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wssspe.bib
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@INPROCEEDINGS{5069157,
author={Heroux, M.A. and Willenbring, J.M.},
booktitle={ICSE Workshop on Software Engineering for Computational Science and Engineering (SECSE '09)},
title={Barely sufficient software engineering: 10 practices to improve your CSE software},
year={2009},
pages={15-21},
keywords={software engineering;CSE software teams;Trilinos project;computational science and engineering;formal methods;formal software engineering;Application software;Automotive engineering;Laboratories;Programming;Research and development;Software algorithms;Software engineering;Software libraries;Software quality;US Department of Energy},
doi={10.1109/SECSE.2009.5069157},
month={May},}
@article{McCall2015_credit,
Author = {Jordan G. McCall and Ream Al-Hasani and Edward R. Siuda and Daniel Y. Hong and Aaron J. Norris and Christopher P. Ford and Michael R. Bruchas},
Title = {{CRH} Engagement of the Locus Coeruleus Noradrenergic System Mediates Stress-Induced Anxiety},
Journal = {Neuron},
Year = {2015},
Volume = {87},
Number = {3},
Pages = {605--620},
Month = aug,
Doi = {10.1016/j.neuron.2015.07.002}
}
@article{Lin2015_credit,
Author = {I-Chun Lin and Michael Okun and Matteo Carandini and Kenneth D. Harris},
Title = {The Nature of Shared Cortical Variability},
Journal = {Neuron},
Year = {2015},
Volume = {87},
Number = {3},
Pages = {644--656},
Month = aug,
Doi = {10.1016/j.neuron.2015.06.035}
}
@article{Howison2015,
Author = {Howison, James and Bullard, Julia},
Journal = {Journal of the Association for Information Science and Technology},
Title = {Software in the scientific literature: {Problems} with seeing, finding, and using software mentioned in the biology literature},
Doi = {10.1002/asi.23538},
Year = {2015},
Note = {In press, available at \url{http://dx.doi.org/10.1002/asi.23538}}
}
@article{Katz:2014_tc,
author = {Katz, Daniel S},
title = {Transitive Credit as a Means to Address Social and Technological Concerns Stemming from Citation and Attribution of Digital Products},
journal = {Journal of Open Research Software},
year = {2014},
volume = {2},
number = {1},
pages = {e20},
month = sep,
doi = {10.5334/jors.be}
}
@misc{WSSSPE3-SC-github-issues,
Author = {{{WSSSPE3} Software Credit Working Group}},
Howpublished = {\url{https://github.com/WSSSPE/meetings/issues/51}},
Note = {Accessed: 2015-10-1},
Title = {{WSSSPE3} Software Credit Working Group {GitHub} Issues},
Year = {2015}}
@misc{WSSSPE2-google-notes,
author = {{WSSSPE2} attendees},
Howpublished = {\url{https://docs.google.com/document/d/1-BxkYWDQ6nNNBXBStUL0xcKF9qCTlEALwf928J_MemI/}},
Note = {Accessed: 2015-02-15},
Title = {{WSSSPE2} Collaborative Notes}}
@misc{NSF_software_vision,
Author = {{National Science Foundation}},
Note = {NSF 12-113, \url{http://www.nsf.gov/publications/pub_summ.jsp?ods_key=nsf12113}},
Title = {A Vision and Strategy for Software for Science, Engineering, and Education: Cyberinfrastructure Framework for the 21st Century},
Year = {2012}}
@book{Bourque2014,
Editor = {Pierre Bourque and Richard E. Fairley},
Publisher = {IEEE Press},
Title = {SWEBOK v3.0: Guide to the Software Engineering Body of Knowledge},
Year = {2014}}
@misc{iso25010,
Author = {ISO/IEC},
Howpublished = {\url{http://www.iso.org/iso/catalogue_detail.htm?csnumber=35733}},
Title = {ISO/IEC 25010:2011 Systems and software engineering: Systems and Software Quality Requirements and Evaluation (SQuaRE): System and software quality models},
Url = {http://www.iso.org/iso/catalogue_detail.htm?csnumber=35733},
Urldate = {2015-05-25},
Bdsk-Url-1 = {http://www.iso.org/iso/catalogue_detail.htm?csnumber=35733}}
@techreport{Miller_WSSSPE,
Author = {Miller, Mark C. and Diachin, Lori and Balay, Satish and McInnes, Lois Curfman and Smith, Barry},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.789055}},
Number = {789055},
Title = {Package Management Practices Essential for Interoperability: Lessons Learned and Strategies Developed for FASTMath},
Year = {2013}}
@techreport{Broman_WSSSPE,
Author = {Karl W. Broman},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1192}},
Number = {1309.1192},
Title = {Thirteen years of R/qtl: Just barely sustainable},
Year = {2013}}
@techreport{Ferenbaugh_WSSSPE,
Author = {Charles R. Ferenbaugh},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1428}},
Number = {1309.1428},
Title = {Experiments in Sustainable Software Practices for Future Architectures},
