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http://glare.sourceforge.net/

A software that facilitates and improves the design of chemical combinatorial libraries.

Proper citation: GLARE (RRID:SCR_012083) Copy   

•   Source: SciCrunch Registry

http://mfpaq.sourceforge.net/

Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).

Proper citation: MFPaQ (RRID:SCR_012049) Copy   

•   Source: SciCrunch Registry

http://proteowizard.sourceforge.net/

Software that enables rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations.

Proper citation: ProteoWizard (RRID:SCR_012056) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/adtex/

A software tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.

Proper citation: ADTEx (RRID:SCR_012059) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/multiplierz/

An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.

Proper citation: multiplierz (RRID:SCR_012058) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/te-locate/

A software tool to locate all copies of sequences in a reference sequence using read-pairs.

Proper citation: TE-locate (RRID:SCR_012063) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/laitor/

A text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.

Proper citation: LAITOR (RRID:SCR_012101) Copy   

•   Source: SciCrunch Registry

http://matnmr.sourceforge.net/

A highly flexible software toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB.

Proper citation: MatNMR (RRID:SCR_012060) Copy   

•   Source: SciCrunch Registry

http://mzmine.sourceforge.net/

Software for mass-spectrometry data processing, with the main focus on LC-MS data.

Proper citation: MZmine (RRID:SCR_012040) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/exorca/

A Matlab package extending the scope of established COBRA metabolic modelling.

Proper citation: ORCA (RRID:SCR_012097) Copy   

•   Source: SciCrunch Registry

http://opencobra.sourceforge.net/openCOBRA/Welcome.html

Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.

Proper citation: COBRApy (RRID:SCR_012096) Copy   

•   Source: SciCrunch Registry

http://knowtator.sourceforge.net/

A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.

Proper citation: Knowtator (RRID:SCR_012099) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pb-jelly/

Software that automates the finishing process using long sequence reads in a reference-guided assembly process.

Proper citation: PBJelly (RRID:SCR_012091) Copy   

•   Source: SciCrunch Registry

http://www.mindtouch.com/

A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more.

Proper citation: Mindtouch DekiWiki (RRID:SCR_003425) Copy   

•   Source: SciCrunch Registry

http://www.evoio.org/wiki/MIAPA

Central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard.

Proper citation: MIAPA (RRID:SCR_003777) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/seqexpress/

A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.

Proper citation: SeqExpress (RRID:SCR_004013) Copy   

•   Source: SciCrunch Registry

http://unoseq.sourceforge.net/

A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists.

Proper citation: UnoSeq (RRID:SCR_005116) Copy   

•   Source: SciCrunch Registry

http://orman.sourceforge.net/Home

A software tool for resolving multi-mappings within an RNA-Seq SAM file.

Proper citation: ORMAN (RRID:SCR_005188) Copy   

•   Source: SciCrunch Registry

http://seqant.genetics.emory.edu/

A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest.

Proper citation: SeqAnt (RRID:SCR_005186) Copy   

•   Source: SciCrunch Registry

http://ergatis.sourceforge.net/

A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level.

Proper citation: Ergatis (RRID:SCR_005377) Copy   

•   Source: SciCrunch Registry