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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 toolkit, software resource | 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 | 2026-08-02 09:02:53 | 5 | |||||||
|
HTQC Resource Report Resource Website 10+ mentions |
HTQC (RRID:SCR_006448) | HTQC | software toolkit, software resource | A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. | c++, illumina, command-line |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23363224 DOI:10.1186/1471-2105-14-33 |
GNU General Public License, v3 | OMICS_01052 | https://sources.debian.org/src/htqc/ | SCR_006448 | HTQC - Quality control and filtration for illumina sequencing data | 2026-08-02 09:04:55 | 42 | |||||
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Avalon Cheminformatics Toolkit Resource Report Resource Website |
Avalon Cheminformatics Toolkit (RRID:SCR_014273) | software toolkit, software resource | 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 | 2026-08-02 09:06:48 | 0 | ||||||||||
|
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 | 2026-08-04 09:43:09 | 4 | ||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-08-04 09:40:11 | 0 | ||||||
|
Xournal Resource Report Resource Website |
Xournal (RRID:SCR_003233) | Xournal | software application, software resource | Free software application for notetaking, sketching, keeping a journal using a stylus that runs on Linux (recent distributions) and other GTK+/Gnome platforms. It is similar to Microsoft Windows Journal or to other alternatives such as Jarnal, Gournal, and NoteLab. Note: is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations. | annotation, markup |
is listed by: FORCE11 has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_157272 | SCR_003233 | 2026-08-04 09:40:51 | 0 | ||||||||
|
TARQUIN Resource Report Resource Website 50+ mentions |
TARQUIN (RRID:SCR_002598) | TARQUIN | software application, software resource | An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses. | magnetic resonance, mrs, mas, molecule, nmr spectroscopy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:20878762 | Free, Available for download, Freely available | nlx_156002 | http://www.nitrc.org/projects/tarquin | SCR_002598 | TARQUIN MRS analysis package | 2026-08-04 09:40:41 | 58 | |||||
|
Monte Carlo eXtreme Resource Report Resource Website 1+ mentions |
Monte Carlo eXtreme (RRID:SCR_007001) | MCX | software application, simulation software, software resource | A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470. | c, console (text based), macos, microsoft, modeling, monte carlo, optical imaging, other programming language, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155817 | http://www.nitrc.org/projects/mcextreme | SCR_007001 | Monte Carlo eXtreme (MCX) | 2026-08-05 10:44:35 | 2 | ||||||
|
Multiscale Object Orientation Simulation Environment Resource Report Resource Website 100+ mentions |
Multiscale Object Orientation Simulation Environment (RRID:SCR_008031) | software application, simulation software, software resource | MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. it is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML. MOOSE is coordinating with the GENESIS-3 project towards the goals of developing educational resources for modeling. MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty. Sponsors: - National Center of Biological Sciences (NCBS) - National Institutes of Health (NIH) Collaboration - EU-India grid - Department of Atomic Energy Science Research Council (DAE/SRC) - Department of Biotechnology (DBT) | cell, computational, molecule, network, neuronal, neuroscience, simulation, subcellular, systems biology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MUlti SImulation Coordinator has parent organization: SourceForge |
nif-0000-10307 | http://www.nitrc.org/projects/moose | SCR_008031 | MOOSE | 2026-08-05 10:44:53 | 302 | ||||||||
|
MaryGold Resource Report Resource Website 1+ mentions |
MaryGold (RRID:SCR_000528) | MaryGold | software toolkit, software resource | Software package that enables detection of sequence variation between metagenomic samples. | sequence variation, metagenomic, c++, python |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available, | OMICS_01495 | SCR_000528 | MaryGold - Variation analysis of metagenomic samples | 2026-08-05 10:43:11 | 1 | |||||||
|
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 | database, data or information resource | 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 | 2026-08-06 09:26:36 | 2 | |||||||
|
RUbioSeq Resource Report Resource Website 10+ mentions |
