Application Note BIAS: Bioinformatics Integrated Application Software

Motivation: We introduce a development platform especially tailored to Bioinformatics research and software development. BIAS (Bioinformatics Integrated Application Software) provides the tools necessary for carrying out integrative Bioinformatics research requiring multiple datasets and analysis tools. It follows an object-relational strategy for providing persistent objects, allows third-party tools to be easily incorporated within the system, and supports standards and data-exchange protocols common to Bioinformatics. Availability: BIAS is an OpenSource project and is freely available to all interested users at http://www.mcb.mcgill.ca/∼bias. This web site also contains a paper containing a more detailed description of BIAS and an example implementation of a Bayesian network approach for the simultaneous prediction of gene regulation events and of mRNA expression from combinations of gene regulation events. Contact: [email protected] There now exists a wide range of ontologies, standards, databases, and applications available to the Bioinformatics community. However, the vast majority of these objects exist independently and are not tightly integrated into a single system. This situation makes it difficult for research groups to quickly and effectively use state-of-the-art Bioinformatics tools. Furthermore, it necessitates a great effort on their part to both integrate all the relevant objects together into a usable platform and to maintain this system over time. The slow progress towards a development framework for Bioinformatics is due to a complex set of reasons including the heterogeneity and diversity of biological data [1]. Additionally, the development of fields such as systems biology bring with it a need to integrate multiple types of information within a coherent statistical model [2, 3, 4]. There remains however a general lack of tools available to help the community manage these complex analyses. Existing development platforms such at [5, 6] are generally not offered at a price accessible to academic laboratories. We make available a new development platform entitled BIAS (Bioinformatics Integrated Application Software). The mandate of BIAS is to provide infrastructure to integrate many different Bioinformatics objects together into one easy to use, easy to expand, and computationally powerful system. Although the system currently has infrastructure for gene expression, tran-