438480 New Standard Resources for Systems Biology: BiGG 2 Database and Visual Pathway Editing with Escher

Wednesday, September 16, 2015
Crowne Plaza Heidelberg City Centre
Andreas Dräger1,2, Zachary A. King2, Justin S. Lu2, Ali Ebrahim2, Nikolaus Sonnenschein3, Philip C. Miller2, Joshua A. Lerman4, Bernhard O. Palsson5,6,7 and Nathan E. Lewis7, (1)Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany, (2)Bioengineering, University of California, San Diego, La Jolla, CA, (3)Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark, (4)Total New Energies USA, Inc., Amyris, Inc., Emeryville, CA, (5)Department of Bioengineering, University of California, San Diego, La Jolla, CA, (6)Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark, (7)Department of Pediatrics, University of California, San Diego, La Jolla, CA

Background: Genome-scale metabolic network reconstructions enable the simulation and analysis of complex biological networks, thus providing insights into how thousands of genes together influence cell phenotypes. Accuracy in systems biology research requires standards in model construction, a variety of specific software tools, and access to high-quality metabolic networks.

Results: To meet these needs, we present the BiGG 2 database and a collection of software solutions for model building, curation, visualization, and simulation.
BiGG 2 currently contains 76 high-quality manually-curated genome-scale metabolic network reconstructions, which can be easily searched and browsed and include interactive pathway map visualizations.
These visualizations have been generated with the web-based Escher pathway builder. Escher allows users to draw pathways in a semi-automated way and can visualize data related to genes or proteins that are associated to pathways. An export function facilitates storing Escher maps in the community formats SBML and SBGN-ML. These features make Escher an ideal interactive model development tool.
In order to make all models in BiGG 2 MIRIAM compliant, BiGG 2 itself has become part of the MIRIAM registry and provides links a plethora of external databases for each model component. This rich annotation enables rapid comparison across models. New Systems Biology Ontology terms have been defined that are used to better highlight the role of model components.
A comprehensive web API for programmatically accessing the database content enables interfacing with diverse modeling and analysis tools.

Conclusions:With these features and tools, BiGG 2 provides a valuable database, structured for easy access and to help improve the quality, standardization, and accessibility of all genome-scale models. The development of this resource has boosted the development of community standards for constraint-based modeling.

Availability: http://bigg.ucsd.edu, http://escher.github.io


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