Year = {2013}}
@techreport{Stephan_WSSSPE,
Author = {Stephan, Eric G. and Elsethagen, Todd O. and Kleese van Dam, Kerstin and Riihimaki, Laura},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790738}},
Number = {790738},
Title = {What Comes First, the {OWL} or the Bean?},
Year = {2013}}
@techreport{Gaston_WSSSPE,
Author = {Gaston, Derek R. and Peterson, John and Permann, Cody J. and Andrs, David and Slaughter, Andrew E. and Miller, Jason M.},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790755}},
Number = {790755},
Title = {Continuous Integration for Concurrent Computational Framework and Application Development},
Year = {2013}}
@techreport{Dubey_WSSSPE,
Author = {A. Dubey and B. Van Straalen},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1781}},
Number = {1309.1781},
Title = {Experiences from Software Engineering of Large Scale {AMR} Multiphysics Code Frameworks},
Year = {2013}}
@techreport{Blatt_WSSSPE,
Author = {Makus Blatt},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1783}},
Number = {1309.1783},
Title = {{DUNE} as an Example of Sustainable Open Source Scientific Software Development},
Year = {2013}}
@techreport{Koop_WSSSPE,
Author = {David Koop and Juliana Freire and Cl\'{a}udio T. Silva},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1784}},
Number = {1309.1784},
Title = {Enabling Reproducible Science with {VisTrails}},
Year = {2013}}
@techreport{Ahern_WSSSPE,
Author = {Sean Ahern and Eric Brugger and Brad Whitlock and Jeremy S. Meredith and Kathleen Biagas and Mark C. Miller and Hank Childs},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1796}},
Number = {1309.1796},
Title = {{VisIt}: Experiences with Sustainable Software},
Year = {2013}}
@techreport{Choi_WSSSPE,
Author = {Sou-Cheng T. Choi},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791562}},
Number = {791562},
Title = {{MINRES-QLP Pack} and Reliable Reproducible Research via Staunch Scientific Software},
Year = {2013}}
@techreport{Crusoe_WSSSPE,
Author = {Michael Crusoe and C. Titus Brown},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791567}},
Number = {791567},
Title = {Walking the talk: adopting and adapting sustainable scientific software development processes in a small biology lab},
Year = {2013}}
@techreport{Panda_WSSSPE,
Author = {Panda, Dhabaleswar K. and Tomko, Karen and Schulz, Karl and Majumdar, Amitava},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791563}},
Number = {791563},
Title = {The {MVAPICH} Project: Evolution and Sustainability of an Open Source Production Quality {MPI} Library for {HPC}},
Year = {2013}}
@techreport{Heien_WSSSPE,
Author = {Eric M. Heien and Todd L. Miller and Becky Gietzel and Louise H. Kellogg},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1199}},
Number = {1309.1199},
Title = {Experiences with Automated Build and Test for Geodynamics Simulation Codes},
Year = {2013}}
@techreport{Casanova_WSSSPE,
Author = {Henri Casanova and Arnaud Giersch and Arnaud Legrand and Martin Quinson and Fr\'{e}d\'{e}ric Suter},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1630}},
Number = {1309.1630},
Title = {{SimGrid}: a Sustained Effort for the Versatile Simulation of Large Scale Distributed Systems},
Year = {2013}}
@techreport{Trainer_WSSSPE,
Author = {Erik Trainer and Chalalai Chaihirunkarn and James Herbsleb},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790754}},
Number = {790754},
Title = {The Big Effects of Short-term Efforts: A Catalyst for Community Engagement in Scientific Software},
Year = {2013}}
@techreport{Cohen_WSSSPE,
Author = {Jeremy Cohen and Chris Cantwell and Neil {Chue Hong} and David Moxey and Malcolm Illingworth and Andrew Turner and John Darlington and Spencer Sherwin},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1101}},
Number = {1309.1101},
Title = {Simplifying the Development, Use and Sustainability of {HPC} Software},
Year = {2013}}
@techreport{Slawinski_WSSSPE,
Author = {Jaroslaw Slawinski and Vaidy Sunderam},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791570}},
Number = {791570},
Title = {Towards Semi-Automatic Deployment of Scientific and Engineering Applications},
Year = {2013}}
@article{Prlic_WSSSPE,
Author = {Andreas Prli\'{c} and James B. Procter},
Journal = {PLOS Computational Biology},
Note = {\url{http://dx.doi.org/10.1371/journal.pcbi.1002802}},
Number = {12},
Title = {Ten Simple Rules for the Open Development of Scientific Software},
Volume = {8},
Year = {2012}}
@techreport{Dubey2_WSSSPE,
