From 6bcbc131bfa1431065884d7c552265bad6880dd7 Mon Sep 17 00:00:00 2001 From: Blaise Thompson Date: Wed, 4 Apr 2018 00:18:19 -0500 Subject: 2018-04-04 00:18 --- bibliography.bib | 226 +++++++++++++++++++++++++++++++++++++++++---------- software/chapter.tex | 4 +- 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. -- cgit v1.2.3