Scientific Software

Non-Commercial Software

• Catalog of Free Flow Cytometry Software
• CellBuster - Cell tracking tool. (Andrea Giacosi)
• Eisen Lab Software - ScanAlyze for microarray image analysis, Cluster and TreeView for cluster analysis and visualization, as well as other software for expression data and sequence analysis. (Michael Eisen, Lawrence Berkeley National Laboratory)
• European Bioinformatics Institute BioCatalog - "The Biocatalog is a software directory of general interest in molecular biology and genetics."
• Folding@Home - Use your computer's unused clock cycles to help fold proteins.
• ImageJ - Newer Java version of NIH Image software; continued software development is focused on ImageJ not NIH Image. (Wayne Rasband, National Institutes of Health)
• IUBio Archive - Biology data and software. (Indiana University)
• MDL Chemscape and Chime
• Microarray Software Comparison - Comparison of a broad range of different microarray-related programs with links.
• NIH Image - Public domain imaging and analysis software. (Wayne Rasband, National Institutes of Health)
• Open Microscopy Environment (OME) - "OME is an open source software project to develop a database-driven system for the quantitative analysis of biological images."
• PHYLIP - A "free package of programs for inferring phylogenies." (University of Washington)
• Phylogeny Programs
• Significance Analysis of Microarrays (SAM) - "Supervised learning software for genomic expression data mining." (Stanford University)
• Software and Databases for Computational Biology on the Internet (Steven Salzberg, Johns Hopkins University)
• Software in Molecular Biology and Bioinformatics (Weizmann Institute of Science)
• SoftwareSeek - Database of shareware and commercial applications for use in genetics, molecular biology, biochemistry and biophysics.
• Stanford Microarray Database: Software and Tools (Stanford University)
• 3-D Laser Scanning Confocal Microscopy - Resources and graphics software (shareware/freeware).

See also the Scientific Databases and Tools page for Web-based nucleotide and amino acid sequence-based bioinformatics tools.

Structural Biology Software

Structure and Function Prediction Servers

Specialized Software and Computer Languages for Systems Biology

Commercial Software and Information Services

• CambridgeSoft - The makers of ChemDraw.
• Chemistry-Software.com - Software for organic, analytical and synthetic chemistry.
• Genome Discovery Tools - Genomics and proteomics software.
• GraphPad Software - The makers of Prism and InStat.
• Improvision - Makers of the excellent cell imaging package OpenLab and other imaging software.
• Niles Software - The makers of EndNote.
• Protein Lounge - Web-based databases for systems biology.
• Sample Tracking Laboratory Software (MediaData Systems)
• Solltech - Image analysis software.
• Tetranode - Design autmoation software for research and development in the life sciences.
• TRANSPATH - "TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database. It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal transduction pathways like hormones, receptors, enzymes and transcription factors are stored together with information about their interaction and references in an object-oriented database. All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, Swissprot, EMBL, PubMed and others)."

Online Software Vendors

• Academic Superstore - Online academic software vendor.
• CampusTech
• SchoolWorld Software
• Sprysoft

See also the Vendors of Scientific Products and Services page.

Discussion Groups

• The Virtual Library of Biochemistry and Cell Biology Discussion Board - Conceptual, practical and technical discussions and questions/answers for scientists and students.

• Usenet Newsgroup Archives (from BIOSCI/bionet):
  • ACEDB/bionet.software.acedb - Discussions by users of genome databases using ACEDB.
  • BIO-SOFTWARE/bionet.software - Information about software for biology.
  • BIO-SRS/bionet.software.srs - Discussions about Sequence Retrieval System (SRS) software.
  • INFO-GCG/bionet.software.gcg - Discussions about using GCG software.
  • STADEN/bionet.software.staden - The Staden molecular sequence analysis software.
  • X-PLOR/bionet.software.x-plor - X-PLOR software for 3D macromolecular structure determination.

See also the Discussion Groups section of the General Biochemistry and Cell Biology page.