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Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) Cover

Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1)

Open Access
|Jul 2014

References

  1. WSSSPE1 attendees WSSSPE1 Collaborative Notes. Available at: https://docs.google.com/document/ d/1eVfioGNlihXG_1Y8BgdCI6tXZKrybZgz5XuQHjT1 oKU/ [Last accessed 03 February 2014]
  2. National Science Foundation A Vision and Strategy for Software for Science, Engineering, and Education: Cyberinfrastructure Framework for the 21st Century 2012 Available at: http://www.nsf.gov/publications/pub_summ.jsp?ods_key=nsf12113 [Last accessed 03 April 2014]
  3. arXiv.org e-Print archive [Cited 03 February 2014]. Available at: http://arxiv.org
  4. figshare [Cited 03 February 2014]. Available at: http://figshare.com
  5. Katz D S Allen G Hong N C Parashar M Proctor D First Workshop on on Sustainable Software for Science: Practice and Experiences (WSSSPE): Submission and Peer-Review Process, and Results arXiv 2013 1311.3523 Available at: http://arxiv.org/abs/1311.3523
  6. Bourne P E A Recipe for Sustainable Software The First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) 17 November 2013 2013 Denver, Colorado, USA Abstract available online: http://wssspe.researchcomputing.org.uk/wssspe1/keynotes/#bourne. Slides available online: www.slideshare.net/pebourne/a-recipe-for-sustainable-software
  7. Public Library of Science [Cited 11 February 2014]. Available at: http://www.plos.org/
  8. Protein Data Bank >[Cited 05 February 2014]. Available at: http://www.rcsb.org/pdb/
  9. GitHub [Cited 11 February 2014]. Available at: https://github.com/
  10. The BioJava Project [Cited 07 February 2014]. Available at: http://biojava.org
  11. Open Science Data Cloud [Cited 07 February 2014]. Available at: https://www.opensciencedatacloud.org/
  12. Veretnik S Fink J L Bourne P E Computational Biology Resources Lack Persistence and Usability PLoS Computational Biology 2008 4 7 e1000136 10.1371/journal.pcbi.1000136
  13. National Science Foundation Small Business Innovation Research [Cited 07 February 2014]. Available at: http://www.nsf.gov/eng/iip/sbir/
  14. National Science Foundation Facilitation Awards for Scientists and Engineers with Disabilities [Cited 07 February 2014]. Available at: http://www.nsf.gov/pubs/policydocs/pappguide/nsf09_1/gpg_2.jsp#IID2
  15. Dickin R What does peer review mean when applied to computer code? [cited 2014–02–07]. Available at: http://blogs.plos.org/biologue/2013/08/08/what-does-peer-review-mean-when-applied-to-computer-code/
  16. Bourne P E Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia PLoS Computational Biology 2011 7 1 e1002001 10.1371/journal.pcbi.1002001
  17. Smith A Scientific Software and the Open Collaborative Web The First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) 17 November 2013 2013 Denver, Colorado, USA. Abstract available online: http://wssspe.researchcomputing.org.uk/wssspe1/keynotes/#smith. Slides available online: http://is.gd/wssspe
  18. Stodden V Why Science is an Open Endeavor The Open Knowledge Conference 16–18 September 2013 2013 Geneva, Switzerland. Slides available online: http://www.stanford.edu/~vcs/talks/OKcon2013-Sept172013-STODDEN.pdf
  19. Brown C T Laboratory of Genomics, Evolution and Development [Cited 07 February 2014]. Available at: http://ged.msu.edu.
