Knowledge-Based Approach to Scientific Software Development},
year = {2016},
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@article{KitchenhamAndPfleeger1996,
acmid = {625544},
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url = {http://dx.doi.org/10.1109/52.476281},
volume = {13},
year = {1996},
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@article{KellyEtAl2014,
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url = {http://scitation.aip.org/content/aapm/journal/medphys/41/9/10.1118/1.4883877},
volume = {41},
year = {2014},
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@@ -13376,7 +13389,7 @@ Best practices in software engineering specifically aim to increase software rob
school = {Port-Said},
title = {Optimized Automatic Code Generation for Geometric Algebra Based Algorithms with Ray Tracing Application},
year = {2010},
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bdsk-url-1 = {http://128.84.21.199/abs/1607.04767}}
@article{SmithEtAl2016,
@@ -13389,7 +13402,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {State of Practice for Mesh Generation Software},
volume = {100},
year = {2016},
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pages = {48-57},
title = {Techniques for testing scientific programs without an oracle},
year = {2013},
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@article{FarhoodiEtAl2013,
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volume = {23},
year = {2013},
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@inproceedings{ShepardAndKelly2001,
@@ -13433,7 +13446,7 @@ Best practices in software engineering specifically aim to increase software rob
pages = {718},
title = {How to do inspections when there is no time},
year = {2001},
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@article{KellyAndShepard2004,
author = {Kelly, Diane and Shepard, Terry},
@@ -13446,7 +13459,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Eight maxims for software inspectors},
volume = {14},
year = {2004},
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@inproceedings{KellyAndShepard2000,
author = {Diane Kelly and Terry Shepard},
@@ -13460,7 +13473,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Task-directed software inspection technique: an experiment and case study},
url = {http://portal.acm.org/citation.cfm?id=782040#},
year = {2000},
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bdsk-url-1 = {http://portal.acm.org/citation.cfm?id=782040#}}
@article{Easterbrook2014,
@@ -13486,7 +13499,7 @@ Best practices in software engineering specifically aim to increase software rob
url = {http://dx.doi.org/10.1038/ngeo2283},
volume = {7},
year = {2014},
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bdsk-url-1 = {http://dx.doi.org/10.1038/ngeo2283}}
@inproceedings{LundgrenAndKanewala2016,
@@ -13506,7 +13519,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Experiences of Testing Bioinformatics Programs for Detecting Subtle Faults},
url = {http://doi.acm.org/10.1145/2897676.2897678},
year = {2016},
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bdsk-url-2 = {http://dx.doi.org/10.1145/2897676.2897678}}
@@ -13528,7 +13541,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Documentation Generation from Annotated Source Code of Scientific Software: Position Paper},
url = {http://doi.acm.org/10.1145/2897676.2897679},
year = {2016},
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bdsk-url-2 = {http://dx.doi.org/10.1145/2897676.2897679}}
@@ -13550,7 +13563,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {Nmag Micromagnetic Simulation Tool: Software Engineering Lessons Learned},
url = {http://doi.acm.org/10.1145/2897676.2897677},
year = {2016},
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bdsk-url-1 = {http://doi.acm.org/10.1145/2897676.2897677},
bdsk-url-2 = {http://dx.doi.org/10.1145/2897676.2897677}}
@@ -13566,7 +13579,7 @@ Best practices in software engineering specifically aim to increase software rob
title = {{Dependently-Typed Programming in Scientific Computing --- Examples from Economic Modelling}},
volume = 8241,
year = 2012,
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bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-642-41582-1_9}}
@inproceedings{Nguyen-HoanEtAl2010,
@@ -13599,7 +13612,7 @@ The most common reasons for and against the production of documentation and thei
title = {A Survey of Scientific Software Development},
url = {http://doi.acm.org/10.1145/1852786.1852802},
year = {2010},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1852786.1852802},
bdsk-url-2 = {http://dx.doi.org/10.1145/1852786.1852802}}