Author = {A. Dubey and S. Brandt and R. Brower and M. Giles and P. Hovland and D.Q. Lamb and F. L\"{o}ffler and B. Norris and B. OShea and C. Rebbi and M. Snir and R. Thakur},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1780}},
Number = {1309.1780},
Title = {Software Abstractions and Methodologies for {HPC} Simulation Codes on Future Architectures},
Year = {2013}}
@techreport{Carver_WSSSPE,
Author = {Jeffrey C. Carver and George K. Thiruvathukal},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.830442}},
Number = {830442},
Title = {Software Engineering Need not be Difficult},
Year = {2013}}
@techreport{Stewart_WSSSPE,
Author = {Craig A. Stewart and Julie Wernert and Eric A. Wernert and William K. Barnett and Von Welch},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1817}},
Number = {1309.1817},
Title = {Initial Findings from a Study of Best Practices and Models for Cyberinfrastructure Software Sustainability},
Year = {2013}}
@techreport{Brown_WSSSPE,
Author = {Jed Brown and Matthew Knepley and Barry Smith},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791571}},
Number = {791571},
Title = {Run-time extensibility: anything less is unsustainable},
Year = {2013}}
@techreport{Swenson_WSSSPE,
Author = {Shel Swenson and Yogesh Simmhan and Viktor Prasanna and Manish Parashar and Jason Riedy and David Bader and Richard Vuduc},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1828}},
Number = {1309.1828},
Title = {Sustainable Software Development for Next-Gen Sequencing ({NGS}) Bioinformatics on Emerging Platforms},
Year = {2013}}
@techreport{Calero_WSSSPE,
Author = {Coral Calero and M.Angeles Moraga and Manuel F. Bertoa},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1640}},
Number = {1309.1640},
Title = {Towards a Software Product Sustainability Model},
Year = {2013}}
@techreport{Venters_WSSSPE,
Author = {Colin Venters and Lydia Lau and Michael K. Griffiths and Violeta Holmes and Rupert R. Ward and Jie Xu},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790758}},
Number = {790758},
Title = {The Blind Men and the Elephant: Towards a Software Sustainability Architectural Evaluation Framework},
Year = {2013}}
@techreport{Pierce_WSSSPE,
Author = {Marlon Pierce and Suresh Marru and Chris Mattmann},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790761}},
Number = {790761},
Title = {Sustainable Cyberinfrastructure Software Through Open Governance},
Year = {2013}}
@techreport{Katz_WSSSPE,
Author = {Daniel S. Katz and David Proctor},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790767}},
Number = {790767},
Title = {A Framework for Discussing e-Research Infrastructure Sustainability},
Year = {2013}}
@techreport{Lenhardt_WSSSPE,
Author = {Christopher Lenhardt and Stanley Ahalt and Brian Blanton and Laura Christopherson and Ray Idaszak},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791561}},
Number = {791561},
Title = {Data Management Lifecycle and Software Lifecycle Management in the Context of Conducting Science},
Year = {2013}}
@techreport{Weber_WSSSPE,
Author = {Nicholas Weber and Andrea Thomer and Michael Twidale},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791564}},
Number = {791564},
Title = {Niche Modeling: Ecological Metaphors for Sustainable Software in Science},
Year = {2013}}
@techreport{Knepley_WSSSPE,
Author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.785731}},
Number = {785731},
Title = {Accurately Citing Software and Algorithms Used in Publications},
Year = {2013}}
@techreport{Priem_WSSSPE,
Author = {Jason Priem and Heather Piwowar},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790651}},
Number = {790651},
Title = {Toward a comprehensive impact report for every software project},
Year = {2013}}
@techreport{Katz2_WSSSPE,
Author = {Daniel S. Katz},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791606}},
Number = {791606},
Title = {Citation and Attribution of Digital Products: Social and Technological Concerns},
Year = {2013}}
@techreport{Chue_Hong_WSSSPE,
Author = {Neil {Chue Hong} and Brian Hole and Samuel Moore},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.795303}},
Number = {795303},
Title = {Software Papers: improving the reusability and sustainability of scientific software},
Year = {2013}}
@techreport{Loffler_WSSSPE,
Author = {Frank L\"{o}ffler and Steven R. Brandt and Gabrielle Allen and Erik Schnetter},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1812}},
Number = {1309.1812},
