diff options
| -rw-r--r-- | bibliography.bib | 226 | ||||
| -rw-r--r-- | 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.
|