@@ -13617,7 +13630,7 @@ The most common reasons for and against the production of documentation and thei
primaryclass = {cs.PL},
title = {{Array Program Transformation with Loo.py by Example: High-Order Finite Elements}},
year = 2016,
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@article{SmithAndKoothoor2016,
abstract = {This paper presents a documentation and development method to facilitate the certification of scientific computing software used in the safety analysis of nuclear facilities. To study the problems faced during quality assurance and certification activities, a case study was performed on legacy software used for thermal analysis of a fuelpin in a nuclear reactor. Although no errors were uncovered in the code, 27 issues of incompleteness and inconsistency were found with the documentation. This work proposes that software documentation follow a rational process, which includes a software requirements specification following a template that is reusable, maintainable, and understandable. To develop the design and implementation, this paper suggests literate programming as an alternative to traditional structured programming. Literate programming allows for documenting of numerical algorithms and code together in what is termed the literate programmer's manual. This manual is developed with explicit traceability to the software requirements specification. The traceability between the theory, numerical algorithms, and implementation facilitates achieving completeness and consistency, as well as simplifies the process of verification and the associated certification.},
@@ -13635,7 +13648,7 @@ The most common reasons for and against the production of documentation and thei
url = {http://www.sciencedirect.com/science/article/pii/S1738573315002582},
volume = {48},
year = {2016},
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bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S1738573315002582},
bdsk-url-2 = {http://dx.doi.org/10.1016/j.net.2015.11.008}}
@@ -13647,7 +13660,7 @@ The most common reasons for and against the production of documentation and thei
pages = {408-419},
title = {The modular structure of complex systems},
year = {1984},
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@article{BeckhausEtAl2009,
author = {Arne Beckhause and Dirk Neumann and Lars Karg},
@@ -13660,7 +13673,7 @@ The most common reasons for and against the production of documentation and thei
title = {The Impact of Communcation Structure on Issue Tracking Efficiency at a Large Business Software Vendor},
volume = {X},
year = {2009},
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@article{HuttonEtAl2014,
author = {Eric W. H. Hutton and Mark D. Piper and Irina Overeem and Albert J. Kettner and James P. M. Syvitski},
@@ -13674,7 +13687,7 @@ The most common reasons for and against the production of documentation and thei
url = {http://arxiv.org/abs/1407.4106},
volume = {abs/1407.4106},
year = {2014},
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bdsk-url-1 = {http://arxiv.org/abs/1407.4106}}
@book{LoggEtAl2012,
@@ -13688,7 +13701,7 @@ The most common reasons for and against the production of documentation and thei
url = {http://dx.doi.org/10.1007/978-3-642-23099-8},
volume = {84},
year = {2012},
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bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-642-23099-8}}
@article{GewaltigAndCannon2012,
@@ -13700,7 +13713,7 @@ The most common reasons for and against the production of documentation and thei
pages = {20 pp},
title = {Quality and sustainability of software tools in neuroscience},
year = {2012},
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@incollection{DavisonEtAl2014,
address = {Boca Raton, Florida.},
@@ -13716,7 +13729,7 @@ The most common reasons for and against the production of documentation and thei
publisher = {Chapman \& Hall/CRC},
title = {Sumatra: A Toolkit for Reproducible Research},
year = {2014},
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@book{Malvern1969,
address = {Englewood Cliffs, New Jersey},
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publisher = {Prentice Hall},
title = {Introduction to the Mechanics of Continuous Medium},
year = {1969},
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@unpublished{Mileta2016,
author = {Ernest Mileta},
@@ -13736,7 +13749,7 @@ The most common reasons for and against the production of documentation and thei
note = {Presentation for Annual Review of NSERC CRD: A Literate Process for the Certification of Scientific and Engineering Software},
title = {Management System Requirements in new edition 15/16 Standard},
year = {2016},