Title = {Cactus: Issues for Sustainable Simulation Software},
Year = {2013}}
@techreport{Stodden_WSSSPE,
Author = {Victoria Stodden and Sheila Miguez},
Institution = {Social Science Research Network},
Note = {\url{http://dx.doi.org/10.2139/ssrn.2322276}},
Number = {2322276},
Title = {Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research},
Year = {2013}}
@techreport{Heiland_WSSSPE,
Author = {Randy Heiland and Betsy Thomas and Von Welch and Craig Jackson},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1677}},
Number = {1309.1677},
Title = {Toward a Research Software Security Maturity Model},
Year = {2013}}
@techreport{Blanton_WSSSPE,
Author = {Brian Blanton and Christopher Lenhardt},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.789028}},
Number = {789028},
Title = {A User Perspective on Sustainable Scientific Software},
Year = {2013}}
@techreport{Huang_WSSSPE,
Author = {Daisie Huang and Hilmar Lapp},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791560}},
Number = {791560},
Title = {Software Engineering as Instrumentation for the Long Tail of Scientific Software},
Year = {2013}}
@techreport{Krintz_WSSSPE,
Author = {Chandra Krintz and Hiranya Jayathilaka and Stratos Dimopoulos and Alexander Pucher and Rich Wolski},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790746}},
Number = {790746},
Title = {Developing Systems for {API} Governance},
Year = {2013}}
@techreport{Christopherson_WSSSPE,
Author = {Laura Christopherson and Ray Idaszak and Stan Ahalt},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790723}},
Number = {790723},
Title = {Developing Scientific Software through the Open Community Engagement Process},
Year = {2013}}
@techreport{Moore_WSSSPE,
Author = {Reagan W. Moore},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.5372}},
Number = {1309.5372},
Title = {Extensible Generic Data Management Software},
Year = {2013}}
@techreport{Cranston_WSSSPE,
Author = {Karen Cranston and Todd Vision and Brian O'Meara and Hilmar Lapp},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790739}},
Number = {790739},
Title = {A grassroots approach to software sustainability},
Year = {2013}}
@techreport{Vay_WSSSPE,
Author = {Jean-Luc Vay and Cameron G. R. Geddes and Alice Koniges and Alex Friedman and David P. Grote and David Bruhwiler},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.793816}},
Number = {793816},
Title = {White Paper on {DOE-HEP} Accelerator Modeling Science Activities},
Year = {2013}}
@techreport{Pierce2_WSSSPE,
Author = {Marlon Pierce and Suresh Marru and Borries Demeler and Amitava Majumdar and Mark Miller},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790760}},
Number = {790760},
Title = {Science Gateway Operational Sustainability: Adopting a Platform-as-a-Service Approach},
Year = {2013}}
@techreport{Zentner_WSSSPE,
Author = {Lynn Zentner and Michael Zentner and Victoria Farnsworth and Michael McLennan and Krishna Madhavan and Gerhard Klimeck},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1805}},
Number = {1309.1805},
Title = {{nanoHUB.org}: Experiences and Challenges in Software Sustainability for a Large Scientific Community},
Year = {2013}}
@techreport{Terrel_WSSSPE,
Author = {Andy Terrel},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791565}},
Number = {791565},
Title = {Sustaining the {Python} Scientific Software Community},
Year = {2013}}
@techreport{Maheshwari_WSSSPE,
Author = {Ketan Maheshwari and David Kelly and Scott J. Krieder and Justin M. Wozniak and Daniel S. Katz and Mei Zhi-Gang and Mainak Mookherjee},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.1813}},
Number = {1309.1813},
Title = {Reusability in Science: From Initial User Engagement to Dissemination of Results},
Year = {2013}}
@techreport{Wilkins-Diehr_WSSSPE,
Author = {Nancy Wilkins-Diehr and Katherine Lawrence and Linda Hayden and Marlon Pierce and Suresh Marru and Michael McLennan and Michael Zentner and Rion Dooley and Dan Stanzione},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790764}},
Number = {790764},
Title = {Science Gateways and the Importance of Sustainability},
Year = {2013}}
@techreport{Hart_WSSSPE,
Author = {Edmund Hart and Carl Boettiger and Karthik Ram and Scott Chamberlain},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791569}},
Number = {791569},
Title = {rOpenSci - a collaborative effort to develop R-based tools for facilitating Open Science},
Year = {2013}}
@techreport{Hanwell_WSSSPE,
