BOSC 2004 Bioperl Validation presentation available

Electric Genetics supports the widely used Bioperl project by validating the Bioperl code base with test suites, semantic checks and documentation clearly explaining the use of the code. Understand how software validation improves your pipeline. [View the Powerpoint presentation]

Electric Genetics Corporation provides specialized services aimed to increase the utility and effectiveness of open source bioinformatics tools through value-added activities such as documentation, validation, packaging, integration and training. BioPerl validation services are available and Ensemble technical and user documentation is currently underway.

BioPerl Validation

Electric Genetics Corporation proposes to provide companies with professional services for validating the open source Bioperl modules incorporated within in-house bioinformatics developments. As part of the service, Electric Genetics will not only validate those Bioperl modules currently in use, but will also validate the other Bioperl modules so that companies can feel free to use any or all of these in future in-house developments. The use of Bioperl modules in custom software code will be verified as part of the process. Background Recent pressure by the US Food and Drug Administration for validation of software and computer systems used in the medical industry have focused attention on third-party software, especially open source software which is difficult to validate due to the lack of detailed software development processes and up-front design. This poses a potential risk for pharmaceutical and medical device companies who wish to take advantage of open source developments.

Companies may have developed several in-house systems using modules from the Bioperl project. Due to its nature as an open source project, Bioperl has not undergone rigorous, commercial-standard validation testing. Because Bioperl has been developed by a large community of contributors, the level of quality and documentation across modules is necessarily inconsistent.

Electric Genetics have a long-standing history of positive interaction with the open source community. Activities such as the initiation and co-hosting of the first annual Biohackathon held in Jan/Feb 2002, participation in the Bioinformatics Open Source Conference since 2000 and our recent contract with the Sanger Institute to produce user and technical documentation for the Ensembl genome browser have established the seriousness of our intentions toward open source software in bioinformatics.

Electric Genetics utilizes open source tools and data in our commercial and freely available products and understands both the power - and the hazards - of relying on community-based developments. As part of our corporate mission, we aim to increase the utility and effectiveness of open source bioinformatics tools through value-added activities such as documentation, validation, packaging, integration and training.