2018-04-04 00:18

2 files changed, 186 insertions, 44 deletions

diff --git a/bibliography.bib b/bibliography.bib
index ec8138a..5f8fb24 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -1,43 +1,3 @@
-@article{DiracPaulAdrienMaurice1939a,

-  doi = {10.1017/s0305004100021162},

-  year  = {1939},

-  month = {jul},

-  publisher = {Cambridge University Press ({CUP})},

-  volume = {35},

-  number = {03},

-  pages = {416},

-  author = {P. A. M. Dirac},

-  title = {A new notation for quantum mechanics},

-  journal = {Mathematical Proceedings of the Cambridge Philosophical Society}

-}

-

-@article{BiggsJasonD2012a,

-  doi = {10.1098/rsta.2011.0219},

-  url = {https://doi.org/10.1098/rsta.2011.0219},

-  year  = {2012},

-  month = {jul},

-  publisher = {The Royal Society},

-  volume = {370},

-  number = {1972},

-  pages = {3709--3727},

-  author = {J. D. Biggs and J. A. Voll and S. Mukamel},

-  title = {Coherent nonlinear optical studies of elementary processes in biological complexes: diagrammatic techniques based on the wave function versus the density matrix},

-  journal = {Philosophical Transactions of the Royal Society A: Mathematical,  Physical and Engineering Sciences}

-}

-

-@article{WardJF1965a,

-  doi = {10.1103/revmodphys.37.1},

-  year  = {1965},

-  month = {jan},

-  publisher = {American Physical Society ({APS})},

-  volume = {37},

-  number = {1},

-  pages = {1--18},

-  author = {J. F. WARD},

-  title = {Calculation of Nonlinear Optical Susceptibilities Using Diagrammatic Perturbation Theory},

-  journal = {Reviews of Modern Physics}

-}

-

 @article{AartsmaThijsJ1976a,

   author =       {Aartsma, Thijs J and Wiersma, Douwe A},

   title =        {{Photon-echo relaxation in molecular mixed crystals}},

@@ -65,6 +25,19 @@
   month =        {apr},

 }

 

+@article{ArmstrongDeborahJ2006a,

+  author =       {Deborah J. Armstrong},

+  title =        {The quarks of object-oriented development},

+  journal =      {Communications of the {ACM}},

+  volume =       49,

+  number =       2,

+  pages =        {123--128},

+  year =         2006,

+  doi =          {10.1145/1113034.1113040},

+  month =        {feb},

+  publisher =    {Association for Computing Machinery ({ACM})},

+}

+

 @article{ArmstrongJA1962a,

   author =       {Armstrong, J. A. and Bloembergen, N. and Ducuing, J. and Pershan, P. S.},

   title =        {{Interactions between Light Waves in a Nonlinear Dielectric}},

@@ -148,6 +121,22 @@
   month =        {jul},

 }

 

+@article{BiggsJasonD2012a,

+  author =       {J. D. Biggs and J. A. Voll and S. Mukamel},

+  title =        {Coherent nonlinear optical studies of elementary processes in biological

+                  complexes: diagrammatic techniques based on the wave function versus the density

+                  matrix},

+  journal =      {Philosophical Transactions of the Royal Society A: Mathematical, Physical and

+                  Engineering Sciences},

+  volume =       370,

+  number =       1972,

+  pages =        {3709--3727},

+  year =         2012,

+  doi =          {10.1098/rsta.2011.0219},

+  month =        {jul},

+  publisher =    {The Royal Society},

+}

+

 @article{BirkedaDl1996a,

   author =       {D. Birkedal and V. G. Lyssenko and J. M. Hvam and K. El Sayed},

   title =        {Continuum contribution to excitonic four-wave mixing due to interaction-induced

@@ -234,6 +223,19 @@
   pmid =         15332970,

 }

 