Author = {Marcus Hanwell and Amitha Perera and Wes Turner and Patrick O'Leary and Katie Osterdahl and Bill Hoffman and Will Schroeder},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790756}},
Number = {790756},
Title = {Sustainable Software Ecosystems for Open Science},
Year = {2013}}
@techreport{Elster_WSSSPE,
Author = {Anne C. Elster},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1309.2357}},
Number = {1309.2357},
Title = {Software for Science: Some Personal Reflections},
Year = {2013}}
@techreport{Foster_WSSSPE,
Author = {Ian Foster and Vas Vasiliadis and Steven Tuecke},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.791604}},
Number = {791604},
Title = {Software as a Service as a path to software sustainability},
Year = {2013}}
@techreport{Girotto_WSSSPE,
Author = {Ivan Girotto and Axel Kohlmeyer and David Grellscheid and Shawn T. Brown},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.796439}},
Number = {796439},
Title = {Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages at the {ICTP}},
Year = {2013}}
@techreport{Crawford_WSSSPE,
Author = {T. Daniel Crawford},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.790757}},
Number = {790757},
Title = {On the Development of Sustainable Software for Computational Chemistry},
Year = {2013}}
@article{Veretnik,
Author = {Veretnik, Stella AND Fink, J. Lynn AND Bourne, Philip E.},
Doi = {10.1371/journal.pcbi.1000136},
Journal = {PLoS Comput Biol},
Month = {07},
Number = {7},
Pages = {e1000136},
Publisher = {Public Library of Science},
Title = {Computational Biology Resources Lack Persistence and Usability},
Url = {\url{http://dx.plos.org/10.1371%2Fjournal.pcbi.1000136}},
Volume = {4},
Year = {2008},
Bdsk-Url-1 = {http://dx.plos.org/10.1371%2Fjournal.pcbi.1000136},
Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pcbi.1000136}}
@article{bourne_ten,
Author = {Bourne, Philip E.},
Doi = {10.1371/journal.pcbi.1002001},
Journal = {PLoS Comput Biol},
Month = {01},
Number = {1},
Pages = {e1002001},
Publisher = {Public Library of Science},
Title = {Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia},
Url = {\url{http://dx.doi.org/10.1371%2Fjournal.pcbi.1002001}},
Volume = {7},
Year = {2011},
Bdsk-Url-1 = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1002001},
Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pcbi.1002001}}
@misc{arXiv-web,
Howpublished = {\url{http://arxiv.org}},
Key = {{arXiv.org e-Print archive}},
Note = {Accessed: 2014-02-03},
Title = {{arXiv.org e-Print archive}}}
@misc{figshare-web,
Howpublished = {\url{https://figshare.com}},
Key = {{figshare}},
Note = {Accessed: 2014-02-03},
Title = {{figshare}}}
@misc{zenodo-web,
Howpublished = {\url{https://zenodo.org}},
Key = {{zenodo}},
Note = {Accessed: 2015-10-28},
Title = {{Zenodo}}}
@techreport{WSSSPE1-pre-report,
Author = {Daniel S. Katz and Gabrielle Allen and Neil {Chue Hong} and Manish Parashar and David Proctor},
Institution = {arXiv},
Note = {\url{http://arxiv.org/abs/1311.3523}},
Number = {1311.3523},
Title = {First Workshop on Sustainable Software for Science: Practice and Experiences {(WSSSPE)}: Submission and Peer-Review Process, and Results},
Year = {2013}}
@misc{WSSSPE1-google-notes,
Author = {{WSSSPE1 attendees}},
Howpublished = {\url{https://docs.google.com/document/d/1eVfioGNlihXG_1Y8BgdCI6tXZKrybZgz5XuQHjT1oKU/}},
Note = {Accessed: 2014-02-03},
Title = {{WSSSPE1} Collaborative Notes}}
@misc{WSSSPE3-SC-google-notes,
Author = {{WSSSPE3 Software Credit Working Group}},
Date-Modified = {2015-10-01 23:59:39 +0000},
Howpublished = {\url{https://docs.google.com/document/d/1oN0ZYqIoWtOE1LBMIlWY9N8nn5LHTncj8GjUKPh62pA}},
Note = {Accessed: 2015-10-1},
Title = {{WSSSPE3} Software Credit Working Group Collaborative Notes},
Year = {2015}}
@misc{WSSSPE1-keynote1,
Author = {Philip E. Bourne},
Note = {A keynote presentation given at the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1), November 17, Denver, Colorado, USA. Abstract available online: \url{http://wssspe.researchcomputing.org.uk/wssspe1/keynotes/#bourne}. Slides available online: \url{www.slideshare.net/pebourne/a-recipe-for-sustainable-software}},
Title = {A Recipe for Sustainable Software},
Year = {2013}}
@misc{WSSSPE1-keynote2,
Author = {Arfon Smith},
Note = {A keynote presentation given at the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1), November 17, Denver, Colorado, USA. Abstract available online: \url{http://wssspe.researchcomputing.org.uk/wssspe1/keynotes/#smith}. Slides available online: \url{http://is.gd/wssspe}},
Title = {Scientific Software and the Open Collaborative Web},
