Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)
By: Daniel S. Katz, Sou-Cheng T. Choi, Kyle E. Niemeyer, James Hetherington, Frank Löffler, Dan Gunter, Ray Idaszak, Steven R. Brandt, Mark A. Miller, Sandra Gessing, Nick D. Jones, Nic Weber, Suresh Marru, Gabrielle Allen, Birgit Penzenstadler, Colin C. Venters, Ethan Davis, Lorraine Hwang, Ilian Todorov, Abani Patra and Miguel de Val-Borro
References
-
Katz
DS
Allen
G
Chue Hong
N
Parashar
M
Proctor
D
First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE): Submission and Peer-Review Process, and Results
2013
arXiv; 1311.3523.
http://arxiv.org/abs/1311.3523 - Katz DS Choi SCT Lapp H Maheshwari K Löffler F Turk M Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) Journal of Open Research Software 2014 2 1 10.5334/jors.an
-
Katz
DS
Allen
G
Chue Hong
N
Cranston
K
Parashar
M
Proctor
D
Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2): Submission, Peer-Review and Sorting Process, and Results
2014
arXiv; 1411.3464.
http://arxiv.org/abs/1411.3464 -
Katz
DS
Choi
SCT
Wilkins-Diehr
N
Chue Hong
N
Venters
CC
Howison
J
Report on the Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2)
Journal of Open Research Software
2016
Accepted. Available at
http://arxiv.org/abs/1507.01715 - Turk MJ Smith BD Oishi JS Skory S Skillman SW Abel T yt: A Multi-code Analysis Toolkit for Astrophysical Simulation Data ApJS 2011 Jan 192 10.1088/0067-0049/192/1/9 9
-
Becker
C
Chitchyan
R
Duboc
L
Easterbrook
S
Mahaux
M
Penzenstadler
B
The Karlskrona manifesto for sustainability design
2014
arXiv; 1410.6968.
http://arxiv.org/abs/1410.6968 - Patra AK Bauer AC Nichita CC Pitman EB Sheridan MF Bursik M Parallel adaptive numerical simulation of dry avalanches over natural terrain Journal of Volcanology and Geothermal Research. Modeling and Simulation of Geophysical Mass Flows 2005 139 1 1 21 10.1016/j.jvolgeores.2004.06.014
- Meng H Kommineni R Pham Q Gardner R Malik T Thain D An invariant framework for conducting reproducible computational science Journal of Computational Science. Computational Science at the Gates of Nature 2015 9 137 142 10.1016/j.jocs.2015.04.012
-
Meng
H
Thain
D
Umbrella: A Portable Environment Creator for Reproducible Computing on Clusters, Clouds, and Grids
Proceedings of the 8th International Workshop on Virtualization Technologies in Distributed Computing. VTDC ’15
2015
New York, NY, USA
ACM 23 30 10.1145/2755979.2755982 - Meng H Wolf M Ivie P Woodard A Hildreth M Thain D A case study in preserving a high energy physics application with Parrot Journal of Physics: Conference Series 2015 664 3 032022 10.1088/1742-6596/664/3/032022
-
Huo
D
Nabrzyski
J
Vardeman
C
An Ontology Design Pattern towards Preservation of Computational Experiments
Proceedings of the 5th Workshop on Linked Science 2015 – Best Practices and the Road Ahead (LISC 2015) co-located with 14th International Semantic Web Conference
2015 2015ISWC -
Baxter
R
Chue Hong
N
Gorissen
D
Hetherington
J
Todorov
I
The Research Software Engineer
Digital Research 2012
2012
http://digital-research-2012.oerc.ox.ac.uk/papers/the-research-software-engineer -
Parr
C
Save your work – give software engineers a career track
Times Higher Education
2013
August
15
https://www.timeshighereducation.com/news/save-your-work-give-software-engineers-a-career-track/2006431.article - Gil Y David CH Demir I Essawy BT Fulweiler RW Goodall JL Towards the Geoscience Paper of the Future: Best Practices for Documenting and Sharing Research from Data to Software to Provenance Earth and Space Science 2016
