Computational Resources for GTL

This final report summarizes the work conducted under our three year DOE GTL grant ($459,402). The work involved a number of areas, including standardization, the Systems Biology Workbench, Visual Editors, collaboration with other groups and the development of new theory and algorithms. Our work has played a key part in helping to further develop SBML, the de facto standard for System Biology Model exchange and SBGN, the developing standard for visual representation for biochemical models. Our work has also made significant contributions to developing SBW, the systems biology workbench which is now very widely used in the community (roughly 30 downloads per day for the last three years, which equates to about 30,000 downloads in total). We have also used the DOE funding to collaborate extensively with nine different groups around the world. Finally we have developed new methods to reduce model size which are now used by all the major simulation packages, including Matlab. All in all, we consider the last three years to be highly productive and influential in the systems biology community. The project resulted in 16 peer review publications.