Year = {2013}}
@misc{okcon-stodden-talk,
Author = {Victoria Stodden},
Note = {A talk given at the Open Knowledge Conference, September 16--18, Geneva, Switzerland. Slides available online:\url{http://www.stanford.edu/~vcs/talks/OKcon2013-Sept172013-STODDEN.pdf}},
Title = {Why Science is an Open Endeavor},
Year = {2013}}
@misc{plos-web,
Howpublished = {\url{http://www.plos.org/}},
Key = {{PLOS}},
Note = {Accessed: 2014-02-11},
Title = {{Public Library of Science}}}
@misc{pdb-web,
Howpublished = {\url{http://www.rcsb.org/pdb/}},
Key = {{PDB}},
Note = {Accessed: 2014-02-05},
Title = {{Protein Data Bank}}}
@misc{biojava-web,
Howpublished = {\url{http://biojava.org}},
Key = {{BioJava}},
Note = {Accessed: 2014-02-07},
Title = {{The BioJava Project}}}
@misc{osdc-web,
Howpublished = {\url{https://www.opensciencedatacloud.org/}},
Key = {OSDC},
Note = {Accessed: 2014-02-07},
Title = {{Open Science Data Cloud}}}
@misc{github-web,
Howpublished = {\url{https://github.com/}},
Key = {GitHub},
Note = {Accessed: 2014-02-11},
Title = {{GitHub}}}
@misc{sbir-web,
Howpublished = {\url{http://www.nsf.gov/eng/iip/sbir/}},
Key = {SBIR},
Note = {Accessed: 2014-02-07},
Title = {{Small Business Innovation Research}}}
@misc{emcee-web,
Author = {Dan Foreman-Mackey and contributors},
Howpublished = {\url{https://github.com/dfm/emcee}},
Key = {EMCEE},
Note = {Accessed: 2014-02-07},
Title = {{The Python ensemble sampling toolkit for affine-invariant MCMC}}}
@misc{ged-web,
Author = {C. Titus Brown},
Howpublished = {\url{http://ged.msu.edu}},
Key = {GED},
Note = {Accessed: 2014-02-07},
Title = {{Laboratory of Genomics, Evolution and Development}}}
@misc{rubygems-web,
Howpublished = {\url{http://rubygems.org/}},
Key = {RubyGems},
Note = {Accessed: 2014-02-07},
Title = {{RubyGems.org}}}
@misc{pypi-web,
Howpublished = {\url{https://pypi.python.org/pypi}},
Key = {PyPI},
Note = {Accessed: 2014-02-07},
Title = {{PyPI -- The Python Package Index}}}
@misc{cpan-web,
Howpublished = {\url{http://www.cpan.org/}},
Key = {CPAN},
Note = {Accessed: 2014-02-07},
Title = {{The Comprehensive Perl Archive Network (CPAN)}}}
@misc{peer-review-code,
Author = {Rosemary Dickin},
Howpublished = {\url{http://blogs.plos.org/biologue/2013/08/08/what-does-peer-review-mean-when-applied-to-computer-code/}},
Note = {Accessed: 2014-02-07},
Title = {{What does peer review mean when applied to computer code?}}}
@misc{perez-open-src-reproducible,
Author = {Fernando Perez},
Howpublished = {\url{http://blog.fperez.org/2013/11/an-ambitious-experiment-in-data-science.html}},
Title = {{An ambitious experiment in Data Science takes off: a biased, Open Source view from Berkeley}},
Year = {2013}}
@misc{fased-web,
Author = {{National Science Foundation}},
Date-Modified = {2015-10-01 23:54:58 +0000},
Howpublished = {\url{http://www.nsf.gov/pubs/policydocs/pappguide/nsf09_1/gpg_2.jsp\#IID2}},
Key = {FASED},
Title = {{Facilitation Awards for Scientists and Engineers with Disabilities}}}
@misc{OSS-ssmm-web,
Author = {Ross Gardler},
Howpublished = {\url{http://oss-watch.ac.uk/resources/ssmm}},
Note = {Accessed: 2014-02-06},
Title = {Software Sustainability Maturity Model}}
@techreport{lenhardt-wssspe1-panel,
Author = {Lenhardt, Christopher},
Institution = {figshare},
Note = {\url{http://dx.doi.org/10.6084/m9.figshare.853817}},
Number = {853817},
Title = {Summary of Papers on Science Software Sustainability Models for {WSSSPE} Panel {II}},
Year = {2013}}
@inproceedings{howison_incentives_2013,
Address = {San Antonio, {TX}},
Author = {Howison, James and Herbsleb, James D.},
Booktitle = {Proceedings of the {ACM} Conference on Computer Supported Cooperative Work},
Doi = {10.1145/2441776.2441828},
Month = feb,
Pages = {459--470},
Title = {Incentives and integration in scientific software production},
Year = {2013}}
@article{bietz_synergizing_2010,
Author = {Bietz, Matthew J. and Baumer, Eric P. and Lee, Charlotte P.},
Doi = {10.1007/s10606-010-9114-y},
Issn = {0925-9724},
Journal = {Comput. Supported Coop. Work},
Month = aug,
Number = {3-4},
Pages = {245--281},
Title = {Synergizing in Cyberinfrastructure Development},
Urldate = {2012-05-30},
Volume = {19},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10606-010-9114-y}}
@inproceedings{howison_scientific_2011,
Address = {Hangzhou, China},
Author = {Howison, James and Herbsleb, James D.},
Booktitle = {Proceedings of the {ACM} Conference on Computer Supported Cooperative Work},
Doi = {10.1145/1958824.1958904},
Pages = {513--522},