-
Duffy
CJ
David
C
Peckham
S
Venayagamoorthy
K
Gil
Y
Geoscience Papers of the Future: An Introduction to the Special Issue
Earth and Space Science
[In press], Accessible from:
http://agupubs.onlinelibrary.wiley.com/agu/issue/10.1002/(ISSN)2333-5084(CAT)SpecialIssues(VI)GPF1/ - Nanthaamornphong A Carver JC Test-Driven Development in scientific software: a survey Software Quality Journal 2015 1 30 10.1007/s11219-015-9292-4
-
Heaton
D
Carver
JC
Claims about the use of software engineering practices in science: A systematic literature review
Information and Software Technology
2015
67
207
219
10.1016/j.infsof.2015.07.011
Available from:
http://www.sciencedirect.com/science/article/pii/S0950584915001342 - Basili VR Carver JC Cruzes D Hochstein LM Hollingsworth JK Shull F Understanding the High-Performance-Computing Community: A Software Engineer’s Perspective IEEE Software 2008 July 25 4 29 36 10.1109/MS.2008.103
- Carver JC Kendall RP Squires SE Post DE Software Development Environments for Scientific and Engineering Software: A Series of Case Studies 29th International Conference on Software Engineering (ICSE’07) 2007 550 559 10.1109/ICSE.2007.77
-
Sempervirens
Accessed: 2015-11-07.
https://github.com/njsmith/sempervirens - Allen A Schmidt J Looking before leaping: Creating a software registry Journal of Open Research Software 2015 3 1 e15
-
Ahalt
S
Berriman
B
Brown
M
Carver
J
Chue Hong
N
Fish
A
Toward a Framework for Evaluating Software Success: A Proposed First Step
Computational Science and Engineering Software Sustainability and Productivity Challenges (CSESSP) Workshop
2015
Available from:
https://www.orau.gov/csessp2015/whitepapers/ahalt_stan.pdf -
Heroux
MA
Willenbring
JM
Barely sufficient software engineering: 10 practices to improve your CSE software
Software Engineering for Computational Science and Engineering, 2009. SECSE ’09
2009
ICSE Workshop 15 21 -
Blatt
M
DUNE as an Example of Sustainable Open Source Scientific Software Development
2013
arXiv; 1309.1783.
http://arxiv.org/abs/1309.1783 -
Ahern
S
Brugger
E
Whitlock
B
Meredith
JS
Biagas
K
Miller
MC
VisIt: Experiences with Sustainable Software
2013
arXiv; 1309.1796.
http://arxiv.org/abs/1309.1796 -
van Vliet
H
Software Engineering: Principles and Practice 2008 3rd ed. Wiley Publishing - Merali Z Computational science: … Error … why scientific programming does not compute Nature 2010 467 775 777 10.1038/467775a
- Hettrick S UK Research Software Survey 2014 2014 10.5281/zenodo.14809
-
Becker
C
Betz
S
Chitchyan
R
Duboc
L
Easterbrook
SM
Penzenstadler
B
Requirements: The Key to Sustainability Software 2016 IEEE Jan 33 1 56 65 10.1109/MS.2015.158 - Becker C Chitchyan R Duboc L Easterbrook S Penzenstadler B Seyff N Sustainability Design and Software: The Karlskrona Manifesto Proc. 2015 Int’l Conf. Software Eng. (ICSE’15) 2015 10.1109/icse.2015.179
-
Tate
K
Sustainable Software Development: An Agile Perspective 2005 Addison-Wesley Professional -
Bourque
P
Fairley
RE
SWEBOK, version 3.0: Guide to the Software Engineering Body of Knowledge 2014 IEEE Computer Society Press -
Working towards Sustainable Software for Science: Practice Experiences
Accessed: 2015-12-03.
http://wssspe.researchcomputing.org.uk/ -
International Workshop on Software Engineering for High Performance Computing in Computational Science Engineering
Accessed: 2015-12-03.
http://se4science.org/workshops/ -
Workshop on Software Engineering for Sustainable Systems
Accessed: 2015-12-03.
