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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Cake Resource Report Resource Website 10+ mentions |
Cake (RRID:SCR_002133) | software resource | A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. | standalone software, unix/linux, mac os x, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23803469 | Free, Available for download, Freely available | OMICS_03613, biotools:cake | https://bio.tools/cake | SCR_002133 | SciCrunch Registry | 2026-11-07 11:54:37 | 11 | |||||||
|
Matchprot Resource Report Resource Website |
Matchprot (RRID:SCR_002163) | software resource | A pairwise protein structure alignment software. | standalone software, c |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17338826 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03666 | SCR_002163 | SciCrunch Registry | 2026-11-07 11:54:42 | 0 | ||||||||
|
RUbioSeq Resource Report Resource Website 10+ mentions |
RUbioSeq (RRID:SCR_002508) | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | 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 | SciCrunch Registry | RUbioSeq+ | 2026-11-07 11:54:57 | 12 | |||||
|
Batch Oligo Selection Script Resource Report Resource Website |
Batch Oligo Selection Script (RRID:SCR_002808) | BOSS | software resource | Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps. | primer, pcr, oligo, contig, scaffold, command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Freely available, Available for download | OMICS_02334 | SCR_002808 | SciCrunch Registry | 2026-11-07 11:54:46 | 0 | ||||||||
|
MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | data or information resource, interchange format, narrative resource, software resource, standard specification | 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 | SciCrunch Registry | Minimal Information for PCR Experiments | 2026-11-07 11:55:02 | 32 | |||||||
|
mrsFAST Resource Report Resource Website 10+ mentions |
mrsFAST (RRID:SCR_003128) | mrsFAST | software resource | A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter) | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:20676076 | Free, Available for download, Freely available | biotools:mrsfast, nlx_156780 | https://bio.tools/mrsfast | SCR_003128 | SciCrunch Registry | mrsFAST: micro-read substitution-only Fast Alignment Search Tool, micro-read substitution-only Fast Alignment Search Tool | 2026-11-07 11:55:09 | 22 | |||||
|
SobekCM Resource Report Resource Website |
SobekCM (RRID:SCR_003225) | SobekCM | software resource | Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories. | archiving, resource management, metadata standard, ontology, data repository, research object, c#, windows |
is listed by: FORCE11 has parent organization: University of Florida; Florida; USA has parent organization: Google Code has parent organization: SourceForge |
NEH ; NSF ; NHPRC ; IMLS |
Free, Available for download, Freely available | nlx_157266 | SCR_003225 | SciCrunch Registry | SobekCM Digital Repository Software, SobekCM : Digital Content Management System, SobekCM Digital Repository | 2026-11-07 11:55:04 | 0 | ||||||
|
Metabolomics Standards Initiative Resource Report Resource Website 10+ mentions |
Metabolomics Standards Initiative (RRID:SCR_003246) | MSI | controlled vocabulary, data or information resource, knowledge environment, narrative resource, ontology, standard specification | 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. | metabolomics, biological context, metadata, chemical analysis, data processing, exchange format |
is related to: NMR-Instrument Component of Metabolomics Investigations Ontology has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_157308 | https://github.com/MSI-Metabolomics-Standards-Initiative/CIMR | SCR_003246 | SciCrunch Registry | 2026-11-07 11:55:04 | 15 | |||||||
|
SpliCQ Resource Report Resource Website |
SpliCQ (RRID:SCR_003266) | SpliCQ | software resource | A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01341 | SCR_003266 | SciCrunch Registry | 2026-11-07 11:55:04 | 0 | ||||||||
|
ORFprimer Resource Report Resource Website 1+ mentions |
ORFprimer (RRID:SCR_003269) | ORFprimer | software resource | An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. | java, java swing, open reading frame, protein, high throughput sequencing, primer, primer design, pcr, pcr primer design |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02331 | SCR_003269 | SciCrunch Registry | ORFprimer - primer design for ORFs | 2026-11-07 11:54:59 | 1 | |||||||
|
Gemi Resource Report Resource Website 10+ mentions |
Gemi (RRID:SCR_003211) | Gemi | software resource | Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences. | polymerase chain reaction, primer, pcr primer design, pcr primer, dna sequence, rna sequence, c#, .net/mono, windows, probe, multiple aligned sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23316117 | Free, Available for download, Freely available | OMICS_02332 | SCR_003211 | SciCrunch Registry | Gemi - PCR oligos / primers design from multiple sequence alignments | 2026-11-07 11:55:11 | 13 | ||||||