  20. RubyGems.org [Cited 07 February 2014]. Available at: http://rubygems.org/
  21. PyPI – The Python Package Index [Cited 07 February 2014]. Available at: https://pypi.python.org/pypi
  22. The Comprehensive Perl Archive Network (CPAN) [Cited 07 February 2014]. Available at: http://www.cpan.org/
  23. Foreman-Mackey D contributors The Python ensemble sampling toolkit for affine-invariant MCMC [Cited 07 February 2014]. Available at: https://github.com/dfm/emcee
  24. Perez F An ambitious experiment in Data Science takes off: a biased, Open Source view from Berkeley 2013 [Cited 07 February 2014]. Available at: http://blog.fperez.org/2013/11/an-ambitious-experiment-in-data-science.html
  25. Hanwell M Perera A Turner W O’Leary P Osterdahl K Hoffman B Sustainable Software Ecosystems for Open Science figshare 2013 790756 10.6084/m9.figshare.790756
  26. Ahern S Brugger E Whitlock B Meredith J S Biagas K Miller M C VisIt: Experiences with Sustainable Software arXiv 2013 1309.1796 Available at: http://arxiv.org/abs/1309.1796
  27. Koop D Freire J Silva C T Enabling Reproducible Science with VisTrails arXiv 2013 1309.1784 Available at: http://arxiv.org/abs/1309.1784
  28. Panda D K Tomko K Schulz K Majumdar A The MVAPICH Project: Evolution and Sustainability of an Open Source Production Quality MPI Library for HPC figshare 2013 791563 10.6084/m9.figshare.791563
  29. Broman K W Fourteen years of R/qtl: Just barely sustainable Journal of Open Research Software 2014 2 1 e11 10.5334/jors.at
  30. Blatt M DUNE as an Example of Sustainable Open Source Scientific Software Development arXiv 2013 1309.1783 Available at: http://arxiv.org/abs/1309.1783
  31. Crusoe M Brown C T Walking the talk: adopting and adapting sustainable scientific software development processes in a small biology lab figshare 2013 791567 10.6084/m9.figshare.791567
  32. Christopherson L Idaszak R Ahalt S Developing Scientific Software through the Open Community Engagement Process figshare 2013 790723 10.6084/m9.figshare.790723
  33. Cranston K Vision T O’Meara B Lapp H A grassroots approach to software sustainability figshare 2013 790739 10.6084/m9.figshare.790739
  34. Terrel A Sustaining the Python Scientific Software Community figshare 2013 791565 10.6084/m9.figshare.791565
  35. Fitzpatrick B W Collins-Sussman B Team geek : a software developer’s guide to working well with others 2012 Sebastopol, CA O’Reilly Available at: http://opac.inria.fr/record=b1134063
  36. Turk M J Scaling a Code in the Human Dimension Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery. XSEDE ’13 2013 New York, NY, USA ACM 69:1 69:7 Available at: http://doi.acm.org/10.1145/2484762.2484782
  37. Crawford T D On the Development of Sustainable Software for Computational Chemistry figshare 2013 790757 10.6084/m9.figshare.790757
  38. Trainer E H Chaihirunkarn C Herbsleb J D The Big Effects of Short-term Efforts: Mentorship and Code Integration in Open Source Scientific Software Journal of Open Research Software 2014 2 1 e18 10.5334/jors.bc
  39. Dubey A Van Straalen B Experiences from Software Engineering of Large Scale AMR Multiphysics Code Frameworks Journal of Open Research Software 2014 2 1 e7 10.5334/jors.am
  40. Girotto I Kohlmeyer A Grellscheid D Brown S T Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages at the ICTP figshare 2013 796439 10.6084/m9.figshare.796439
  41. Prlić A Procter J B Ten Simple Rules for the Open Development of Scientific Software PLOS Computational Biology 2012 8 12 10.1371/journal.pcbi.1002802
  42. Lenhardt C Summary of Papers on Science Software Sustainability Models for WSSSPE Panel II figshare 2013 853817 10.6084/m9.figshare.853817
  43. Calero C Moraga M A Bertoa M F Towards a Software Product Sustainability Model arXiv 2013 1309.1640 Available at: http://arxiv.org/abs/1309.1640
  44. Venters C C Lau L Griffiths M K Holmes V Ward R R Jay C Dibsdale C E Xu J The Blind Men and the Elephant: Towards an Empirical Evaluation Framework for Software Sustainability Journal of Open Research Software 2014 2 1 e8 10.5334/jors.ao
  45. Pierce M Marru S Mattmann C Sustainable Cyberinfrastructure Software Through Open Governance figshare 2013 790761 10.6084/m9.figshare.790761
  46. Katz D S Proctor D A Framework for Discussing e-Research Infrastructure Sustainability Journal of Open Research Software 2014 2 1 e13 10.5334/jors.av
  47. Lenhardt W C Ahalt S Blanton B Christopherson L Idaszak R Data Management Lifecycle and Software Lifecycle Management in the Context of Conducting Science Journal of Open Research Software 2014 2 1 e15 10.5334/jors.ax
  48. Weber N Thomer A Twidale M Niche Modeling: Ecological Metaphors for Sustainable Software in Science figshare 2013 791564 10.6084/m9.figshare.791564
  49. Katz D S Transitive Credit as a Means to Address Social and Technological Concerns Stemming from Citation and Attribution of Digital Products Journal of Open Research Software 2014 2 1 e20 10.5334/jors.be