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@unpublished{Mileta2015,
author = {Ernest Mileta},
@@ -13746,8 +13759,8 @@ The most common reasons for and against the production of documentation and thei
note = {Presentation for Annual Review of NSERC CRD: A Literate Process for the Certification of Scientific and Engineering Software},
title = {Management System Requirements \& Analytical Software},
year = {2015},
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@inproceedings{Parnas2010,
annote = {- never mix reference documents with introductions
@@ -13764,7 +13777,7 @@ The most common reasons for and against the production of documentation and thei
title = {Precise Documentation: The Key to Better Software},
url = {http://dx.doi.org/10.1007/978-3-642-15187-3_8},
year = {2010},
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bdsk-url-1 = {http://dx.doi.org/10.1007/978-3-642-15187-3_8}}
@@ -13788,7 +13801,7 @@ The most common reasons for and against the production of documentation and thei
title = {Documentation for Safety Critical Software.},
url = {http://dblp.uni-trier.de/db/conf/icse/icse93.html#CourtoisP93},
year = 1993,
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bdsk-url-1 = {http://dblp.uni-trier.de/db/conf/icse/icse93.html#CourtoisP93}}
@article{ParnasEtAl1994,
@@ -13811,7 +13824,7 @@ The most common reasons for and against the production of documentation and thei
url = {http://dx.doi.org/10.1109/32.368133},
volume = {20},
year = {1994},
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@inproceedings{HannayEtAl2009,
@@ -13830,7 +13843,7 @@ The most common reasons for and against the production of documentation and thei
title = {How Do Scientists Develop and Use Scientific Software?},
url = {http://dx.doi.org/10.1109/SECSE.2009.5069155},
year = {2009},
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@article{AckroydEtAl2008,
@@ -13845,7 +13858,7 @@ The most common reasons for and against the production of documentation and thei
title = {Scientific Software Development at a Research Facility},
volume = {25},
year = {2008},
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@article{SegalAndMorris2008,
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title = {Developing Scientific Software},
volume = {25},
year = {2008},
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@article{Easterbrook2009,
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title = {Engineering the Software for Understanding Climate Change},
volume = {11},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2009.193}}
@@ -13908,7 +13921,7 @@ The most common reasons for and against the production of documentation and thei
title = {Predicting Metamorphic Relations for Testing Scientific Software: A Machine Learning Approach Using Graph Kernels},
volume = {preprint},
year = {2015},
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@article{Kelly2015,
author = {Diane Kelly},
@@ -13924,7 +13937,7 @@ The most common reasons for and against the production of documentation and thei
url = {http://dx.doi.org/10.1016/j.jss.2015.07.027},
volume = {109},
year = {2015},
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bdsk-url-1 = {http://dx.doi.org/10.1016/j.jss.2015.07.027}}
@book{Zobel2004,
@@ -13935,7 +13948,7 @@ The most common reasons for and against the production of documentation and thei
publisher = {SpringerVerlag},
title = {Writing for Computer Science},
year = {2004},
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@article{HofnerEtAl2011,
added-at = {2011-05-30T00:00:00.000+0200},
@@ -13954,7 +13967,7 @@ The most common reasons for and against the production of documentation and thei
title = {An algebra of product families},
volume = {10},
year = {2011},
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bdsk-url-1 = {http://dblp.uni-trier.de/db/journals/sosym/sosym10.html#HofnerKM11}}
@book{Leveson2011,
@@ -13968,7 +13981,7 @@ The most common reasons for and against the production of documentation and thei
title = {Engineering a Safer World: Systems Thinking Applied to Safety},
url = {https://books.google.ca/books?id=0gZ\_7n5p8MQC},
year = {2011},
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bdsk-url-1 = {https://books.google.ca/books?id=0gZ%5C_7n5p8MQC}}
@techreport{Rushby2015,
@@ -13982,7 +13995,7 @@ The most common reasons for and against the production of documentation and thei
number = {SRI-CSL-15-01},
title = {The Interpretation and Evaluation of Assurance Cases},
year = 2015,
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@book{HoffmanAndStrooper1995,
address = {New York, NY, USA},