+@article{CardDavidN1986a,

+  author =       {David N. Card and Victor E. Church and William W. Agresti},

+  title =        {An empirical study of software design practices},

+  journal =      {{IEEE} Transactions on Software Engineering},

+  volume =       {{SE}-12},

+  number =       2,

+  pages =        {264--271},

+  year =         1986,

+  doi =          {10.1109/tse.1986.6312942},

+  month =        {feb},

+  publisher =    {Institute of Electrical and Electronics Engineers ({IEEE})},

+}

+

 @article{CarlsonRogerJ1990a,

   author =       {Carlson, Roger J. and Wright, John C.},

   title =        {{Line narrowing in multiresonant third order molecular spectroscopies}},

@@ -290,6 +292,19 @@
   month =        {jul},

 }

 

+@inproceedings{CarverJeffreyC2007a,

+  author =       {Jeffrey C. Carver and Richard P. Kendall and Susan E. Squires and Douglass E.

+                  Post},

+  title =        {Software Development Environments for Scientific and Engineering Software: A

+                  Series of Case Studies},

+  booktitle =    {29th International Conference on Software Engineering

+                  ({ICSE}{\textquotesingle}07)},

+  year =         2007,

+  doi =          {10.1109/icse.2007.77},

+  month =        {may},

+  publisher =    {{IEEE}},

+}

+

 @article{CastellanosGomezA2012a,

   author =       {A. Castellanos-Gomez and M. Barkelid and A. M. Goossens and V. E. Calado and H.

                   S. J. van der Zant and G. A. Steele},

@@ -431,6 +446,19 @@ year = {1998}
   month =        {mar},

 }

 

+@article{DiracPaulAdrienMaurice1939a,

+  author =       {P. A. M. Dirac},

+  title =        {A new notation for quantum mechanics},

+  journal =      {Mathematical Proceedings of the Cambridge Philosophical Society},

+  volume =       35,

+  number =       03,

+  pages =        416,

+  year =         1939,

+  doi =          {10.1017/s0305004100021162},

+  month =        {jul},

+  publisher =    {Cambridge University Press ({CUP})},

+}

+

 @article{DochertyCallumJ2014a,

   author =       {Callum J. Docherty and Patrick Parkinson and Hannah J. Joyce and Ming-Hui Chiu

                   and Chang-Hsiao Chen and Ming-Yang Lee and Lain-Jong Li and Laura M. Herz and

@@ -489,7 +517,6 @@ year = {1998}
   month =        {jun},

 }

 

-

 @article{DonaldsonPaulMurray2010a,

   author =       {Donaldson, Paul M and Willison, Keith R and Klug, David R},

   title =        {{Generation of Simplified Protein Raman Spectra Using Three-Color Picosecond

@@ -624,6 +651,7 @@ year = {1998}
   pmid =         18832166,

 }

 

+

 @article{FurutaKoichi2012a,

   author =       {Furuta, Koichi and Fuyuki, Masanori and Wada, Akihide},

   title =        {Cross-Term Selective, Two-Pulse Correlation Measurements by Phase-Shifted

@@ -739,6 +767,7 @@ year = {1998}
   issn =         {0021-9606},

   month =        {jan},

 }

+

 @inproceedings{HannayJoErskine2009a,

   author =       {Jo Erskine Hannay and Carolyn MacLeod and Janice Singer and Hans Petter

                   Langtangen and Dietmar Pfahl and Greg Wilson},

@@ -854,7 +883,6 @@ year = {1998}
   month =        {apr},

   pmid =         19745871,

 }

-

 @book{KahnemanDaniel2013a,

 	author = {Kahneman, Daniel},

 	title = {Thinking, Fast and Slow},

@@ -1177,6 +1205,19 @@ year = {1998}
   month =        {dec},

 }

 