  50. Priem J Piwowar H Toward a comprehensive impact report for every software project figshare 2013 790651 10.6084/m9.figshare.790651
  51. Knepley M G Brown J McInnes L C Smith B Accurately Citing Software and Algorithms Used in Publications figshare 2013 785731 10.6084/m9.figshare.785731
  52. Howison J Herbsleb J D Incentives and integration in scientific software production Proceedings of the ACM Conference on Computer Supported Cooperative Work 2013 San Antonio, TX 459 470 10.1145/2441776.2441828
  53. Howison J Herbsleb J D Scientific software production: incentives and collaboration Proceedings of the ACM Conference on Computer Supported Cooperative Work. CSCW ’11 2011 Hangzhou, China ACM 513 522 10.1145/1958824.1958904
  54. Bietz M J Baumer E P Lee C P Synergizing in Cyberinfrastructure Development Computer Supported Cooperative Work 2010 19 3–4 245 281 10.1007/s10606-010-9114-y
  55. Chue Hong N Hole B Moore S Software Papers: improving the reusability and sustainability of scientific software figshare 2013 795303 10.6084/m9.figshare.795303
  56. Krintz C Jayathilaka H Dimopoulos S Pucher A Wolski R Developing Systems for API Governance figshare 2013 790746 10.6084/m9.figshare.790746
  57. Heiland R Thomas B Welch V Jackson C Toward a Research Software Security Maturity Model arXiv 2013 1309.1677 Available at: http://arxiv.org/abs/1309.1677
  58. Blanton B Lenhardt C A Scientist's Perspective on Sustainable Scientific Software Journal of Open Research Software 2014 2 1 e17 10.5334/jors.ba
  59. Huang D Lapp H Software Engineering as Instrumentation for the Long Tail of Scientific Software figshare 2013 791560 10.6084/m9.figshare.791560
  60. Goff S A Vaughn M McKay S Lyons E Stapleton A E Gessler D The iPlant Collaborative: Cyberinfrastructure for Plant Biology Frontiers in Plant Science 2011 2 July 1 16 10.3389/fpls.2011.00034
  61. Goecks J Nekrutenko A Taylor J Galaxy Team Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biology 2010 11 8 R86 10.1186/gb-2010-11-8-r86
  62. Caporaso J G Kuczynski J Stombaugh J Bittinger K Bushman F D Costello E K QIIME allows analysis of high-throughput community sequencing data Nature Methods 2010 7 5 335 336 10.1038/nmeth.f.303
  63. Boettiger C Ram K Chamberlain S Hart E rOpenSci - open source tools for open science [Cited 06 April 2014]. Available at: http://ropensci.org/.
  64. Wilson G Software Carpentry: Getting Scientists to Write Better Code by Making Them More Productive Computing in Science & Engineering 2006 8 6 66 10.1109/mcse.2006.122
  65. Vay J L Geddes C G R Koniges A Friedman A Grote D P Bruhwiler D White Paper on DOE-HEP Accelerator Modeling Science Activities figshare 2013 793816 10.6084/m9.figshare.793816
  66. Maheshwari K Kelly D Krieder S J Wozniak J M Katz D S Zhi-Gang M Reusability in Science: From Initial User Engagement to Dissemination of Results arXiv 2013 1309.1813 Available at: http://arxiv.org/abs/1309.1813
  67. Hart E Boettiger C Ram K Chamberlain S rOpenSci - a collaborative effort to develop R-based tools for facilitating Open Science figshare 2013 791569 10.6084/m9.figshare.791569
  68. Pierce M Marru S Demeler B Majumdar A Miller M Science Gateway Operational Sustainability: Adopting a Platform-as-a-Service Approach figshare 2013 790760 10.6084/m9.figshare.790760
  69. Zentner L Zentner M Farnsworth V McLennan M Madhavan K Klimeck G nanoHUB.org: Experiences and Challenges in Software Sustainability for a Large Scientific Community Journal of Open Research Software 2014 2 1 e19 10.5334/jors.bd
  70. Löffler F Brandt S R Allen G Schnetter E Cactus: Issues for Sustainable Simulation Software Journal of Open Research Software 2014 2 1 e12 10.5334/jors.au
  71. Wilkins-Diehr N Lawrence K Hayden L Pierce M Marru S McLennan M Science Gateways and the Importance of Sustainability figshare 2013 790764 10.6084/m9.figshare.790764
  72. Millington R Buzzing Communities: How to Build Bigger, Better, and More Active Online Communities 2012 FeverBee
  73. Deelman E Livny M Howison J Examining the Scientific Software Ecosystem [Cited 06 April 2014]. Available at: https://sites.google.com/site/scientificsoftwaremetrics/
  74. Prlić A Procter J B Ten simple rules for the open development of scientific software PLoS Computational Biology 2012 8 12 e1002802+ 10.1371/journal.pcbi.1002802
  75. Bangerth W Heister T What makes computational open source software libraries successful? Computational Science & Discovery 2013 6 1 015010 Available at: http://stacks.iop.org/1749-4699/6/i=1/a=015010
  76. Bacon J The Art of Community. Building the New Age of Participation 2009
  77. Trapani G Your Community is Your Best Feature 2011 Available at: http://smarterware.org/7819/my-codeconf-talk-your-community-is-your-best-feature.
