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Lists of Software for
Bioinformatics: Pathway Analysis Tools

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[ A, B, C ] -- [ D, E, F ] -- [ G, H, I ] -- [ J, K, L ]
[ M, N, O ] -- [ P, Q, R ] -- [ S, T, U ] --
[ V, W ] -- [ X, Y, Z]




--- A, B, C ---





 

BIOCARTA is a web-based, user contributed collection of pathways and the tools to study them. Observe how genes interact in dynamic graphical models. The online maps depict molecular relationships from areas of active research. In an "open source" approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species. Find both classical pathways as well as current suggestions for new pathways. Check the Biocarta website for additional information.



 

Cell Illustrator is a biopathway modeling and simulation tool. It provides graphical drag and drop user interface for constructing a pathway model, or reads one from a public database. Processes and reactions are specified in terms of their input and output entities and their rate. This anables the simulation of the pathway once intial conditions of the various entities and processes are set. Simulations poduce graphs of vaious entities, and data that can be used by Cell Animator--a free component, to generate a "live" animation. Cell Illustrator accepts data from pathway databases like KEGG, BioCyc. The program uses a proprietary XML representation of a pathway. Sites/databases like KEGG, BioCYC, BioPACS, provide some pathways in this format, or convert databases to this format. Contact:

Gene Networks
560 South Winchester Blvd.-Suite 500
San Jose, CA 95128
Tel: 408-572-5567
Web: http://www.gene-networks.com


 

Cognia Molecular is a tool for managing biological information. It allows clients to integrate proprietary data with information from public sources. Cognia developed the Cognia Molecular information management system to give researchers a powerful, cost-effective, and easy to use system to efficiently integrate , intelligently manage , and effectively utilize biological and chemical information.

Cognia Molecular is a system for researchers to coalesce important information and create an integrated centralized knowledge base. The transformed information is organized and standardized, making it amenable to precise and complex querying and network building. Researchers will more easily make sense of their findings in the context of what is already known.

Cognia Molecular's easy-to-use curation clients, precise relational database, automated batch loading tools for experimental information, parsed datasets, well documented API, simple linking tools and built in links, and powerful search and visualization interfaces enable researchers to:

  • Integrate your information with public and third party datasets and provide context within the literature for interpreting findings
  • Efficiently curate and document literature-derived and internal analyzed information on proteins, complexes, genes, interactions, and compounds in your own centralized database
  • Capture and share institutional knowledge and curated information within your research group or company
  • Search highly discrete biological and chemical information with intelligent query tools
  • Build and visualize molecular interaction networks dynamically with information in your database

Contact:

Cognia Corporation
117 East 55th Street
New York, NY 10022
Email: info@cognia.com
Tel.: 212.331.7850
Fax: 646.349.1835
Web: http://www.cognia.com




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ExPASy (Expert Protein Analysis System), is the proteomics server of the Swiss Institute of Bioinformatics. This page gives access to the digitized version of the Roche Applied Science "Biochemical Pathways" wall chart. Please note that the publishing company Elsevier GmbH, Slevogtstr. 3 - 5 69126 Heidelberg Germany, owns the rights for commercial applications of the Biochemical Pathways. If you wish to use any of the information obtained from this site commercially please contact Ms. Ina Schibel at Elsevier GmbH for approval. For enquiries on how to obtain a paper copy of the wall chart, please contact Roche Applied Science directly.





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GenMAPP (Gene Map Annotator and Pathway Profiler), is a computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes. The project is run by GenMAPP.org at the University of California at San Francisco. We continuously improve the GenMAPP software and databases to address the needs of the bioinformatics community. GenMAPP the application is available with over 50 curated MAPPs, hundreds of MAPPs derived from KEGG pathways and thousands of functional groupings of genes derived from the Gene Ontology Project. GenMAPP.org seeks collaborators in the biological community to assist in the development of a library of pathways that will encompass all known genes in the major model organisms. GenMAPP is pleased to announce that we are collaborating with BioPAX (Biological Pathways Exchange). Biopax is a community based initiative whose mission is to develop a flexible and extensible common exchange format for biological pathways data. GenMAPP's efforts initial involvement will focus on implementing a Biopax to GenMAPP pathway converter.