+@article{MillmanJarrodK2011a,

+  author =       {K. Jarrod Millman and Michael Aivazis},

+  title =        {Python for Scientists and Engineers},

+  journal =      {Computing in Science {\&} Engineering},

+  volume =       13,

+  number =       2,

+  pages =        {9--12},

+  year =         2011,

+  doi =          {10.1109/mcse.2011.36},

+  month =        {mar},

+  publisher =    {Institute of Electrical and Electronics Engineers ({IEEE})},

+}

+

 @article{MolinaSanchezAlejandro2013a,

   author =       {Alejandro Molina-S{\'{a}}nchez and Davide Sangalli and Kerstin

                   Hummer and Andrea Marini and Ludger Wirtz},

@@ -1213,6 +1254,15 @@ year = {1998}
   month =        {oct},

 }

 

+@inproceedings{MullerMatthiasM2001a,

+  author =       {M.M. Muller and W.F. Tichy},

+  title =        {Case study: extreme programming in a university environment},

+  booktitle =    {Proceedings of the 23rd International Conference on Software Engineering. {ICSE}

+                  2001},

+  doi =          {10.1109/icse.2001.919128},

+  publisher =    {{IEEE} Comput. Soc},

+}

+

 @article{NieZhaogang2014a,

   author =       {Zhaogang Nie and Run Long and Linfeng Sun and Chung-Che Huang

                   and Jun Zhang and Qihua Xiong and Daniel W. Hewak and Zexiang

@@ -1448,6 +1498,17 @@ year = {1998}
   pmid =         1463575,

 }

 

+@inproceedings{PrabuPrakash2011a,

+  author =       {Prakash Prabhu and Yun Zhang and Soumyadeep Ghosh and David I. August and Jialu

+                  Huang and Stephen Beard and Hanjun Kim and Taewook Oh and Thomas B. Jablin and

+                  Nick P. Johnson and Matthew Zoufaly and Arun Raman and Feng Liu and David Walker},

+  title =        {A survey of the practice of computational science},

+  booktitle =    {State of the Practice Reports on - {SC} {\textquotesingle}11},

+  year =         2011,

+  doi =          {10.1145/2063348.2063374},

+  publisher =    {{ACM} Press},

+}

+

 @misc{QMutex,

   note =         {Accessed: 2018-03-27},

   title =        {QMutex Class.},

@@ -1467,6 +1528,19 @@ year = {1998}
   month =        {jul},

 }

 

+@article{RewRuss1990a,

+  author =       {R. Rew and G. Davis},

+  title =        {{NetCDF}: an interface for scientific data access},

+  journal =      {{IEEE} Computer Graphics and Applications},

+  volume =       10,

+  number =       4,

+  pages =        {76--82},

+  year =         1990,

+  doi =          {10.1109/38.56302},

+  month =        {jul},

+  publisher =    {Institute of Electrical and Electronics Engineers ({IEEE})},

+}

+

 @article{RiebeMichaelT1988a,

   author =       {Riebe, Michael T. and Wright, John C.},

   title =        {{Spectral line‐narrowing and saturation effects in fully resonant nondegenerate

@@ -1538,6 +1612,24 @@ year = {1998}
   month =        {mar},

 }

 

+@inproceedings{SeamanCarolynB1997a,

+  author =       {Carolyn B. Seaman and Victor R. Basili},

+  title =        {An empirical study of communication in code inspections},

+  booktitle =    {Proceedings of the 19th international conference on Software engineering - {ICSE}

+                  {\textquotesingle}97},

+  year =         1997,

+  doi =          {10.1145/253228.253248},

+  publisher =    {{ACM} Press},

+}

+

+@inproceedings{SegalJudith2004a,

+  author =       {Segal, Judith},

+  title =        {Models of scientific software development},

+  booktitle =    {SECSE 08, First International Workshop on Software Engineering in Computational

+                  Science and Engineering},

+  year =         2008,

+}

+

 @article{SegalJudith2005a,

 	author = {Judith Segal},

 	title = {When Software Engineers Met Research Scientists: A Case Study},

@@ -1681,6 +1773,18 @@ year = {1998}
   month =        {nov},

 }

 

+@article{TreinshLloydA1987a,

+  author =       {Lloyd A. Treinish and Michael L. Gough},

+  title =        {A software package for the data-independent management of multidimensional data},