http://sustainabilitydesign.org/initiatives/se4susy/ -
Entertainment Identifier Registry
Accessed: 2015-10-28.
http://eidr.org - Katz DS 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 Sep 2 1 10.5334/jors.be e20
- Katz DS Smith AM Transitive Credit and JSON-LD Journal of Open Research Software 2015 3 1 e7
- Mayes AC zee-moz Collins A Niemeyer K Jabbari A Leadership-Training: “Working Open” Guide – WSSSPE3 version 2015 10.5281/zenodo.33748
- Bacon J The Art of Community. Building the New Age of Participation 2009
-
Howison
J
Sustaining scientific infrastructures: transitioning from grants to peer production (work-in-progress)
iConference 2015 Proceedings
2015
http://hdl.handle.net/2142/73439 - Geels FW Schot J Typology of sociotechnical transition pathways Research Policy 2007 36 3 399 417 10.1016/j.respol.2007.01.003
-
WSSSPE3 Software Credit Working Group
WSSSPE3 Software Credit Working Group GitHub Issues
2015
Accessed: 2015-10-1.
https://github.com/WSSSPE/meetings/issues/51 -
WSSSPE3 Software Credit Working Group
WSSSPE3 Software Credit Working Group Collaborative Notes
2015
Accessed: 2015-10-1.
https://docs.google.com/document/d/1oN0ZYqIoWtOE1LBMIlWY9N8nn5LHTncj8GjUKPh62pA -
CASRAI
Project Credit
Accessed: 2015-03-31.
http://credit.casrai.org -
Mayes
AC
Contributorship Badges
2015
Accessed: 2015-10-26.
https://www.mozillascience.org/projects/contributorship-badges -
Open Researcher Contributor ID (ORCID)
Accessed: 2015-03-31.
http://orcid.org/ - McCall JG Al-Hasani R Siuda ER Hong DY Norris AJ Ford CP CRH Engagement of the Locus Coeruleus Noradrenergic System Mediates Stress-Induced Anxiety Neuron 2015 Aug 87 3 605 620 10.1016/j.neuron.2015.07.002
- Lin IC Okun M Carandini M Harris KD The Nature of Shared Cortical Variability Neuron 2015 Aug 87 3 644 656 10.1016/j.neuron.2015.06.035
- Howison J Bullard J Software in the scientific literature: Problems with seeing, finding, and using software mentioned in the biology literature Journal of the Association for Information Science and Technology 2015 10.1002/asi.23538 In press
- Brin S Page L The anatomy of a large-scale hypertextual Web search engine Computer Networks and ISDN Systems 1998 30 1–7 107 117
-
SIG SP
Astronomy software citation examples and ideas
2015
Accessed: 2015-10-29.
https://docs.google.com/document/d/1q9ULl7alA3veL7Qwg7jGteRWeJwlrkvRHSXjvt-rTs0 -
Data Citation Synthesis Group
Martone
M
Joint Declaration of Data Citation Principles 2014 San Diego, CA FORCE11 Accessed: 2015-10-28.http://www.force11.org/group/joint-declaration-data-citation-principles-final -
Zenodo
Accessed: 2015-10-28.
https://zenodo.org -
Figshare
Accessed: 2014-02-03.
https://figshare.com -
IPython
A gallery of interesting IPython Notebooks
2015
Accessed: 2015-10-28.
https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks#reproducible-academic-publications
DOI: https://doi.org/10.5334/jors.118 | Journal eISSN: 2049-9647
Language: English
Submitted on: Feb 6, 2016
Accepted on: Sep 5, 2016
Published on: Oct 21, 2016
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
© 2016 Daniel S. Katz, Sou-Cheng T. Choi, Kyle E. Niemeyer, James Hetherington, Frank Löffler, Dan Gunter, Ray Idaszak, Steven R. Brandt, Mark A. Miller, Sandra Gessing, Nick D. Jones, Nic Weber, Suresh Marru, Gabrielle Allen, Birgit Penzenstadler, Colin C. Venters, Ethan Davis, Lorraine Hwang, Ilian Todorov, Abani Patra, Miguel de Val-Borro, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.