Amira: Visualize, Analyze, Present - Software platform for visualizing, manipulating and understanding life science and bio-medical data coming from all types of sources and modalities.
Biosoft - Programs for data analysis, graphics and statistics.
BioVis3D: Research All Dimensions - Flexible and easy-to-use software designed for researchers to reconstruct 3D models from histological serial sections. A new feature is that single neurons can now be modeled in a 3D environment along with their interconnections.
Dynamic Clamp - DYNCLAMP4 is a program to insert artificial synapses and conductances in up to 4 neurons in real time.
eBioSys - Provides eLab, an easy-to-use laboratory information management system that improves sample throughput and reduces IT costs. Also offers IT consulting services for the biological sciences.
Feeding Frenzy - Bean There Grown That is an educational software CD-ROM and a seed-growing science kit. User grows seeds and performs experiments.
The Frangakis Group - Provides an electron tomography toolbox for Amira. The EMPackage is a powerful toolbox for three-dimensional electron microscopy in Amira.
ImStar - Bio-imaging software and fully automated systems for research and clinical diagnostic with focus on genetic diseases and cancers.
Java Biology Lab - A wide variety of free online biology software programs.
Jumper - Open source, web-infrastructure platform that allows users to tag and link any data object. It can be used for organizing and searching assay data across multiple storage repositories.
Kalaimoscope Motion Tracker for Live Cell Imaging - Provides biological insights by finding, measuring and tracking image objects. High level statistical analysis tools and grid-computing capabilities are built in.
LabLife - Lab management software for academic biology research labs. Organize data and materials, coordinate purchasing, analyze sequences and share information.
LabSys - Provides Laboratory Information Management Systems for all laboratory data management issues.
LIMS - Laboratory Information Management Systems. Compendium of information on state-of-the-art data management software.
MCID Core - Image analysis software solutions for neuroscience, biology and other life sciences.
MetaSystems - Manufacturer of automatic microscopy imaging systems for research and routine labs.
Minnesota Biomedical Business Network - MBBNet lists health-related software and information management, device, and display companies in Minnesota.
MireSoft - Provides CiteSmart, a software program to manage bibliographic references when working with PubMed. CiteClick and RefClick can cite and store references with a single click.
Nonlinear Dynamics - Product range includes analysis software for 1D and 2D electrophoresis gels, mass spectrometry and LC-MS as well as tools for multivariate statistical analysis.
RefNavigator - A software program to search biology references from Pubmed and other online libraries. It also downloads full text and makes bibliographies in Word.
Ruro, Inc - Development and production of computer software for research, biotechnological, pharmaceutical, healthcare and government laboratories. Range includes FreezerPro, ezColony, LIMS 247, and ElegantDS tools.
Serf - A Windows-based program for electrophysiologists for analysis of single channel currents and spike trains.
SimBiotic Software - Provides a range of interactive software for biology education including virtual labs which simulate real life experiments.
Spellex Development - Biotechnology spell checking software for spelling words in the bioscience field including molecular biology, biomedicine, biophysics, microbiology, genetics and biochemistry
Stat-Ease, Inc. - Statistical software, training, and consulting on Design of Experiments for scientists and engineers.
Statistical Computation Website - Online software for calculating probability, linear correlation and regression, chi-square, t-procedures and ANOVA from Vassar College.
Alice Software - Database system to build and publish synonymised checklists of species. Species descriptions include pre-established fields and detailed descriptions employing any number of user-defined fields.
Alternative Splice Site Predictor - ASSP predicts putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons.
Binary State Pattern Clustering - BSPC is a method for pattern discovery in gene expression microarray data, that makes use of a perspective that interprets gene activity as being in two or more discrete functional states.
Broad Institute Genetics Software - Offers a wide range of software for genome sequence analysis, genetic variation, linkage analysis, expression analysis, and PCR primer selection.
CellProfiler - Open source image analysis software designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
CounterTrace II DNA Sequencing - Software and reagent for improving the quality and read length of DNA sequence traces collected on the ABI 3730 DNA sequencer.
CREME: Cis-REgulatory Module Explorer - Identifies modules of putative transcription factor binding sites that are specific to promoters of co-expressed human genes. Provides a resource for decoding microarray experiments.
Gene Array Analyzer Software - Software for the efficient management, analysis and visualization of large amounts of gene expression data.
Gene Expression Open Source System - Open source database and analysis package used to store and analyze gene expression data. Includes microarray center workflow management, and researcher tools to analyze final data.
GeneSifter - Web-based microarray analysis system that combines data management and analytical functions with integrated, current gene annotation from public databases. Product overview in pdf format.
Genetic Linkage Analysis - Offers links and other resources for genetic analysis software from the Rockefeller University.
Genetic Network Maps as Java Applets - Genetic networks controlling development in Sea Urchin represented as Java applets. Formal scheme. Molecular interactions modelled as Petri Net.
Genex Open Source Gene Expression Database - Genex is an open source database for storing, processing, and analyzing gene expression microarray data.It is intended for local installation by medium sized laboratories with some system administration support. No activity since 2003.
GENtle - GPL software for viewing and editing DNA and amino acid sequences. Integrated alignment, PCR, BLAST searches, and shared databases. Windows version is available for download (English and German).
Hands on Genetics - Instructional software for basic genetics, such as DNA, PCR, Mendel, Hardy-Weinberg, meiosis and computer simulations. Freeware for Mac and Windows.
MapMakerDrawer - Program that draws chromosome maps (as EMF files) using the output of MapMaker EXP. Delphi source code is freely available upon request. The software is available under the MIT licence.
MuStaR Sequence Variant Database Software - Designed to create a database of mutation loci, to make this information available to as many people as possible. No longer being maintained.
Mutation Explorer - Software to automatically detect mutations from DNA sequence data, including homozygous, heterozygous, insertion and deletion.
OpenBiomind - OpenBiomind is an open source toolkit for analysis of gene expression, SNP and other biological datasets using advanced machine learning and pattern mining techniques, and includes traditional clustering, hybrid clustering, and other techniques.
PeakTrace Basecaller - Software for base and quality scoring ABI DNA sequencing traces. Works with all ABI DNA sequencers including the ABI 377, ABI 310, ABI 3700, ABI 3100, ABI 3130 and ABI 3730.
Phenosystems - Software company developing user friendly tools for the molecular genetics community. Provides details of products, R and D collaborations and news.
Progeny Software - Supply pedigree drawing and genetic data management software for genetic research with a built-in customizable relational database.
PyMoods - A software application for visualizing genomic data. Can be used to analyze and display relations between complete genomes, genomic fragments, proteins, ESTs, full length cDNAs, and gene expression data.
Random Genetic Optimization - Genetic algorithms are a new approach to modeling based on the evolution theory in biology and use concepts such as population, descendant, parents, mutations, chromosomes, genes, etc.
Seqool - Free Windows software tool for the analysis of DNA and RNA sequences. It includes several sequence statistics and a comprehensive set of signal search methods.
The Sequence Manipulation Suite - The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.
STRand - Open-source program, provided by Davis' Veterinary Genetics Lab at the University of California, to automate or speed up the analysis of DNA fragment length polymorphism samples.
Synopsis - Commercial Windows software for visualization and annotation of genomic data.
Help build the largest human-edited
directory on the web.