A Recipe for Sustainable Software

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Presented at the Workshop for Sustaonable Software for Science: Practice and Experiment (WSSSPE). Part of Supercomputing 2013 (SC13) in denver Colorado.

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  • DELSA – Data enabled life sciences alliance
  • A Recipe for Sustainable Software

    1. 1. http://www.carlmason-liebenberg.com/raw-chocolate-mousse-recipe/ A Recipe for Sustainable Software Philip E. Bourne University of California San Diego pbourne@ucsd.edu 11/17/13 WSSSPE 1
    2. 2. Outline • My Perspective/Bias • Motivation • Experiences providing ingredients to the recipe: – The role of journals – The role of institutions – The role of the community – The role of funders – A business model 11/17/13 WSSSPE 2
    3. 3. My Perspective/Bias • • • • • • • Basic scientist in the biomedical sciences Not coded anything for years Built computing infrastructure Manage software project teams of ~10 people Formed 4 software-based companies 15 years with a community resource – PDB Helped to establish communities – PLOS, FORCE11, DELSA, NIF • University Administrator • Journal co-founder 11/17/13 WSSSPE 3
    4. 4. Motivation – The Good News • Those iconic DNA and protein representations were drawn by hand • Molecular graphics emerged to automate this process • Today cell contents are drawn by hand • Automating that conceptualization is is just one next step We are at the beginning of what software will bring to the life sciences 11/17/13 WSSSPE 4
    5. 5. Motivation – The Bad News 11/17/13 WSSSPE 5
    6. 6. Thinking on Software back in 2008.. • • • • • Costs too much Is located in silos Does not foster reproducibility Is poorly maintained – is unsustainable Does not meet the needs of 21st century biology • Is a major time waster Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 2008 . 4(7): e1000136 11/17/13 WSSSPE 6
    7. 7. What Got Me Thinking More • Software development in science has improved thanks to open source, github etc. but for the most part remains arcane • Software (and data) atrophy is a problem • There is much we can learn from the app model – Consistent user interface – intuitive – Common calling interface – App store – ratings commentary etc. 11/17/13 WSSSPE 7
    8. 8. The Protein Data Bank (PDB) • My Perspective/Bias • Motivation • Experiences providing ingredients to the recipe: – The role of journals – The role of institutions – The role of the community – The role of funders – A business model 11/17/13 WSSSPE 8
    9. 9. The Protein Data Bank (PDB) • The single community owned worldwide repository containing structures of publically accessible biological macromolecules • A resource used by ~ 300,000 individuals per month • A resource distributing worldwide the equivalent to ¼ the National Library of Congress each month • A bicoastal resource • 1TB 11/17/13 WSSSPE
    10. 10. PDB: Looking Back Over the Past 15 Years – In General • Everything was harder and took longer than we thought • There are a lot of politics associated with data and software • Emphasis has shifted from archive to + analytical tool to + educational tool • Consequently outreach is our most important yet least understood activity today • Staff needed to change accordingly • It has become a worldwide enterprise • Prorated our budget has decreased 11/17/13 WSSSPE 10
    11. 11. PDB: Looking Back Over the Past 15 Years – Infrastructure • It took about 5 years to achieve and subsequently sustain 99.99% uptime • We have gone through 3 distinct code refreshes another is needed – Object model / Perl CGI – Enterprise Java – Code rewrite Enterprise Java Bluhm et al. 2011 Quality Assurance doi: 10.1093/database/bar003 11/17/13 WSSSPE 11
    12. 12. PDB: Looking Back Over the Past 15 Years – Open Source • Only considered in the past 7 years or so • Had “PDB in a Box” but abandoned that • Now new components are made available through biojava and github • Don’t really use community contributions enough 11/17/13 WSSSPE 12
    13. 13. PDB: Trends Today • Constant demand for better performance • Use of Web services increasing • Widgets have not taken off • Mobile use is increasing fast • PDB 2.0 services are in demand 11/17/13 WSSSPE 13
    14. 14. PDBMobile Objective: PDB Data Access On-The-Go • Fast, low bandwidth data access • iPhone in production ~ 10,000 users • Android in beta • HTML 5-based web application • Client-side database stores data for offline-access • Tight integration with MyPDB 11/17/13 WSSSPE 14
    15. 15. PDB Sustainability • Its easier when the data are seen as vital to the scientific enterprise • Quality breeds trust which breeds support • The community must be involved in every major decision • Different people/skills are needed at different time points • The Google bus is inevitable – make allowances for it 11/17/13 WSSSPE 15
    16. 16. Sustainability Through the Private Sector • My Perspective/Bias • Motivation • Experiences providing ingredients to the recipe: – The role of journals – The role of institutions – The role of the community – The role of funders – A business model 11/17/13 WSSSPE 16