RUbioSeq (RRID:SCR_002508) | sequence analysis software, software resource, standalone software, data analysis software, data processing software, software application | 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. | resequencing analysis, exome variant detection, pipeline, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
BLUEPRINT Consortium FP7/2007-2013 282510; Spanish Ministry of Economy and Competitiveness BIO2007-666855 |
PMID:23630175 | Free, Available for download | biotools:rubioseq, OMICS_00072 | https://sourceforge.net/projects/rubioseq/files/, https://bio.tools/rubioseq | SCR_002508 | RUbioSeq+ | 2026-08-06 09:25:40 | 12 | |||||
|
MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | software resource, interchange format, data or information resource, standard specification, narrative resource | 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. | standalone software, pcr, xml, data storage, data exchange |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02358 | http://mipe.sourceforge.net/, https://sources.debian.org/src/mipe/ | SCR_003065 | Minimal Information for PCR Experiments | 2026-08-06 09:25:47 | 31 | |||||||
|
GeneVenn Resource Report Resource Website 100+ mentions |
GeneVenn (RRID:SCR_012117) | data analysis service, production service resource, analysis service resource, service resource | A web application creating Venn diagrams from two or three gene lists. | web app |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:17597932 | OMICS_05568 | SCR_012117 | 2026-08-06 09:27:50 | 101 | |||||||||
|
Magnolya Resource Report Resource Website 1+ mentions |
Magnolya (RRID:SCR_000164) | software application, data analytics software, software resource | A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets. | algorithm, copy number, next-generation, reference genome, dataset comparison |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23047563 | Free, Available for download, Freely available | OMICS_00347 | SCR_000164 | 2026-08-06 09:25:07 | 2 | ||||||||
|
UTR Resource Report Resource Website |
UTR (RRID:SCR_000045) | standalone software, software application, software resource | Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq. | java, 3 prime utr, rna sequence, change point model, detecting 3-prime UTR changes, RNA-Seq |
uses: R Project for Statistical Computing has parent organization: SourceForge |
PMID:24728858 | Free, Available for download, Freely available | OMICS_04052 | SCR_000045 | 2026-08-06 09:25:06 | 0 | ||||||||
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metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | standalone software, software application, software resource | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Erik and Edith Fernström foundation ; Cancer Research UK |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | 2026-08-06 09:25:22 | 0 | ||||||
|
HOLLOW Resource Report Resource Website 10+ mentions |
HOLLOW (RRID:SCR_005729) | HOLLOW | data visualization software, software application, software resource, data processing software | 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 | 2026-08-06 09:26:28 | 37 | ||||||
|
Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, source code, software resource | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-08-06 09:25:17 | 0 | |||||||
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CHEBI Resource Report Resource Website 100+ mentions |
CHEBI (RRID:SCR_002088) | ChEBI | database, data or information resource | Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. | complex, conformer, ion, ion pair, isotope, molecular entity, molecule, radical, radical ion, small molecule, obo, gold standard, biochemistry, metabolomics, bio.tools |
uses: IUPAC uses: Nomenclature Committee of IUBMB is used by: Open PHACTS is used by: Ultimate Rough Aggregation of Metabolic Map is used by: RHEA is used by: GEROprotectors is used by: SwissLipids is listed by: OBO is listed by: BioPortal is listed by: NIF Data Federation is listed by: SourceForge is listed by: bio.tools is listed by: Debian is related to: Pathway Commons is related to: Integrated Manually Extracted Annotation has parent organization: European Bioinformatics Institute is parent organization of: Physico-Chemical Process is parent organization of: Physico-Chemical Methods and Properties works with: MiMeDB |
BBSRC BB/G022747/1 | PMID:19854951 PMID:19496059 PMID:17932057 |
Freely available | nif-0000-02655, biotools:chebi, r3d100012626 | http://bioportal.bioontology.org/ontologies/1007, http://www.obofoundry.org/cgi-bin/detail.cgi?id=chebi, ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo, http://chebi.wiki.sourceforge.net/, https://bio.tools/chebi | http://www.ebi.ac.uk/chebi/ | SCR_002088 | CHEBI, Chemical Entities of Biological Interest | 2026-08-06 09:25:35 | 126 |
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