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title = {Software Design, Automated Testing, and Maintenance: A Practical Approach},
url = {http:// citeseer.ist.psu.edu/428727.html},
year = {1995},
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@techreport{SmithEtAl2015-Seism-TR,
@@ -14017,7 +14030,7 @@ The most common reasons for and against the production of documentation and thei
school = {McMaster University, Hamilton, Ontario, Canada},
title = {A Document Driven Approach to Certifying Scientific Computing Software},
year = {2013},
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@inproceedings{CaretteEtAl2011,
abstract = {We present the design and implementation of a generative geometric kernel. The kernel generator is generic, type-safe, parametrized by many design-level choices and extensible. The resulting code has minimal traces of the design abstractions. We achieve genericity through a layered design deriving concepts from affine geometry, linear algebra and abstract algebra. We achieve parametrization and type-safety by using OCaml's module system, including higher order modules. The cost of abstraction is removed by using MetaOCaml's support for code generation coupled with some annotations atop the code type.},
@@ -14059,7 +14072,7 @@ The most common reasons for and against the production of documentation and thei
title = {Testing for Trustworthiness in Scientific Software},
url = {http://dx.doi.org/10.1109/SECSE.2009.5069163},
year = {2009},
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bdsk-url-1 = {http://dx.doi.org/10.1109/SECSE.2009.5069163}}
@article{Carver2006,
@@ -14074,7 +14087,7 @@ The most common reasons for and against the production of documentation and thei
url = {http://www.ctwatch.org/quarterly/archives/november-2006-a},
volume = {2},
year = {2006},
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bdsk-url-1 = {http://www.ctwatch.org/quarterly/archives/november-2006-a}}
@article{MatthewsEtAl2008,
@@ -14097,7 +14110,7 @@ The most common reasons for and against the production of documentation and thei
url = {http://dx.doi.org/10.1109/MCSE.2008.144},
volume = {10},
year = {2008},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2008.144}}
@article{Dubois2005,
@@ -14112,7 +14125,7 @@ The most common reasons for and against the production of documentation and thei
title = {Maintaining Correctness in Scientific Programs},
volume = {7},
year = {2005},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MCSE.2005.54}}
@inproceedings{RemmelEtAll2013,
@@ -14132,7 +14145,7 @@ The most common reasons for and against the production of documentation and thei
title = {Design and Rationale of a Quality Assurance Process for a Scientific Framework},
url = {http://dl.acm.org/citation.cfm?id=2663370.2663379},
year = {2013},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2663370.2663379}}
@inproceedings{RemmelEtAl2011,
@@ -14153,7 +14166,7 @@ The most common reasons for and against the production of documentation and thei
title = {Supporting the Testing of Scientific Frameworks with Software Product Line Engineering: A Proposed Approach},
url = {http://doi.acm.org/10.1145/1985782.1985785},
year = {2011},
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bdsk-url-1 = {http://doi.acm.org/10.1145/1985782.1985785},
bdsk-url-2 = {http://dx.doi.org/10.1145/1985782.1985785}}
@@ -14168,7 +14181,7 @@ The most common reasons for and against the production of documentation and thei
title = {Iterative and incremental development: A brief history},
volume = {36},
year = {2003},
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@phdthesis{Yu2011,
address = {Hamilton, ON, Canada},
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school = {McMaster University},
title = {{FASCS}: A Family Approach for Developing Scientific Computing Software},
year = {2011},
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@article{RosselEtAl2014,
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url = {http://dx.doi.org/10.1016/j.advengsoft.2014.01.011},
volume = {70},
year = {2014},
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@inproceedings{BastarricaEtAl2006,
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username = {quantentunnel},
volume = 12,
year = 2014,
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bdsk-url-2 = {http://dx.doi.org/10.1371/journal.pbio.1001745}}
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title = {Best Practices for Scientific Computing},
volume = {abs/1210.0530},
year = {2013},
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@article{Wilson2006,
author = {Gregory V.~Wilson},
