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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software resource, software toolkit | 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. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-09-12 01:02:23 | 5 | |||||||
|
Avalon Cheminformatics Toolkit Resource Report Resource Website |
Avalon Cheminformatics Toolkit (RRID:SCR_014273) | software resource, software toolkit | Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting. | software toolkit, chemistry, canonicalize smiles, render smiles, manipulate mol file, structure fingerprinting | is listed by: SourceForge | Free, Available for download | SCR_014273 | 2026-09-12 01:02:50 | 0 | ||||||||||
|
BVA import/export EEGLAB plugin Resource Report Resource Website 1+ mentions |
BVA import/export EEGLAB plugin (RRID:SCR_016333) | bva-io | software application, software resource, software toolkit | Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software. | interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB |
is related to: SourceForge is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016333 | Brain Vision Analyser | 2026-09-12 01:02:53 | 4 | ||||||||
|
MIGen Resource Report Resource Website 10+ mentions |
MIGen (RRID:SCR_006959) | MIGen | data or information resource, knowledge environment, narrative resource, standard specification | Standard specification for the information required to report a genotyping experiment, covering: study and experiment design, subject information, genotyping procedure, and data analysis methods. The goal is to set a reporting standard for adoption by the research community to facilitate consistent data interpretation and independent validation/reproduction, and to serve as guidance for database design for storing genotyping experiment data. MIGen is being developed as a collaborative project involving international domain experts and is a registered project under MIBBI: Minimum Information for Biological and Biomedical Investigations. | genotyping, genotype, genotyping experiment, data archiving, data management, data sharing, data transfer, data analysis, experiment |
is listed by: OMICtools is related to: Minimum Information for Biological and Biomedical Investigations has parent organization: SourceForge has parent organization: UT Southwestern Medical Center Department of Pathology |
The community can contribute to this resource | OMICS_01786 | SCR_006959 | Minimum Information about a Genotyping Experiment | 2026-09-12 01:00:12 | 20 | |||||||
|
SAM format Resource Report Resource Website 1000+ mentions |
SAM format (RRID:SCR_012093) | data or information resource, interchange format, narrative resource, standard specification | A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19505943 | OMICS_05115 | SCR_012093 | Sequence Alignment/Map format | 2026-09-12 01:00:15 | 1274 | |||||||||
|
HOLLOW Resource Report Resource Website 10+ mentions |
HOLLOW (RRID:SCR_005729) | HOLLOW | data processing software, data visualization software, software application, software resource | HOLLOW facilitates the production of surface images of proteins. HOLLOW is a portable command-line utility written in Python 2.4-2.7; it does not have any other dependencies (although running under the PyPy JIT interpreter, it runs much faster). The input is a PDB file. The output is a PDB file of dummy water atoms that forms a cast of the voids and channels of a protein. HOLLOW generates a surface from a cast of the protein surface. HOLLOW fills the interior spaces of a protein structure with dummy atoms defined on an overlapping grid. The surface generated by these dummy atoms can be shown to reproduce the surface of the protein at the ideal limit. The use of the surface of the dummy atoms allows us to focus on a specific piece of the interior surface. Simply by deleting dummy atoms, the interior surface can be trimmed to produce a custom portion of the interior space. For advanced coloring of the surface, the B-factor of the dummy atoms can be calculated as the average of the B-factor of the protein atoms surrounding the dummy atoms. This allows various colorings of the surface to be conveyed through the B-factor field of the PDB files. The volume filling representation facilitated by HOLLOW is meant to complement other programs that identify voids, pockets and channels, such as SPHGEN and CASTp, which identify binding sites but cannot produce output that can be rendered in standard molecular graphics software. HOLLOW can be used to help render these binding pockets. | surface image, protein, protein image, protein structure, image, channel surface, electrostatic surface, interior pathway surface, ligand-binding surface, molecular structure, python |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
Center for Membrane Protein Structure ; Membrane Protein Expression Center ; Howard Hughes Medical Institute |
PMID:19014592 | nlx_149186 | SCR_005729 | HOLLOW - Volume Filling of Protein Structures, HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures | 2026-09-12 01:00:35 | 37 | ||||||
|
FMAToolbox Resource Report Resource Website 50+ mentions |
