a recipe for sustainable software

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A Recipe for Sustainable Software

Philip E. BourneUniversity of California San Diego

[email protected]

11/17/13

http://www.carlmason-liebenberg.com/raw-chocolate-mousse-recipe/

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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

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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

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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

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We are at the beginning of what software will bring to the life sciences

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Motivation – The Bad News

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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

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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.

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The Protein Data Bank (PDB)



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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

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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

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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

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Bluhm et al. 2011 Quality Assurance doi: 10.1093/database/bar003

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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

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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

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PDBMobile

• 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

Objective: PDB Data Access On-The-Go

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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

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Sustainability Through the Private Sector



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Founded 4 Companies

• ViSoft Inc.

• Protein Vision Inc.

• Film Frontiers

• SciVee Inc.

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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

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Journals & Sustainability



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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

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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 suitability11/17/13

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The PLOS/Mozilla Experiment

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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?

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Institutions Can Sustain Developers and Software



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University 2.0 Is Yet to Happen – Demand Appears to be There

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Institutions Underrate Software as Scholarship, But There is a Glimmer of Hope – But You Must Do Your Bit

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PLoS Comp. Biol. 7(1) e1002001

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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

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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

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Funders & Sustainability



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NIH As An Example

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http://acd.od.nih.gov/Data%20and%20Informatics%20Working%20Group%20Report.pdf

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NIH As An Example

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Features of the Software Catalog (Maybe)

• Driven by the community• Registration service• Rating service• Discovery service• Long term sustainability?

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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

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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

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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

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Acknowledgements

• Stephanie Hagstrom• The PDB Team• The FORCE11 Team• The PLOS Team• The 3DVC Community

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a recipe for sustainable software

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