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url = {http://www.americanscientist.org/issues/pub/wheres-the-real-bottleneck-in-scientific-computing},
volume = {94},
year = {2006},
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bdsk-url-1 = {http://www.americanscientist.org/issues/pub/wheres-the-real-bottleneck-in-scientific-computing}}
@article{Parnas1972a,
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title = {On the Criteria To Be Used in Decomposing Systems into Modules},
volume = {15},
year = {1972},
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@inproceedings{Moore1996,
abstract = {The assurance argument that a trusted system satisfies
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url = {http://comjnl.oxfordjournals.org/content/27/2/97.abstract},
volume = {27},
year = {1984},
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bdsk-url-1 = {http://comjnl.oxfordjournals.org/content/27/2/97.abstract},
bdsk-url-2 = {http://dx.doi.org/10.1093/comjnl/27.2.97}}
@@ -14376,7 +14389,7 @@ The most common reasons for and against the production of documentation and thei
title = {Automated Capture of Experiment Context for Easier Reproducibility in Computational Research},
volume = {14},
year = {2012},
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@book{GhezziEtAl2003,
@@ -14443,7 +14456,7 @@ Chapter 8, Productivity
title = {A Product-Focused Approach to Software Certification},
volume = {41},
year = {2008},
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@article{Dubois2002,
author = {Paul F. Dubois},
@@ -14457,7 +14470,7 @@ Chapter 8, Productivity
title = {Designing Scientific Components},
volume = {4},
year = {2002},
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@article{SandersAndKelly2008,
annote = {``None of our interviewees created an up-front formal requirements specification. If regulations in their field mandated a requirements document, they wrote it when the software was almost complete. Customers of the scientific software might provide a vision statement, but nothing more. In all cases, customers ceded decisions about the software to the scientists, giving them broad sway in deciding what to include in the software.''},
@@ -14471,7 +14484,7 @@ Chapter 8, Productivity
title = {Dealing with Risk in Scientific Software Development},
volume = {4},
year = {2008},
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@article{KellyEtAl2011,
author = {Diane F. Kelly and W. Spencer Smith and Nicholas Meng},
@@ -14484,7 +14497,7 @@ Chapter 8, Productivity
title = {Software Engineering for Scientists},
volume = {13},
year = {2011},
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@inproceedings{KellyEtAl2007,
address = {St.\ John, New Brunswick},
@@ -14505,7 +14518,7 @@ Chapter 8, Productivity
title = {Assessing the Quality of Scientific Software},
url = {http://www.cse.msstate.edu/~SECSE08/schedule.htm},
year = {2008},
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@inproceedings{Kelly2013,
@@ -14523,7 +14536,7 @@ Chapter 8, Productivity
title = {Industrial Scientific Software: A Set of Interviews on Software Development},
url = {http://dl.acm.org/citation.cfm?id=2555523.2555555},
year = {2013},
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bdsk-url-1 = {http://dl.acm.org/citation.cfm?id=2555523.2555555}}
@inproceedings{Segal2008,
@@ -14537,7 +14550,7 @@ Chapter 8, Productivity
title = {Models of Scientific Software Development},
url = {http://www.cse.msstate.edu/~SECSE08/schedule.htm},
year = {2008},
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bdsk-url-1 = {http://secse08.cs.ua.edu/schedule.htm},
bdsk-url-2 = {http://www.cse.msstate.edu/~SECSE08/schedule.htm}}
@@ -14550,7 +14563,7 @@ Chapter 8, Productivity
title = {End-User Software Engineering and Professional End-User Developers},
url = {http://drops.dagstuhl.de/opus/volltexte/2007/1095},
year = {2007},
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bdsk-url-1 = {http://drops.dagstuhl.de/opus/volltexte/2007/1095}}
@inproceedings{Segal2007,
@@ -14566,7 +14579,7 @@ Chapter 8, Productivity
publisher = {IEEE Computer Society},
title = {Some Problems of Professional End User Developers},
year = {2007},
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bdsk-url-1 = {http://dx.doi.org/10.1109/VLHCC.2007.50}}
@article{Segal2005,
@@ -14620,7 +14633,7 @@ Chapter 8, Productivity
title = {Defining families: The commonality analysis},
url = {http://www.research.avayalabs.com/user/weiss/Publications.html},
year = {1997},
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@inproceedings{YuAndSmith2009,
@@ -14638,7 +14651,7 @@ Chapter 8, Productivity
title = {Reusability of {FEM} Software: A Program Family Approach},