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KEGG (The Kyoto Encyclopedia of Genes and Genomes) is a resource for metabolic pathways and regulatory pathways. A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic information. Towards this end we have been developing a bioinformatics resource named KEGG, Kyoto Encyclopedia of Genes and Genomes, as part of the research projects in the Kanehisa Laboratory of Kyoto University Bioinformatics Center.



 

LION Target Engine(™) is a suite of programs for pathway and sequence analysis. Features include:

  • Summary Sheets provide a thorough overview of all information available about gene targets and sequences of interest.
  • The Gene Hub provides a comprehensive reference data set for genes, transcripts and proteins.
  • Annotation supports you in collecting all available information about any sequence, as the starting point for the target validation process.
  • Pathway and Interaction - Now recognized as the key technology for target validation and discovery, the creation and interpretation of pathways in the context of R&D is crucial for target validation.
  • Text Mining supports the user in the extraction of valuable scientific knowledge.
  • Assay Viewer allows analyses of numerical experimental results, as they are typically produced by the different drug target validation technologies.
  • Registration provides a sequence registration in a similar fashion as a compound registration service.
  • Target Tracking product visualizes the position of targets in the company pipeline.
  • GeneSpring¨ Connector - This is an example for the capability of LION Target Engineª to integrate with desktop applications. The direct connection between GeneSpring¨ (Silicon Genetics) and LION Target Engineª allows the user to exchange information between the two software systems and to switch seamlessly from one product to the other.
  • Genome Viewer visualizes single or multiple genes in context with information from many different sources mapped to a genome sequence.
  • Protein Structure provides an overview of all tertiary structures related to a given target sequence.

For additional information, contact LION Bioscience.





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MetaCore is an integrated software suite for functional analysis of microarrays, SAGE, proteomics and other experimental data. MetaCore is based on the unique, curated database of human protein-protein and protein-DNA interactions, transcriptional factors, signaling, metabolism and bioactive molecules. The analytical package includes intuitive tools for data visualization, mapping and exchage; multiple networking algorithms and in silico filters. MetaCore is available via web access and as a stand-alone server for in-house installations. For additional information, contact:

GeneGo, Inc.
500 Renaissance Drive, Suite 106
St. Joseph, MI 49085
phone (888) 592-3124
Fax (269) 983-7649
Web: http://www.genego.com


 

Multifactor Dimensionality Reduction (MDR) is an open-source, freely available, and user-friendly software package for detecting and characterizing epistasis or gene-gene interactions in genetic and epidemiologic studies of common human diseases. The software is written in JAVA and is platform independent. For a recent review of the method see: Moore JH. Computational analysis of gene-gene interactions using multifactor dimensionality reduction. Expert Rev Mol Diagn. 2004 Nov;4(6):795-803. Please also see Epistasis Blog, http://compgen.blogspot.com for a public discussion on epistasis.





--- P, Q, R ---





 

PathArt is a dynamic pathway articulator, which builds molecular interaction networks from curated databases. This product has comprehensive information on over 900 regulatory as well as signaling pathways. This product allows users to upload and map microarray expression data onto the pathways. The program builds a pathway schematic, which includes all molecules in a pathway and their biological relevance as well as annotated information and a protein-protein interaction network.

Jubilant Biosys Ltd.
8575 Window Latch Way
Columbia, MD 21045
Mobile : (443) 838 6260
Fax: (703) 940 4088
Web: http://www.jubilantbiosys.com


 

PathwayStudio (formerly PathwayAssist) is a powerful, user-friendly software package that allows you to build, visualize and explore biological association networks (BAN). A BAN is an interactive diagram that shows the biological interactions amongst different proteins, small molecules and cellular processes. Each interaction is annotated with the source references and contains hyperlinks to the exact source literature. A BAN is built using a biological fact database, and each copy of PathwayStudio contains ResNet, a database with over 140,000 biological facts extracted from PubMed. Additional facts can be easily added by importing data from GO, BIND, DIP, KEGG or other custom biological databases. PathwayStudio also supports a variety of query options to allow you to see only the types of interactions that are relevant to your research.

