Using CONTEXTS is possible to build rich web applications that integrate the information retrieved from several biological resources.

CONTEXTS and the MIT Registry of Standar Biological Parts

Biological information about the fundamental cell components and their relation is essential not only to understand the mechanisms that operate in living cells but also to help in the rational design of new synthetic biological components. In the typical Synthetic Biology scenario after the formulation of the basic design at the general conceptual-engineering level, the implementation is carried out actual biological parts (i.e. ORFs, promoters, etc) that have to be selected from the set of known ones. The full system is then modelled and simulated, and finally synthesized, assembled and integrated in the biological chassis.

This information however is distributed through different databases and often is difficult to trace a particular gene or protein from one database to other. Tools like BioMart (http://biomart.org) or Galaxy (http://main.g2.bx.psu.edu/) have increased the repositories connectivity building a map between major database identifiers and providing mechanisms to access the information from a common interface. These tools however still do not include main synthetic biology repositories as the Registry of Standard Biological Parts.

CONTEXTS fill this gap by connecting the information stored in the Registry with the annotations provided by these major bioinformatics resources. Sitting over BioMart shoulder and other web services, CONTEXTS provides information that plays an important role to understand the behaviour of a part in a particular experiment and also in the new parts design.