Bioinformatics Software Support and Development

The biotechnology advancements produce large quantity of data, which requires computational support by bioinformatics for storage, analysis, and integration of these data with other research data including clinical trial data. Bioinformatic tools range from biological sequence analysis, functional annotation and literature knowledge databases, as well as specific data mining and artificial intelligence discovery software from both commercial and academic sources. The explosion of data coincides with continued sophistication of the World Wide Web of computer networks that are enabling broad distribution of both information and computational services in real time. Software developers from all over the world are striving to create tools and services that serve their immediate user base, as well as being able to inter-operate across the computer networks. One example of such efforts is the caBIG™ initiative by NCI.

AGTI has been part of bioinformatics software development through our involvements with CEBS database and services development and the caBIG initiative. Our experiences allow us to evaluate the pros and cons from both top-down and bottom-up approaches of software tool development depending on the goals of the intended use. These experiences also helped us recognize various issues associated with software interoperability, such as data standards (e.g. HL-7, CDISC, GO), regulatory restrictions (HIPAA), as well as syntactic and semantic compatibility (caBIG).

Our knowledge and experiences can help clients with the full life cycle of bioinformatics software development. These include use case and requirements development through our understanding of the underlying biological system and experimental data; and software architecture design leveraging existing data and regulatory standards, as well public databases; and software programming, testing, packaging, training, and support.