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http://manatee.sourceforge.net/

Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris

Proper citation: Manatee (RRID:SCR_005685) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cancergrid-tma/

A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis.

Proper citation: cancergrid-tma (RRID:SCR_005595) Copy   

•   Source: SciCrunch Registry

http://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dna-bison/

Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads.

Proper citation: dna-bison (RRID:SCR_005913) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dtailor/

A fully extendable software framework, for property-based design of synthetic DNA sequences.

Proper citation: D-Tailor (RRID:SCR_000115) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sirnarules/

An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.

Proper citation: siRNArules (RRID:SCR_000096) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/abmining/

Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).

Proper citation: AbMining ToolBox (RRID:SCR_000090) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/spdesigner/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

Proper citation: SP-Designer (RRID:SCR_000031) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mysirna/

Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.

Proper citation: MysiRNA-designer (RRID:SCR_000102) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dprimer/

A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.

Proper citation: dprimer (RRID:SCR_000050) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/imethy/

Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.

Proper citation: iMethy (RRID:SCR_000049) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/protms/

A software tool for the proteomics community that may help improving analysis of proteomic experimental data.

Proper citation: Quant (RRID:SCR_000267) Copy   

•   Source: SciCrunch Registry

http://open2dprot.sourceforge.net/Flicker/

An open-source stand-alone computer program for visually comparing 2D gel images.

Proper citation: Flicker (RRID:SCR_000288) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/biogrinder/

An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.

Proper citation: Grinder (RRID:SCR_000168) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/omssapercolator/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results.

Proper citation: OMSSAPercolator (RRID:SCR_000287) Copy   

•   Source: SciCrunch Registry

http://gprox.sourceforge.net/

A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.

Proper citation: GProX (RRID:SCR_000273) Copy   

•   Source: SciCrunch Registry

http://peptideprophet.sourceforge.net/

Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.

Proper citation: PeptideProphet (RRID:SCR_000274) Copy   

•   Source: SciCrunch Registry

http://garm-meta-assem.sourceforge.net/

A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.

Proper citation: GARM (RRID:SCR_006731) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/blox/

A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme

Proper citation: Blox (RRID:SCR_006667) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/powermap/

Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support.

Proper citation: PowerMap (RRID:SCR_006721) Copy   

•   Source: SciCrunch Registry