© 2000 - 2014 Virginia Bioinformatics Institute
Friday, 18 April 2014

RESOURCES AND TOOLS

ADAM (Analysis of Dynamic Algebraic Models)
http://adam.vbi.vt.edu/

ADAM uses a combination of simulation and mathematical algorithms to analyze the dynamics of discrete biological systems.

Biochemical Networks Modeling Group
http://www.comp-sys-bio.org

This project builds methods to infer genetic networks from gene chip or microarray transcription profiles.

CI-TEAM Implementation for Biological Researchers, Educators, and Developers (CIBRED)
https://cibred.vbi.vt.edu/drupal/

CIBRED applies current research in a project-centric and interdisciplinary environment for the development of a sustainable cyberinfrastructure education program.

COPASI (Complex Pathway Simulator)
http://www.copasi.org/tiki-index.php

COPASI is a software package that allows the simulation and detailed analysis of biochemical networks.

Discrete Visualizer of Dynamics
http://dvd.vbi.vt.edu

DVD is a tool for the visualization of the dynamics of multi-state discrete models of biological networks.

Dissecting Soybean Resistance to Phytophthora
http://pmgn.vbi.vt.edu/soybean/

The Dissecting Soybean Resistance to Phytophthora project focuses on the mechanisms of quantitative resistance of soybean against the oomycete pathogen Phytophthora sojae, which is one of the most damaging pathogens of soybean crop.

GenoCAD
http://www.genocad.org/genocad/

GenoCAD allows users to build and verify complex genetic constructs derived from a library of standard genetic parts. See also GenoCAD SourceForge https://sourceforge.net/projects/genocad/, an open source development effort for GenoCAD.

Genome Reverse Compiler
http://staff.vbi.vt.edu/jcslab/grc.html

Genome annotation software available for download from http://dev.vbi.vt.edu/projects/grc/

Middle-Atlantic Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Resear
http://marce.vbi.vt.edu/

MARCE focuses on research to enable rapid defense against bioterror and emerging infectious diseases.

MIEP
http://www.modelingimmunity.org

The Center for Modeling Immunity to Enteric Pathogens (MIEP) is a NIAID funded project with the mission of understanding the mechanisms of action underlying immune responses to enteric pathogens.

Nodulation Mutant Database (NodMutDB)
http://nodmutdb.vbi.vt.edu/

NodMutDB provides a comprehensive and accurate resource for depositing, organizing and retrieving information on symbiosis-related genes, mutants and published literature.

Oomycete Molecular Genetics Research Collaboration Network (OMGN)
http://pmgn.vbi.vt.edu/

The Oomycete Molecular Genetics Research Collaboration Network is helping build an international scientific community interested in oomycete molecular genetics and genomics, either at the experimental or computational level.

Oomycetes Soybean EST Database (EST)
http://est.vbi.vt.edu

The Oomycetes Soybean EST Database is an integrated resource hosting combined Expressed Sequence Tag (EST) data from oomycetes such as Phytophthora sojae, Phytophthora infestans and Hyaloperonospora arabidopsidis.

PAMGO (PAMGO)
http://pamgo.vbi.vt.edu/

PAMGO interest group develops new gene ontology (GO) terms describing the various processes, functions and cellular components related to microbe-host interactions.

Pathogen Portal
http://pathogenportal.org

Pathogen Portal is a repository linking to four Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). The BRCs are providing web-based resources to the scientific community for infectious disease research.

Polynome: Discrete System Identification
http://polymath.vbi.vt.edu/polynome

Polynome is a web-based tool for parameter estimation and simulation of Boolean models of biological networks.

Rhizobiales Bioinformatics Resource Center (RhizobialesBRC)
http://rhizobia.vbi.vt.edu/production_v1/

The goal of the Rhizobiales Bioinformatics Resource Center is to provide a comprehensive and accurate web-based resource for genomic and associated information on the sequenced Rhizobiales.

Seedgenes: Essential gene functions in Arabidopsis thaliana
http://www.seedgenes.org/

The SeedGenes project identifies and analyzes every Arabidopsis gene essential for seed development.

SpLip - Lipoprotein computational prediction in spirochetal genomes
http://jcslab.vbi.vt.edu/splip/

Sequence analysis software available for download from this site.

SysGenSIM
http://sysgensim.sourceforge.net/

SysGenSIM is a bioinformatics toolbox for MATLAB® to create artificial gene expression datasets by simulating Systems Genetics experiments.

The Agrobacterium and Azotobacter projects pages (members only)
http://agro.vbi.vt.edu/

Agrobacterium and Azotobacter community tools and resources for genomics

The Agrobacterium Community Genome Annotation Database
http://agro.vbi.vt.edu/public
Tools and resources for genome sequencing of Agrobacterium biovar type strains.

The Azotobacter Community webpage
http://www.azotobacter.org

The website for the Azotobacter vinelandii genome project

The PathoSystems Resource Integration Center (PATRIC)
http://patricbrc.vbi.vt.edu

PATRIC (PATRIC 2.0) is a multi-faceted bioinformatic website containing genomic and associated information on bacterial pathogens included in the National Institute of Allergy and Infectious Diseases or NIAID's category A-C priority list.

VBI Genome Browser
http://sourceforge.net/projects/vbigenomebrowse

The VBI Genome Browser is a tool that allows viewing of genomic data that adheres to the Genomics Unified Schema (GUSDB) data storage standard.

VBI Microbial Database
http://vmd.vbi.vt.edu

The VBI Microbial Database hosts data from different sources for a range of plant pathogenic oomycetes, fungi and bacteria, primarily those organisms under study at VBI.