Publisher = {{ACM}},
Series = {{CSCW} '11},
Title = {Scientific software production: incentives and collaboration},
Year = {2011},
Bdsk-Url-1 = {http://dx.doi.org/10.1145/1958824.1958904}}
@article{citeulike:11831265,
Author = {Prli\'{c}, Andreas and Procter, James B.},
Citeulike-Article-Id = {11831265},
Citeulike-Linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1002802},
Citeulike-Linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/23236269},
Citeulike-Linkout-2 = {http://www.hubmed.org/display.cgi?uids=23236269},
Day = {6},
Doi = {10.1371/journal.pcbi.1002802},
Issn = {1553-7358},
Journal = {PLoS Computational Biology},
Keywords = {advices, journal, open\_source, research\_practices, software\_development, software\_engineering},
Month = dec,
Number = {12},
Pages = {e1002802+},
Pmid = {23236269},
Posted-At = {2012-12-19 10:49:27},
Priority = {2},
Publisher = {Public Library of Science},
Title = {Ten simple rules for the open development of scientific software},
Url = {http://dx.doi.org/10.1371/journal.pcbi.1002802},
Volume = {8},
Year = {2012},
Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1002802}}
@book{art-of-community,
Author = {Bacon, Jono},
Citeulike-Article-Id = {7888211},
Keywords = {bacon, community, participation},
Posted-At = {2010-09-23 10:59:02},
Priority = {0},
Title = {The Art of Community. Building the New Age of Participation.},
Year = {2009}}
@book{citeulike:478633,
Author = {Fogel, Karl},
Citeulike-Article-Id = {478633},
Citeulike-Linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0596007590},
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Citeulike-Linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0596007590},
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Citeulike-Linkout-6 = {http://www.worldcat.org/isbn/0596007590},
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Day = {07},
Howpublished = {Paperback},
Isbn = {0596007590},
Keywords = {oss},
Month = oct,
Posted-At = {2011-11-09 07:04:10},
Priority = {2},
Publisher = {O'Reilly Media, Inc.},
Title = {Producing Open Source Software: How to Run a Successful Free Software Project},
Url = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0596007590},
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@book{opac-b1134063,
Address = {Sebastopol. CA},
Author = {Fitzpatrick, Brian W. and Collins-Sussman, Ben},
Isbn = {978-1-449-30244-3},
Publisher = {O'Reilly},
Title = {Team geek : a software developer's guide to working well with others},
Url = {http://opac.inria.fr/record=b1134063},
Year = 2012,
Bdsk-Url-1 = {http://opac.inria.fr/record=b1134063}}
@inproceedings{DBLP:conf/cscw/HowisonH11,
Author = {James Howison and James D. Herbsleb},
Bibsource = {DBLP, http://dblp.uni-trier.de},
Booktitle = {CSCW},
Crossref = {DBLP:conf/cscw/2011},
Ee = {http://doi.acm.org/10.1145/1958824.1958904},
Pages = {513-522},
Title = {Scientific software production: incentives and collaboration},
Year = {2011}}
@proceedings{DBLP:conf/cscw/2011,
Bibsource = {DBLP, http://dblp.uni-trier.de},
Booktitle = {CSCW},
Editor = {Pamela J. Hinds and John C. Tang and Jian Wang and Jakob E. Bardram and Nicolas Ducheneaut},
Isbn = {978-1-4503-0556-3},
Publisher = {ACM},
Title = {Proceedings of the 2011 ACM Conference on Computer Supported Cooperative Work, CSCW 2011, Hangzhou, China, March 19-23, 2011},
Year = {2011}}
@misc{Trapani:2011,
Author = {Trapani, Gina},
Month = apr,
Title = {Your Community is Your Best Feature},
Url = {http://smarterware.org/7819/my-codeconf-talk-your-community-is-your-best-feature},
Year = {2011},
Bdsk-Url-1 = {http://smarterware.org/7819/my-codeconf-talk-your-community-is-your-best-feature}}
@misc{Allsopp:2012,
Author = {Allsopp, John},
Month = nov,
Title = {The Proof of the Pudding},
Url = {http://www.webdirections.org/blog/the-proof-of-the-pudding/},
Year = {2012},
Bdsk-Url-1 = {http://www.webdirections.org/blog/the-proof-of-the-pudding/}}
@article{1749-4699-6-1-015010,
Author = {Wolfgang Bangerth and Timo Heister},
Journal = {Computational Science \& Discovery},
Number = {1},
Pages = {015010},
Title = {What makes computational open source software libraries successful?},
Url = {http://stacks.iop.org/1749-4699/6/i=1/a=015010},
Volume = {6},
Year = {2013},
Bdsk-Url-1 = {http://stacks.iop.org/1749-4699/6/i=1/a=015010}}
@inproceedings{Turk:2013:SCH:2484762.2484782,
Acmid = {2484782},
Address = {New York, NY, USA},
Articleno = {69},
Author = {Turk, Matthew J.},
Booktitle = {Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery},
