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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SeqTRACS Resource Report Resource Website |
SeqTRACS (RRID:SCR_013294) | SeqTRACS | software resource | Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01013 | SCR_013294 | SeqTRACS: LIMS for sequencing core facilities | 2026-09-05 06:27:34 | 0 | |||||||
|
SOCS Resource Report Resource Website 50+ mentions |
SOCS (RRID:SCR_013223) | SOCS | software resource | Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00590 | SCR_013223 | 2026-09-05 06:27:33 | 91 | ||||||||||
|
DSP Resource Report Resource Website |
DSP (RRID:SCR_013114) | DSP | software resource | Pipeline for small genome assembly using SOLiD sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
Apache License, v2 | OMICS_00013 | SCR_013114 | denovo_solid_pipeline | 2026-09-05 06:27:32 | 0 | ||||||||
|
Tuxedo Resource Report Resource Website 100+ mentions |
Tuxedo (RRID:SCR_013194) | Tuxedo | software resource | Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01415 | SCR_013194 | Tuxedo: Automated RNA-sequencing Pipeline Script | 2026-09-05 06:27:33 | 103 | |||||||||
|
Crossbow Resource Report Resource Website 1+ mentions |
Crossbow (RRID:SCR_013306) | Crossbow | software resource | A scalable software pipeline for whole genome resequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19930550 DOI:10.1186/gb-2009-10-11-r134 |
biotools:crossbow, OMICS_00284 | https://bio.tools/crossbow | https://sources.debian.org/src/crossbow/ | SCR_013306 | 2026-09-05 06:27:34 | 5 | ||||||
|
MaryGold Resource Report Resource Website 1+ mentions |
MaryGold (RRID:SCR_000528) | MaryGold | software resource, software toolkit | 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 | 2026-09-05 06:30:35 | 1 | |||||||
|
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 | 2026-09-05 06:30:41 | 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 | 2026-09-05 06:30:46 | 1320 | ||||||
|
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 | 2026-09-05 06:30:00 | 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 | 2026-09-05 06:30:03 | 1274 | |||||||||
|
GeneVenn Resource Report Resource Website 100+ mentions |
GeneVenn (RRID:SCR_012117) | analysis service resource, data analysis service, production 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 | 2026-09-05 06:32:02 | 107 | |||||||||
|
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 | 2026-09-05 06:32:22 | 0 | ||||||
|
Magnolya Resource Report Resource Website 1+ mentions |
Magnolya (RRID:SCR_000164) | data analytics software, software application, 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 | 2026-09-05 06:32:20 | 2 | ||||||||
|
UTR Resource Report Resource Website |
UTR (RRID:SCR_000045) | software application, software resource, standalone software | 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 | 2026-09-05 06:32:20 | 0 | ||||||||
|
Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, software resource, source code | 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 | 2026-09-05 06:31:12 | 0 | |||||||
|
CHEBI Resource Report Resource Website 100+ mentions |
CHEBI (RRID:SCR_002088) | ChEBI | data or information resource, database | 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 | 2026-09-05 06:31:16 | 129 | |||
|
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 | 2026-09-05 06:31:35 | 2 | |||||||
|
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 | 2026-09-05 06:30:20 | 37 | ||||||
|
COHCAP Resource Report Resource Website 10+ mentions |
COHCAP (RRID:SCR_006499) | COHCAP | software resource | An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. | java, perl, s/r, java swing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23598999 | Acknowledgement requested, Attribution Assurance License | biotools:cohcap, OMICS_00595 | https://bio.tools/cohcap | SCR_006499 | City of Hope CpG Island Analysis Pipeline, COHCAP - City of Hope CpG Island Analysis Pipeline | 2026-09-05 06:25:55 | 19 | |||||
|
XDrawChem Resource Report Resource Website |
XDrawChem (RRID:SCR_010941) | software resource | A drawing software application designed for drawing and analyzing chemical structures and reactions. | standalone software, c++, fortran |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_04961 | SCR_010941 | 2026-09-05 06:26:50 | 0 |
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