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http://mzmatch.sourceforge.net/
A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.
Proper citation: mzMatch (RRID:SCR_000543) Copy
http://sourceforge.net/projects/htqc/
A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc..
Proper citation: HTQC (RRID:SCR_006448) Copy
https://sourceforge.net/projects/avalontoolkit/
Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting.
Proper citation: Avalon Cheminformatics Toolkit (RRID:SCR_014273) Copy
neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware.
Proper citation: neurospy (RRID:SCR_007016) Copy
http://cudasw.sourceforge.net/
CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher
Proper citation: CUDASW++ (RRID:SCR_008862) Copy
http://purl.bioontology.org/ontology/FB-SP
The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.
Proper citation: Fly Taxonomy (RRID:SCR_003317) Copy
http://sourceforge.net/projects/limsforproteomi/
Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow.
Proper citation: LIPAGE (RRID:SCR_000290) Copy
http://dti-tk.sourceforge.net/pmwiki/pmwiki.php
A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation
Proper citation: Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) Copy
Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.
Proper citation: SNVer (RRID:SCR_002061) Copy
http://rubioseq.sourceforge.net/
Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.
Proper citation: RUbioSeq (RRID:SCR_002508) Copy
http://sourceforge.net/projects/mipe/
A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file.
Proper citation: MIPE (RRID:SCR_003065) Copy
http://www.metabolomics-msi.org
Oversight Committee appointed to monitor, coordinate and review the efforts of working groups (WG) in specialist areas (Biological context metadata WG, Chemical analysis WG, Data processing WG, Ontology WG, Exchange format WG) that will examine standardization and make recommendations.
Proper citation: Metabolomics Standards Initiative (RRID:SCR_003246) Copy
http://sourceforge.net/projects/vtontology/
A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.
Proper citation: Vertebrate Trait Ontology (RRID:SCR_003214) Copy
https://bioportal.bioontology.org/ontologies/NEMO/?p=summary
Ontology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG).
Proper citation: NEMO Ontology (RRID:SCR_003386) Copy
An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).
Proper citation: Software Ontology (RRID:SCR_003493) Copy
http://solexaqa.sourceforge.net/
Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.
Proper citation: SolexaQA (RRID:SCR_005421) Copy
A web-based software package for comparative genomics.
Proper citation: Sybil (RRID:SCR_005593) Copy
http://sourceforge.net/projects/cnvhitseq/
A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.
Proper citation: cnvHiTSeq (RRID:SCR_013160) Copy
An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component.
Proper citation: Jmol (RRID:SCR_003796) Copy
http://mged.sourceforge.net/ontologies/MGEDontology.php
An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.
Proper citation: MGED Ontology (RRID:SCR_004484) Copy
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