[Bioperl-l] Validating Bioperl

Peter van Heusden pvh at egenetics.com
Sun Feb 15 15:29:04 EST 2004

Hi BioPerl people

I have been hired by Electric Genetics to spend no less than 50% of my time "validating" Bioperl. What this means is that I'm slowly going through BioPerl, reviewing the code and documentation, and trying to ensure three related things:

1) The documentation clearly specifies input, output and exception 
conditions for the code.
2) The code complies with the documentation and behaves as expected.
3) The test suite exhaustively tests the code to ensure that 2 is true.

The goal of this 'validation' is to be able to offer some kind of 
assurance to our customers (who includ some big names in the 
pharmaceuticals field) that Bioperl is robust enough to be included 
without worry in their development process. Their fear surrounding open 
source tools is based on past experiences, particularly upgrading across 
various versions of operating systems and tools, and the slow tightening 
of FDA requirements for software included in any clinical development 

The tangible output of the validation work will be:

  - improved code that is submitted back to the Bioperl CVS
  - new features, as requested by our pharma clients, that are implemented by EG and submitted to the Bioperl CVS
  - professional-grade documentation, which is provided to EG's customers as part of the Bioperl validation and support product on offer

Finally to give a bit of background: Electric Genetics is a 
bioinformatics software company based in South Africa and the USA. The 
name should be familiar to a number of BioPerl hackers - we've been 
around for some years and sponsored the first 'BioHackathon' (in Cape 
Town in 2002). We've been open source enthusiasts for years, and with 
this product can finally bridge the gap between our commerical reality 
and our open source aspirations.

Looking forward to lots of BioPerl hacking,

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