|
Vertebrate Trait Ontology Resource Report Resource Website |
Vertebrate Trait Ontology (RRID:SCR_003214) | VT | controlled vocabulary, data or information resource, ontology | A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. | trait, morphology, physiology, development, obo |
is listed by: BioPortal is related to: monarch-ontologies is related to: Rat Genome Database (RGD) is related to: Animal QTLdb is related to: Mouse Phenome Database (MPD) has parent organization: SourceForge |
PMID:23937709 | Free, Available for download, Freely available | nlx_156940 | SCR_003214 | SciCrunch Registry | VT Ontology | 2026-11-07 11:54:52 | 0 | ||||||
|
GEOSS Resource Report Resource Website 1+ mentions |
GEOSS (RRID:SCR_003401) | GEOSS | software resource | A complete software system used to store and analyze gene expression data. |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Virginia; Virginia; USA |
Free, Freely available | OMICS_00764 | SCR_003401 | SciCrunch Registry | Gene Expression Open Source System, GEOSS - Gene Expression Open Source System, GEOSS Gene Expression Open Source System, GeneX Va | 2026-11-07 11:55:03 | 1 | ||||||||
|
NEMO Ontology Resource Report Resource Website |
NEMO Ontology (RRID:SCR_003386) | NEMO Ontology | controlled vocabulary, data or information resource, ontology | 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). | eeg, meg, owl, event-related potential, cognitive, behavioral, data sharing, erp |
is listed by: BioPortal is related to: NEMO Analysis Toolkit has parent organization: Neural ElectroMagnetic Ontologies (NEMO) Project has parent organization: SourceForge |
NIH | Free, Available for download, Freely available | nif-0000-32927 | http://purl.bioontology.org/ontology/NEMO, http://sourceforge.net/projects/nemoontologies/ | http://nemo.nic.uoregon.edu/wiki/NEMO#NEMO_Ontology | SCR_003386 | SciCrunch Registry | Neural ElectroMagnetic Ontology | 2026-11-07 11:55:06 | 0 | ||||
|
Amplicon Resource Report Resource Website 1000+ mentions |
Amplicon (RRID:SCR_003294) | Amplicon | software resource | Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac | python, pcr primer, pcr, primer, tkinter, windows, dna sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:14962918 | Free, Available for download, Freely available | OMICS_02329 | http://www.aad.gov.au/amplicon | SCR_003294 | SciCrunch Registry | 2026-11-07 11:54:54 | 1955 | ||||||
|
Fly Taxonomy Resource Report Resource Website |
Fly Taxonomy (RRID:SCR_003317) | FB-SP, FBsp | controlled vocabulary, data or information resource | The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. | obo, taxonomy, organismal |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge has parent organization: FlyBase |
Free, Available for download, Freely available | nlx_157407 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo | SCR_003317 | SciCrunch Registry | FlyBase Taxa | 2026-11-07 11:54:54 | 0 | ||||||
|
Software Ontology Resource Report Resource Website 1+ mentions |
Software Ontology (RRID:SCR_003493) | SWO | controlled vocabulary, data or information resource, ontology | 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). | owl, software, provenance, version, ontology |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge is related to: Information Artifact Ontology has parent organization: European Bioinformatics Institute has parent organization: University of Manchester; Manchester; United Kingdom |
JISC | The community can contribute to this resource | nlx_157591 | http://www.ebi.ac.uk/efo/swo, http://purl.bioontology.org/ontology/SWO, http://theswo.svn.sourceforge.net/viewvc/theswo/trunk/src/release/swoinowl/swo_merged/swo_merged.owl | SCR_003493 | SciCrunch Registry | 2026-11-07 11:54:58 | 2 | ||||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | SciCrunch Registry | Genome Expression Pathway Analysis Tool | 2026-11-07 11:54:59 | 2 | ||||||
|
Jmol Resource Report Resource Website 100+ mentions |
Jmol (RRID:SCR_003796) | Jmol | d visualization software, software application, software resource, standalone software | 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. | chemical, crystal, material, biomolecule, java |
is used by: Glyco3D is listed by: SoftCite has parent organization: SourceForge |
PMID:28472503 PMID:28316648 |
GNU Lesser General Public License, Acknowledgement requested | nlx_158093 | SCR_003796 | SciCrunch Registry | Jmol: an open-source Java viewer for chemical structures in 3D | 2026-11-07 11:55:02 | 245 | ||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | SciCrunch Registry | 2026-11-07 11:55:45 | 0 |
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