Doi = {10.1145/2484762.2484782},
Isbn = {978-1-4503-2170-9},
Keywords = {XSEDE proceedings, community, open source},
Location = {San Diego, California},
Numpages = {7},
Pages = {69:1--69:7},
Publisher = {ACM},
Series = {XSEDE '13},
Title = {Scaling a Code in the Human Dimension},
Url = {http://doi.acm.org/10.1145/2484762.2484782},
Year = {2013},
Bdsk-Url-1 = {http://doi.acm.org/10.1145/2484762.2484782},
Bdsk-Url-2 = {http://dx.doi.org/10.1145/2484762.2484782}}
@article{iPlant,
Author = {Goff, Stephen A and Vaughn, Matthew and McKay, Sheldon and Lyons, Eric and Stapleton, Ann E and Gessler, Damian and Matasci, Naim and Wang, Liya and Hanlon, Matthew and Lenards, Andrew and Muir, Andy and Merchant, Nirav and Lowry, Sonya and Mock, Stephen and Helmke, Matthew and Kubach, Adam and Narro, Martha and Hopkins, Nicole and Micklos, David and Hilgert, Uwe and Gonzales, Michael and Jordan, Chris and Skidmore, Edwin and Dooley, Rion and Cazes, John and McLay, Robert and Lu, Zhenyuan and Pasternak, Shiran and Koesterke, Lars and Piel, William H. and Grene, Ruth and Noutsos, Christos and Gendler, Karla and Feng, Xin and Tang, Chunlao and Lent, Monica and Kim, Seung-Jin and Kvilekval, Kristian and Manjunath, B S and Tannen, Val and Stamatakis, Alexandros and Sanderson, Michael and Welch, Stephen M. and Cranston, Karen A. and Soltis, Pamela and Soltis, Doug and O'Meara, Brian and Ane, Cecile and Brutnell, Tom and Kleibenstein, Daniel J. and White, Jeffery W. and Leebens-Mack, James and Donoghue, Michael J. and Spalding, Edgar P. and Vision, Todd J and Myers, Christopher R and Lowenthal, David and Enquist, Brian J and Boyle, Brad and Akoglu, Ali and Andrews, Greg and Ram, Sudha and Ware, Doreen and Stein, Lincoln and Stanzione, Dan},
Doi = {10.3389/fpls.2011.00034},
Issn = {1664-462X},
Journal = {Front. Plant Sci.},
Keywords = {bioinformatics; cyberinfrastructure; plant biology},
Number = {July},
Pages = {1--16},
Title = {The iPlant Collaborative: Cyberinfrastructure for Plant Biology},
Url = {http://dx.doi.org/10.3389/fpls.2011.00034},
Volume = 2,
Year = 2011,
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Pmid = {20383131},
Publisher = {Nature Publishing Group},
Title = {{QIIME} allows analysis of high-throughput community sequencing data},
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Pages = {66},
Title = {Software Carpentry: Getting Scientists to Write Better Code by Making Them More Productive},
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@misc{rOpenSci,
Abstract = {rOpenSci develops tools to faciliate open and reproducible
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Author = {Boettiger, Carl and Ram, Karthik and Chamberlain, Scott and Hart, Edmund},
Howpublished = {\url{http://ropensci.org/}},
Note = {Accessed: 2014-04-06},
Title = {{rOpenSci} - open source tools for open science},
Url = {http://ropensci.org/},
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Abstract = {Increased reliance on computational approaches in the life
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reproducible computation-reliant results truly are. Galaxy
http://usegalaxy.org, an open web-based platform for genomic
research, addresses these problems. Galaxy automatically
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capturing the context and intent of computational methods.
Galaxy Pages are interactive, web-based documents that provide
users with a medium to communicate a complete computational
analysis.},
Affiliation = {Department of Biology and Department of Mathematics and Computer Science, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA. jeremy.goecks@emory.edu},
Author = {Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and {Galaxy Team}},
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Pmid = {20738864},
Title = {Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
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@techreport{wssspe2_allen,
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@techreport{wssspe2_blomer,
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@techreport{wssspe2_boettiger,
Author = {Carl Boettiger and Ted Hart and Scott Chamberlain and Karthik Ram},
Institution = {figshare},
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Year = {2014}}
@techreport{wssspe2_chamberlain,
Author = {Ryan Chamberlain and Jennifer Schommer},
Institution = {figshare},
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Year = {2014}}