    17. 17. Founded 4 Companies • ViSoft Inc. • Protein Vision Inc. • Film Frontiers • SciVee Inc. 11/17/13 WSSSPE 17
    18. 18. Sustainability Through Companies • Making a business from scientific software alone is very rare – founders tend to overvalue everything; customers undervalue • Be at the right place on the technology adoption curve • Need to provide value add – either through content (again rare for science) or services – increasingly likely but needs a special skill set • TTOs do not understand the value (or lack) of scientific software – be prepared 11/17/13 WSSSPE 18
    19. 19. Journals & Sustainability • My Perspective/Bias • Motivation • Experiences providing ingredients to the recipe: – The role of journals – The role of institutions – The role of the community – The role of funders – A business model 11/17/13 WSSSPE 19
    20. 20. The Role of Journals • Journals can help elevate the value of software and software developers • However, it propagates a broken reward system • Provide quality control through peer review • Provide copy of record 11/17/13 WSSSPE 20
    21. 21. Example: PLOS Computational Biology Software Articles - Requirements • Outstanding open source software of exceptional importance that has been shown to provide new biological insights, either as a part of the software article, or published elsewhere. • The software must already be widely adopted, or have the promise of wide adoption by a broad community of users. • No enhancements published • The software must be downloadable anonymously in source code form and licensed under an OSI license • Must be documented and testable • Presubmission determines suitability 11/17/13 WSSSPE 21
    22. 22. The PLOS/Mozilla Experiment 11/17/13 WSSSPE 22
    23. 23. The PLOS/Mozilla Experiment • How much scientific software can be reviewed by non-specialists, and how often is domain expertise required? • How much effort does this take compared to reviews of other kinds of software, and to reviews of papers themselves? • How useful do scientists find these reviews? 11/17/13 WSSSPE 23
    24. 24. Institutions Can Sustain Developers and Software • My Perspective/Bias • Motivation • Experiences providing ingredients to the recipe: – The role of journals – The role of institutions – The role of the community – The role of funders – A business model 11/17/13 WSSSPE 24
    25. 25. University 2.0 Is Yet to Happen – Demand Appears to be There 11/17/13 WSSSPE 25
    26. 26. Institutions Underrate Software as Scholarship, But There is a Glimmer of Hope – But You Must Do Your Bit PLoS Comp. Biol. 7(1) e1002001 11/17/13 WSSSPE 26
    27. 27. Your Responsibility for Software as Scholarship • Make it easy for software developers to quantify the use and perceived value of software • Explain to reviewers who do not understand the value the impact you have had • Software is frequently more valuable that a research article – don’t hide that • Make clear the costs and sustainability issues to institutions 11/17/13 WSSSPE 27
    28. 28. The Academic Institutions Responsibility for Software as Scholarship • Accept alternative metrics • Encourage individual departments to put forward promotion files that reflect the value of software to that domain • Educate the committee on academic promotions 11/17/13 WSSSPE 28
    29. 29. Funders & Sustainability • My Perspective/Bias • Motivation • Experiences providing ingredients to the recipe: – The role of journals – The role of institutions – The role of the community – The role of funders – A business model 11/17/13 WSSSPE 29
    30. 30. NIH As An Example http://acd.od.nih.gov/Data%20and%20Informatics%20Working%20Group%20Report.pdf 11/17/13 WSSSPE 30
    31. 31. NIH As An Example 11/17/13 WSSSPE 31
    32. 32. 11/17/13 WSSSPE 32
    33. 33. Features of the Software Catalog (Maybe) • • • • • Driven by the community Registration service Rating service Discovery service Long term sustainability? 11/17/13 WSSSPE 33
    34. 34. The Role of Funders • There needs to be more agency cross-talk – both national and international • Funders can help train institutions not just individuals • Better specification of the software enterprise • Less build it and they will come – more grass roots application driven support but managed 11/17/13 WSSSPE 34
    35. 35. The 3D Virtual Cell & FORCE11 Communities • My Perspective/Bias • Motivation • Experiences driving ingredients to the recipe – The role of journals – The role of institutions – The role of the community – The role of funders – A business model 11/17/13 WSSSPE 35
    36. 36. 11/17/13 WSSSPE 36
    37. 37. Sustainability Lessons from the 3D Virtual Cell • There remains a minimal requirement for funding even with a vibrant community – How? • Communities still need champions & a vision • Self organization is not an option • Members must like each other – face to face is needed 11/17/13 WSSSPE 37
    38. 38. Acknowledgements • • • • • 11/17/13 WSSSPE Stephanie Hagstrom The PDB Team The FORCE11 Team The PLOS Team The 3DVC Community 38

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