FMAToolbox (RRID:SCR_015533) | data analysis software, data processing software, software application, software resource | Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals. | electrophysiology software, behavioral software, freely moving animal, matlab |
uses: MATLAB is listed by: SourceForge |
Available for download, Acknowledgement requested | http://www.buzsakilab.com/content/PDFs/HasanJNeuroscMeth2006.pdf | SCR_015533 | FMA Toolbox, Freely Moving Animal Toolbox | 2026-09-12 12:58:27 | 65 | ||||||||
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Bioelectromagnetism Matlab Toolbox Resource Report Resource Website 1+ mentions |
Bioelectromagnetism Matlab Toolbox (RRID:SCR_006090) | data processing software, software application, software resource, software toolkit | Software toolbox to facilitate quick and easy import, visualization and measurement for Event Related Potential (ERP) data. The toolbox can open and visualise ERP averaged data (Neuroscan, ascii formats), 2D/3D electrode coordinates and 3D cerebral tissue tesselations (meshes). All the features can be explored quickly and easily using the example data provided in the toolbox. The GUI interface is simple and intuitive. | eeg, meg, mri, electrocorticography, event related potential, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ERPLAB has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
GNU General Public License | nif-0000-00268 | http://www.nitrc.org/projects/eeg | SCR_006090 | EEG Toolbox | 2026-09-12 01:00:56 | 1 | |||||||
|
MarsBaR region of interest toolbox for SPM Resource Report Resource Website 1000+ mentions |
MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) | MarsBaR | data processing software, software application, software resource, software toolkit | A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery. | analyze, linear, matlab, magnetic resonance, nifti, os independent, regression, statistical operation, region of interest, spm, analysis |
is used by: BetA-Series COrrelation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: SourceForge |
GNU General Public License | nlx_155806 | http://www.nitrc.org/projects/marsbar | SCR_009605 | MARSeille Boite A Region dInteret, MARSeille Boite a Region dInteret | 2026-09-12 01:00:59 | 1320 | ||||||
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OBO Tracker: Plant Ontology (PO) TERM requests Resource Report Resource Website 1+ mentions |
OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) | OBO SF PO | data or information resource, database | Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users. | plant, ontology, term |
is related to: OBO has parent organization: SourceForge |
The community can contribute to this resource, Account required | nlx_99576 | SCR_006497 | Tracker: PO TERM requests, Tracker: Plant Ontology TERM requests, SourceForge.net: Open Biomedical Ontologies: Plant Ontology (PO) TERM requests, Source Forge OBO Plant Ontology (PO) term request tracker, Tracker: Plant Ontology (PO) TERM requests | 2026-09-12 01:01:42 | 2 | |||||||
|
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-09-12 01:03:12 | 35 | ||||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | software resource, software toolkit, source code | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/, https://github.com/broadinstitute/picard, https://sources.debian.org/src/picard-tools/ | SCR_006525 | 2026-09-12 01:03:16 | 15653 | ||||||||
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neurospy Resource Report Resource Website |
neurospy (RRID:SCR_007016) | neurospy | software resource, source code | 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. | imaging, neuron, microscopy, functional imaging, java, neuronal activity |
has parent organization: SourceForge has parent organization: Howard Hughes Medical Institute has parent organization: Salk Institute for Biological Studies has parent organization: University of California at San Diego; California; USA |
Howard Hughes Medical Institute ; NIH |
PMID:17684546 | Open unspecified license | nlx_149367 | SCR_007016 | 2026-09-12 01:03:16 | 0 | ||||||
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CUDASW++ Resource Report Resource Website 1+ mentions |
CUDASW++ (RRID:SCR_008862) | CUDASW++ | software resource, source code | 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 | smith-waterman, bioinformatics, protein, protein database, sequence, simt, simd, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Nanyang Technological University; Singapore; Singapore |
PMID:19416548 PMID:20370891 |
Open-source | nlx_149212, biotools:cudasw | https://bio.tools/cudasw | SCR_008862 | CUDASW++ (Smith Waterman) | 2026-09-12 01:03:18 | 5 | |||||
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cnvHiTSeq Resource Report Resource Website 1+ mentions |
cnvHiTSeq (RRID:SCR_013160) | cnvHiTSeq | commercial organization, software resource | A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259578 | Commercial license | OMICS_00342 | SCR_013160 | cnvHiTSeq - A set of tools for detecting CNVs using sequencing data | 2026-09-12 01:03:46 | 4 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
