Biomedical Engineering Reference
In-Depth Information
7.4 Lessons learned
7.4.1 Open source, collaborative environment
The ISA software solution is a suite of open source and freely available
modules, with an active community of users (researchers and curators)
and contributing developers. GitHub [41] is the social repository selected
to support an environment for code sharing and collaborative
development, with the ultimate goal to achieve long-term sustainability
and foster self-reliance. Feature requests and bug reports are tracked,
discussed and assigned to specifi c developers.
Due to the modular nature of the ISA software, contributors can take
responsibility for the development of specialized modules, contributions
to and extensions of the core code. In turn, these are reviewed, vetted or
rejected thus making it possible to implement agile practice in an open
framework. The main requirement in such open environment is
compliance to the open source licensing contract, which is essential to
ensure that contributions are duly acknowledged while limiting aggressive
open source 'free loading'.
Augmenting the ISA code base with APIs will also support further
collaborative development and connections to other widely used data
management systems (e.g. [42]). Dealing with feature requests, code
forking and subsequent reviews, however, is always a challenging and
demanding task, particularly when the ecosystem of users, contributors,
and collaborators continues to grow [22, 23].
7.4.2 Curation practices
Generally, even if some good data management practices are in place
when data sets are produced, without community standards any
subsequent curation or re-use is neither simple nor straightforward. The
current crop of minimum information checklists, terminologies and fi le
formats is still growing, lacking control, creating integration headaches
especially when new technologies or combinations of technologies are
employed. The harmonization of standards remains patchy at best and
far from crossing all life science and biomedical domains. Minimum
information checklists are often seen as burdensome and over-prescriptive;
ontologies too rich and complex; formats intractable. Although the ISA
framework can assist in the process of selecting and using the appropriate
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