Bioinformatics and Computational Biology | SRI International
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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.


Deep Adaptive Semantic Logic (DASL)

Harnessing formalized expert knowledge to construct sophisticated deep learning architectures

Using Synthetic Lethality to Identify Predictive Biomarkers of Targeted Therapies

Using synthetic lethality to ID biomarkers for targeted anti-cancer drugs.

two researchers looking at computer screens

MetaCyc Metabolic Pathway Database

MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2500 pathways from 2800 organisms.

silhouette of a man looking at BioCyc software

BioCyc Database Collection

A comprehensive website for sharing fundamental information about biochemical pathways and genomes with researchers around the world.