Simulation models play an increasingly important role in biomedical research. To maximize the value of those models to the scientific community, they must be available, reliable, and searchable. TheBioModels database was created to address all three needs. To ensure availability, models in SBML format are centrally hosted by BioModels, and many journals now recommend that authors submit to BioModels when modeling papers are published. To ensure reliability, models are validated by the BioModels team, to ensure that the hosted file reproduces results from the corresponding paper. To ensure searchability, models are annotated by the BioModels team, to connect model entities to standardized biological databases. The BioModels database has grown rapidly, now hosting over 1400 models. But a lack of manpower means that BioModels team has only curated and annotated roughly half of those models. To relieve this shortage of manpower and to promote student engagement with authentic research models, Dr. Gutenkunst is collaborating with Viji Chelliah to engage students in the curation of BioModels.
In a pilot project during Fall 2015, students in MCB 572 and MCB 315 curated and annotated the following models:
- Coggins 2015 – Activation of the CXCR4 signaling pathway by CXCL12.
- Cellière 2011 – Generic properties of signaling by TGF-β.
- Perez-Rosas 2015 – Caffeine-induced calcium release in smooth muscle cells.
- Stavrum 2013 – Tryptophan metabolism in the human liver.
- Petelenz-Kurdziel 2013a, b, c, d, e, f – Adaptation to osmotic stress in yeast.
This pilot project showed that students could successfully curate and annotate models, and that they found the experience valuable. Over the next several years, Dr. Gutenkunst will develop improved instructional materials and software to ease the student curation process. These resources will be honed through application at the University of Arizona and at the q-bio Summer School. They will then be made widely available, so instructors at other institutions can incorporate BioModels into their systems biology curricula.