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| BioFabric | William Longabaugh | LGPL | BioFabric is a network visualization tool that uses a novel presentation method where nodes are represented using horizontal line segments. | 2012 |  |
| Pubcrawl | Andrea Eakin | LGPL | Pubcrawl is an interactive web application that generates normalized medline distances for terms, and then returns a network topology based on the term distances and protein domain interactions. | 2011 | |
| Dodoma | Brady Bernard | LGPL | DoDoMa is a tool that automatically identifies transcription factors with matching DNA binding domains, and returns all associated position weight matrix (PWM). | 2011 | |
| Golem | Ryan Bressler | LGPL | Golem (Go Launch on Every Machine) is a light weight system for distributing analysis across processes and machines using web technologies and core features of the Go language. | 2011 | |
| RF-ACE | Timo Erkkila | Apache 2.0 | RF-ACE is an efficient implementation of a robust machine learning algorithm for uncovering multivariate associations from large and diverse data sets. | 2010 | |
| Fastbreak | Ryan Bressler | LGPL | Fastbreak is a set of python scripts implementing an O(n) algorithm for detecting translocations and other genetic structural variants from aligned mate pair sequence data in SAM/BAM format. | 2010 | |
| VisQuick | Dick Kreisberg | New BSD | VisQuick is a Javascript library utilizing the Protovis project to provide configurable, interactive, informative data exploration tools. | 2010 | |
| EPEPT | Theo Knijnenburg | LGPL | A web service for enhanced P-value estimation in permutation tests | 2010 | |
| Addama | Hector Rovira | Apache 2.0 | The Adaptive Data Management Service Architecture provides web applications and services, and defines REST APIs to facilitate rapid application development. | 2008 | |
| ProbTF | Harri Lähdesmäki | LGPL | ProbTF is a web server that enables the analysis of DNA sequences using mouse-specific position weight matrices from the TRANSFAC™ database. | 2007 | |
| BioTapestry | William Longabaugh | LGPL | BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. | 2003 | |
| Cytoscape | Sarah Killcoyne | LGPL | Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. | 2001 | |
| Lichen | Ryan Bressler | LGPL | Lichen provides a set of Flash visualizations designed to be easily incorporated as figures and user interface elements in scientific databases or web applications. | 2009 | |
| MotifMogul | Alistair Rust | --- | Web service that enables the analysis of multiple DNA sequences using sets of Position Weight Matrices from the JASPAR and TRANSFAC™ databases, using multiple scanning algorithms. | 2006 | |
| Innate Immune Database (IIDB) | Alistair Rust | --- | The Innate Immune Database (IIDB) is a repository of genomic annotations and experimental data for over 2000 genes associated with immune response behavior in the mouse genome. | | |
| ISB Java | Stephen Ramsey | LGPL | This project is a library (collection) of classes written in the Java programming language, that are intended to be used for research in computational biology. | 2004 | |
| SimCluster | Ricardo Vencio | GNU GPL | Simcluster is a package for clustering analysis of transcript enumeration data on the simplex space. | 2007 | |
| ProbCD | Ricardo Vencio | LGPL | ProbCD is a R package for Probabilistic Categorical Data analysis. ProbCD calculates the statistical association (correlation is one type of association measurement) between the properties encoded in the rows and columns of a k x 2 contingency table in which there is uncertainty in placing each element in any of the 2k possible table cells. | 2007 | |
| AngioQuant | Antti Niemistö | GNU GPL | AngioQuant is an automated image analysis tool for quantification of angiogenesis. It is designed for in vitro angiogenesis assays that are based on co-culturing endothelial cells with fibroblasts. | 2005 | |
| Dizzy | Stephen Ramsey | LGPL | Dizzy is a chemical kinetics stochastic simulation software package written in Java. It provides a model definition environment and an implementation of the Gillespie, Gibson-Bruck, and Tau-Leap stochastic algorithms. | 2003 | |