PathwayStudio also contains MedScan, a Natural Language Processor (NLP) that extracts facts directly from biological text. MedScan can be run on PubMed abstracts, full journal articles on internal documents allowing you to include nonpublic information in your BAN. Microarray gene expression data can be overlaid on a BAN to show how genes and proteins are affected in perturbed or normal states. Pathway Assist runs on PC compatibles and supports Windows® 2000 and XP. Contact:

Ariadne Genomics
9700 Great Seneca Highway, Suite 113
Rockville, MD 20850
Phone: (240) 453-6296
Fax: (240) 453-6208
Web: http://www.ariadnegenomics.com


 

Pathways Analysis is a web-based application that makes use of Ingenuity Systems' Pathways Knowledge Base, a curated database of millions of modeled relationships between proteins, genes, complexes, cells, tissues, drugs and diseases. The Ingenuity Pathways Analysis solution is a new way for scientists to concurrently analyze multiple datasets across different experimentation platforms and identify key functions and pathways that distinguish biological states. This innovative technology is especially useful for dose response assessment, patient stratification for clinical trials, time course experiments, and simultaneous analysis of gene lists and protein lists. Contact Ingenuity at

Ingenuity Systems, Inc.
1565 Charleston Road
Mountain View, CA 94043
Tel: (650) 967-7777
Fax: (650) 623-0810
Email: info@ingenuity.com
Web: http://www.ingenuity.com


 

The Pathway Tools software is a bioinformatics software system for pathway analysis of genomes, and for creating Pathway/Genome Databases (PGDBs). A pathway/genome database (PGDB), such as EcoCyc, is a bioinformatics DB that integrates genomic data with detailed functional annotations of the genome, such as descriptions of metabolic and signaling pathways. A PGDB is a type of model-organism DB. Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.

The Pathway Tools has three software components:

  • PathoLogic: Creates a new PGDB containing the predicted metabolic pathways of an organism, given a Genbank entry as input.
  • Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs.
  • Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.


 

Protein Networker enables an institute to make high throughput protein interaction data generated by two hybrid screens available throughout the institute. It generates graphical protein interaction maps for all protein interactions. It is a web based application allowing access on an intranet to any researcher with a browser. Secure logins ensure only authorized users have access. Secure access can optionally be enabled on the internet.

The database administrator is given additional tools for the addition and modification of interaction data. Addition of interaction data is provided by standard spreadsheet format files to ensure compatibility with other applications. Access for modification of the interaction data is restricted to authorized users. Available from

PREMIER Biosoft International
3786 Corina Way
Palo Alto, CA 94303-4504
Phone: 650-856-2703
Fax: 650-843-1250
http://www.PremierBiosoft.com





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--- V, W ---





 

Vector Xpression and Vector PathBlazer is a combined microarray and pathway analysis tool from Invitrogen. Vector PathBlazer software allows you to view protein-protein interactions identified through your research in the context of biological processes, highlighted using functional gene ontology annotations. New algorithms assist you in discovering previously unknown connections between pathways. Identification of critical control points in these pathways can help in functional validation of targets identified by siRNA. Link microarray analysis results to protein pathways and identify mechanisms of biological activity. Finally, you can use your proprietary data in combination with public data to enhance the discovery process.

Vector Xpression software provides an intuitive and easy-to-use application for microarray analysis and gene expression profiling. The desktop package includes an on-board database and a comprehensive set of software tools in a user-friendly interface. Using Vector Xpression software you can:

  • Store microarray data and annotations
  • Normalize microarray-derived data
  • Identify differentially expressed genes
  • Classify genes or subjects based on expression profiles
  • Link to Biological Pathways using Vector PathBlazer

For additional information, contact:

Invitrogen Corporation
1600 Faraday Avenue
PO Box 6482
Carlsbad, CA 92008
Phone: (760) 603-7200
FAX: (760) 602-6500
Web: http://www.invitrogen.com




--- X, Y, Z ---







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