RDA Plenary 4 - BoF on Sustainability - my experience with ISA tools

1. Data Consultant,
Honorary Academic Editor
Associate Director,
Principal Investigator
!
BoF on the sustainability of eResearch /
cyberinfrastructure!
!
Susanna-Assunta Sansone, PhD!
!
@biosharing!
@isatools!
@scientificdata!
!
RDA Plenary 4, Sunstainability BoF, Sep 23, 2014
Board of Directors; Technical Advisory Board;
Sector Lead

2. Sustainability: definitions and key indicators
• Sustainable open source projects are those that are capable of
supporting themselves:
o meet their ongoing costs
• From the viewpoint of selection and procurement are those that:
o are capable of delivering improvements and fixing problems in a
timely manner
o have a reasonable prospect of continuing into the future
• Key indicators of sustainability:
o code activity: contributors and contributions
o release history: communication and governance
o user community: use cases and directions
o longevity: technology replacement and exit strategy
o ecosystem: a “coral reef” of partners
Credit to:

4. Community involvement and uptake!
Core developments!
ISA software v1!
Straw man
ISA-Tab spec!
2007 2008 2009 2010
2012
1st ISA-Tab
workshop!
3rd ISA-Tab
workshop!
2nd ISA-Tab
workshop!
Final ISA-Tab spec! Database instance !
at EBI!
1st public instance: !
Harvard Stem Cell !
Discovery Engine!
2011
RDF/OWL format starts!
Conversions to !
Pride-XML/SRA-XML/!
MAGE-Tab!
User workshops/visits - start!
Growing number of
systems starts to adopt
ISA framework!
Key publications!
Other tools !
implement ISA-Tab
!
Links to
analysis tools
starts!
2013
The ISA software suite:
supporting standards-compliant
curation at the
community level
Bioinformatics
OntoMaton: a Bioportal
powered ontology widget for
Google Spreadsheets.
Bioinformatics
ISA chapter in : Open Source
Software in Life Science
Research
Woodhead Publishing

5. Our industry needs a Disruptive Innovation.
That Disruption...is Pistoia"
African proverb
If you want to go fast, go alone
If you want to go far, go together

6. Our 7-years long journey – some notes
• Code activity and releases
+ positive
- less positive / negative
+ modifications and extensions, broadening scope and features
-/+ more contributions than contributors
-/+ too many feature requests submitted to our tracker
- depth, breath of develop and maintain (collaborative) documentation (tech and not)
• User community
++ lucky to have mix of developers & data scientists (bio/bench background) in my team
+ large service providers, consortia, individual labs, publishers - academic and industry
+ several components have passed User Acceptance Testing by industrial users
- diversity of use cases, needs, data types to handle and relation with existing workflow
- - too many users have no in-house dev support - extremely time consuming on our side
• Longevity – actual and continuingly funded
++ successfully embedded into many UK, EU, NIH funded projects; exploring NSF and
charities; contract with SME supplying outsources bioinformatics solutions to pharmas
and other industries
++ renewed importance due to data policies, standards-compliance, data publication etc.
• Ecosystem
++ embedded into/ on the map of large international infrastructure projects/programmes
+ good “coral reef” of partners and other tools we link to (converting, exporting or
visualizing data/metadata from our tools)

7. The quest for sustainable software
• “If software is pervasive in research, why is its vital role so often
overlooked by funders, universities, assessment committees, and
even the research community itself”, Carole Goble
• Geoffrey Chang’s discovery of the bug in his software led to his
retraction of three Science papers
• G. Miller, “A Scientist’s Nightmare: Software Problem Leads to Five
Retractions,” Science, 2006, DOI: 10.1126/science.314.5807.1856
• Towards a “healthier software ecosystem” with coordinating hubs and
incubators communities, agents of changes e.g.:
• EU-funded
• NSF-funded Software Institutes for Sustained Innovation
• Sloan Foundation-funded
• …etc