+  journal =      {Eos, Transactions American Geophysical Union},

+  volume =       68,

+  number =       28,

+  pages =        633,

+  year =         1987,

+  doi =          {10.1029/eo068i028p00633},

+  publisher =    {Wiley-Blackwell},

+}

+

 @article{TurnerDanielB2009a,

   author =       {Daniel B. Turner and Katherine W. Stone and Kenan Gundogdu and

                   Keith A. Nelson},

@@ -1742,6 +1846,19 @@ year = {1998}
   publisher =    {Springer Nature},

 }

 

+@article{WardJF1965a,

+  doi = {10.1103/revmodphys.37.1},

+  year  = {1965},

+  month = {jan},

+  publisher = {American Physical Society ({APS})},

+  volume = {37},

+  number = {1},

+  pages = {1--18},

+  author = {J. F. WARD},

+  title = {Calculation of Nonlinear Optical Susceptibilities Using Diagrammatic Perturbation Theory},

+  journal = {Reviews of Modern Physics}

+}

+

 @article{WehnerMU1996a,

   author =       {M. U. Wehner and D. Steinbach and M. Wegener},

   title =        {Ultrafast coherent transients due to exciton-continuum scattering in bulk {GaAs}},

@@ -1769,6 +1886,31 @@ year = {1998}
   month =        {apr},

 }

 

+@article{WellsDC1981a,

+  author =       {{Wells}, D.~C. and {Greisen}, E.~W. and {Harten}, R.~H.},

+  title =        "{FITS - a Flexible Image Transport System}",

+  journal =      {Astronomy and Astrophysics Supplement},

+  volume =       44,

+  pages =        363,

+  year =         1981,

+  month =        jun,

+}

+

+@article{WilsonGreg2017a,

+  author =       {Greg Wilson and Jennifer Bryan and Karen Cranston and Justin Kitzes and Lex

+                  Nederbragt and Tracy K. Teal},

+  title =        {Good enough practices in scientific computing},

+  journal =      {{PLOS} Computational Biology},

+  volume =       13,

+  number =       6,

+  pages =        {e1005510},

+  year =         2017,

+  doi =          {10.1371/journal.pcbi.1005510},

+  editor =       {Francis Ouellette},

+  month =        {jun},

+  publisher =    {Public Library of Science ({PLoS})},

+}

+

 @article{WongCathyY2011a,

   author =       {Cathy Y. Wong and Gregory D. Scholes},

   title =        {Using two-dimensional photon echo spectroscopy to probe the fine structure of the

diff --git a/software/chapter.tex b/software/chapter.tex
index d4a1517..87dee86 100644
--- a/software/chapter.tex
+++ b/software/chapter.tex
@@ -28,7 +28,7 @@ Who makes it, and what is the quality of that product?  %
 Much has been written about these questions.  %

 To this authors knowledge, there are at least 8 case studies and surveys dedicated to how

 scientists develop and use scientific software. \cite{CardDavidN1986a, SeamanCarolynB1997a,

-  MullerMatthias2001a, SegalJudith2004a, SegalJudith2005a, CarverJeffreyC2007a,

+  MullerMatthiasM2001a, SegalJudith2004a, SegalJudith2005a, CarverJeffreyC2007a,

   HannayJoErskine2009a, PrabuPrakash2011a}  %

 Although they focus on different disciplines, and were published at different times, these articles

 present a remarkably consistent perspective on what challenges tend to arise when developing

@@ -377,7 +377,7 @@ In Python, HDF5 is supported primarily through the h5py package. [CITE]  %
 \section{Scientific Python}  % --------------------------------------------------------------------

 

 SciPy is a collection of ``open-source software for mathematics, science, and egnineering.''

-\cite{MillmanKHarrod2011a}  %

+\cite{OliphantTravisE2007a, MillmanJarrodK2011a}  %

 SciPy was an absolute essential component of this dissertation and the work it describes.  %

 There are packages under the SciPy umbrella.  %

 NumPy is a very powerful and fast package for working with multidimensional arrays.