year = {2009},
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@inproceedings{SmithMcCutchanAndCao2007,
@@ -14653,8 +14666,8 @@ Chapter 8, Productivity
pages = {39--47},
title = {Program Families in Scientific Computing},
year = {2007},
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@inproceedings{SmithEtAl2008,
address = {Leipzig, Germany},
@@ -14668,7 +14681,7 @@ Chapter 8, Productivity
title = {Commonality Analysis of Families of Physical Models for use in Scientific Computing},
url = {http://www.cse.msstate.edu/~SECSE08/schedule.htm},
year = {2008},
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@techreport{SmithAndChen2004b,
@@ -14682,9 +14695,9 @@ Chapter 8, Productivity
title = {Commonality analysis for mesh generating systems},
type = {Technical Report},
year = {2004},
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@techreport{CSA1999,
address = {178 Rexdale Blvd.\ Etobicoke, Ontario, Canada M9W 1R3},
@@ -14695,7 +14708,7 @@ Chapter 8, Productivity
number = {N286.7-99},
title = {Quality assurance of analytical, scientific, and design computer programs for nuclear power plants},
year = {1999},
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@techreport{CSA2009,
address = {5060 Spectrum Way, Suite 100, Mississauga, Ontario, Canada L4W 5N6, 1-800-463-6727},
@@ -14706,7 +14719,7 @@ Chapter 8, Productivity
number = {N286.7.1-09},
title = {Guideline for the application of {N286.7-99}, Quality assurance of analytical, scientific, and design computer programs for nuclear power plants},
year = {2009},
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@inproceedings{SmithEtAl2013,
author = {W. Spencer Smith and Nirmitha Koothoor and Nedialko Nedialkov},
@@ -14718,7 +14731,7 @@ Chapter 8, Productivity
pages = {[8 p.]},
title = {Document Driven Certification of Computational Science and Engineering Software},
year = {2013},
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@inproceedings{SmithAndLai2005,
address = {Paris, France},
@@ -14732,9 +14745,9 @@ Chapter 8, Productivity
pages = {107--121},
title = {A New Requirements Template for Scientific Computing},
year = {2005},
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@inproceedings{SmithAndChen2004,
address = {Banff, Alberta},
@@ -14748,7 +14761,7 @@ Chapter 8, Productivity
title = {Commonality and Requirements Analysis for Mesh Generating Software},
year = {2004},
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@inproceedings{Smith2006,
address = {Minneapolis / St.\ Paul, Minnesota},
@@ -14761,8 +14774,8 @@ Chapter 8, Productivity
title = {Systematic Development of Requirements Documentation for General Purpose Scientific Computing Software},
url = {http://www.ifi.unizh.ch/req/events/RE06/},
year = {2006},
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@article{SmithEtAl2014,
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url = {https://doi.org/10.1007/s11155-006-9020-7},
volume = {13},
year = {2007},
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@article{SmithAndYu2009,
@@ -14806,7 +14819,7 @@ Chapter 8, Productivity
title = {A Document Driven Methodology for Improving the Quality of a Parallel Mesh Generation Toolbox},
volume = {40},
year = {2009},
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@article{Ramsey1994,
@@ -14932,7 +14945,7 @@ Chapter 8, Productivity
title = {The Duke University scandal--what can be done?},
volume = {8},
year = {2011},
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@article{JoppaEtAl2013,
author = {Lucas N. Joppa and Greg McInerny and Richard Harper and Lara Salido and Kenji Takeda and Kenton O'Hara and David Gavaghan and Stephen Emmott},
@@ -14949,7 +14962,7 @@ Chapter 8, Productivity
title = {Code review for and by scientists: preliminary findings},
url = {https://arxiv.org/abs/1407.5648},
year = {2014},
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@article{Roache1997,
@@ -14975,7 +14988,7 @@ Chapter 8, Productivity
title = {Ten Simple Rules for Reproducible Computational Research},
volume = {9},
year = {October 2013},
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@article{PNAS2016,
author = {Anders Eklund and Thomas E. Nichols and Hans Knutsson},
@@ -15362,7 +15375,7 @@ Chapter 8, Productivity
url = {http://dx.doi.org/10.1109/MCSE.2009.139},
volume = {11},
year = {2009},
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@article{ShepardandKelly2004,
@@ -15403,7 +15416,7 @@ Chapter 8, Productivity
url = {http://dx.doi.org/10.1109/MS.2008.86},
volume = {25},
year = {2008},
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bdsk-url-1 = {http://dx.doi.org/10.1109/MS.2008.86}}
@article{KendallEtAl2016,