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Scientific Software

Non-Commercial Software

• Catalog of Free Flow Cytometry Software
• Cell Profiler - Open-source cell image analysis software.
• 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 ofNIH 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)
• Tools for Structure Prediction and Analysis Based on Complementarity with Environment (SPACE) (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)

See also theScientific 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 - Makers of ChemDraw.
• Chemistry-Software.com - Software for chemical laboratory management.
• Genomatica - Software for the modeling and simulation of metabolism.
• 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.
• InNetics - Systems biology software.
• Math-for-Health - Makers of the PDB Structural Decomposition Tool for decomposition and repair of PDB files.
• Niles Software - The makers of EndNote.
• Nucleics - DNA sequencing software and reagents.
• Protein Lounge - Web-based databases for systems biology.
• OnScreen DNA - Educational DNA-visualization and simulation software for teaching about DNA structure and function.
• Sample Tracking Laboratory Software (MediaData Systems)
• Soll Technologies - Image analysis software.
• Teranode - Design automation software for research and development in the life sciences.
• Wolfram Research - Makers of Mathematica.

Online Software Vendors

• Academic Superstor
• CampusTech
• CCV Software
• Computational Chemistry Software
• SchoolWorld Software
• Sprysoft

See also theVendors of Scientific Products and Services page.

Discussion Groups

• Usenet newsgroup archives fromBIOSCI/bionet (can also be accessed throughGoogle Groups: 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 theDiscussion Groups section of theGeneral Resources and Tutorials page.

© 1999–2023 Gabriel Fenteany

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