  78. Fogel K Producing Open Source Software: How to Run a Successful Free Software Project O’Reilly Media, Inc 2005 Available at: http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20&path=ASIN/0596007590
  79. Allsopp J The Proof of the Pudding 2012 Available at: http://www.webdirections.org/blog/the-proof-of-the-pudding/.
  80. Foster I Vasiliadis V Tuecke S Software as a Service as a path to software sustainability figshare 2013 791604 10.6084/m9.figshare.791604
  81. Elster A C Software for Science: Some Personal Reflections arXiv 2013 1309.2357 Available at: http://arxiv.org/abs/1309.2357
  82. Gardler R Software Sustainability Maturity Model [Cited 06 February 2014]. Available at: http://oss-watch.ac.uk/resources/ssmm
  83. Ferenbaugh C r Experiments in Sustainable Software Practices for Future Architectures arXiv 2013 1309.1428 Available at: http://arxiv.org/abs/1309.1428
  84. Carver J C Thiruvathukal G K Software Engineering Need not be Difficult figshare 2013 830442 10.6084/m9.figshare.830442
  85. Gordon and Betty Moore Foundation Data Science Environments [Cited 21 April 2014]. Available at: http://www.moore.org/programs/science/data-driven-discovery/data-science-environments
  86. Thaney K Code as a research object: a new project [Cited 21 April 2014]. Available at: http://mozillascience.org/code-as-a-research-object-a-new-project/
  87. Miller M C Diachin L Balay S McInnes L C Smith B Package Management Practices Essential for Interoperability: Lessons Learned and Strategies Developed for FASTMath figshare 2013 789055 10.6084/m9.figshare.789055 [Last accessed 03 April 2014]
  88. Stephan E G Elsethagen T O Kleese van Dam K Riihimaki L What Comes First, the OWL or the Bean? figshare 790738 10.6084/m9.figshare.790738
  89. Gaston D R Peterson J W Permann C J Andrs D Slaughter A E Miller J M Continuous Integration for Concurrent Computational Framework and Application Development Journal of Open Research Software 2014 2 1 e10 10.5334/jors.as
  90. Choi S-C T MINRES-QLP Pack and Reliable Reproducible Research via Supportable Scientific Software Journal of Open Research Software 2014 2 1 e22 10.5334/jors.bb
  91. Heien E M Miller T L Gietzel B Kellogg L H Experiences with Automated Build and Test for Geodynamics Simulation Codes arXiv 2013 1309.1199 Available at: http://arxiv.org/abs/1309.1199
  92. Casanova H Giersch A Legrand A Quinson M Suter F SimGrid: a Sustained Effort for the Versatile Simulation of Large Scale Distributed Systems arXiv 2013 1309.1630 Available at: http://arxiv.org/abs/1309.1630
  93. Cohen J Cantwell C Chue Hong N Moxey D Illingworth M Turner A Simplifying the Development, Use and Sustainability of HPC Software Journal of Open Research Software 2014 2 1 e16 10.5334/jors.az
  94. Slawinski J Sunderam V Towards Semi-Automatic Deployment of Scientific and Engineering Applications figshare 2013 791570 10.6084/m9.figshare.791570
  95. Dubey A Brandt S R Brower R Giles M Hovland P Lamb D Q et al Software Abstractions and Methodologies for HPC Simulation Codes on Future Architectures Journal of Open Research Software 2014 2 1 e14 10.5334/jors.aw
  96. Stewart C A Wernert J Wernert E A Barnett W K Welch V Initial Findings from a Study of Best Practices and Models for Cyberinfrastructure Software Sustainability arXiv 2013 1309.1817 Available at: http://arxiv.org/abs/1309.1817
  97. Brown J Knepley M Smith B Run-time extensibility: anything less is unsustainable figshare 2013 791571 10.6084/m9.figshare.791571
  98. Swenson S Simmhan Y Prasanna V Parashar M Riedy J Bader D Sustainable Software Development for Next-Gen Sequencing (NGS) Bioinformatics on Emerging Platforms arXiv 2013 1309.1828 Available at: http://arxiv.org/abs/1309.1828
  99. Stodden V Miguez S Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research Journal of Open Research Software 2014 2 1 e21 10.5334/jors.ay
  100. Moore R W Rajasekar A Xu H Extensible Generic Data Management Software Journal of Open Research Software 2014 2 1 e9 10.5334/jors.ap
DOI: https://doi.org/10.5334/jors.an | Journal eISSN: 2049-9647
Language: English
Published on: Jul 9, 2014
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2014 Daniel S Katz, Sou-Cheng T Choi, Hilmar Lapp, Ketan Maheshwari, Frank Löffler, Matthew Turk, Marcus D Hanwell, Nancy Wilkins-Diehr, James Hetherington, James Howison, Shel Swenson, Gabrielle D Allen, Anne C Elster, Bruce Berriman, Colin Venters, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.