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Bioinformatics and Computational Biology
Applying computational methods to the study of living systems at all scales—from molecules to ecosystems—advances scientific understanding. For example, researchers can now use computer programs to generate a quantitative metabolic model from a sequenced genome.
SRI's interdisciplinary scientists develop tools, software, databases, and ontologies to manage and analyze the burgeoning quantities of high-throughput, heterogeneousbiological data and knowledge now available. These tools can be applied to applications ranging from accelerating drug discovery and precision medicine applications to developing new biofuels.
Projects and offerings include:
Pathway Logic: a powerful approach to modeling biological entities and processes, such as metabolic networks and signal transduction
BioCyc: a collection of more than 3,000 databases containing information about genomes and biochemical pathways
Pathway Tools: bioinformatics software for pathway analysis of genomes and for creating quantitative metabolic models
HumanCyc: a bioinformatics database linking human metabolic pathways to the human genome
MetaCyc: a database of nonredundant, experimentally elucidated metabolic pathways that contains 2,100 pathways from thousands of different organisms, and is curated from the scientific experimental literature
Biological Simulation Program for Intra- and Inter-Cellular Evaluation (Bio-SPICE): an open-source computing environment that biologists can modify and control
Hybrid qualitative modeling/hybrid quantitative modeling: SRI's approach to analyzing complex biological systems based on simultaneously modeling a system’s continuous and discrete behaviors using the HybridSAL language
Precision Medicine Tools for Cancer: bioinformatics tools to identify mutation-specific therapeutic targets in cancer and predictions of response to targeted drugs based on mining patient genomic and transcriptomic data.
In our work, we often engage researchers, biologists, and computer scientists at other R&D organizations.
Harnessing formalized expert knowledge to construct sophisticated deep learning architectures
Using synthetic lethality to ID biomarkers for targeted anti-cancer drugs.
MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2500 pathways from 2800 organisms.
A comprehensive website for sharing fundamental information about biochemical pathways and genomes with researchers around the world.