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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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BioMoby Resource Report Resource Website 1+ mentions |
BioMoby (RRID:SCR_013386) | controlled vocabulary, data or information resource, ontology | The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. Sponsors: Funding was provided by Genome Prairie and Genome Alberta A Bioinformatics Platform for Genome Canada''; Canadian Institutes for Health Research; The Natural Sciences and Engineering Research Council of Canada; The Heart and Stroke Foundation for BC and Yukon; The EPSRC through the myGrid (GR/R67743/01, EP/C536444/1, EP/D044324/1, GR/T17457/01) e-Science projects; The Spanish National Institute for Bioinformatics (INB) through Fundacin Genoma Espaa; The Generation Challenge Programme (GCP; http://www.generationcp.org) of the Consultative Group for International Agricultural Research. :Keywords: Ontology, Messaging, Standard, Client, Automatically, Discovery, Biological, Data, ANalytical, Service, Model, Organism, Database, Java, Platform, Semantic, Bioinformatics, |
is listed by: SoftCite is related to: BioExtract has parent organization: Pompeu Fabra University; Barcelona; Spain |
nif-0000-30186 | SCR_013386 | SciCrunch Registry | BioMoby | 2026-10-24 12:47:04 | 8 | ||||||||||
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MediaWiki Resource Report Resource Website 10+ mentions |
MediaWiki (RRID:SCR_014045) | authoring tool, software application, software resource | A server-based software wiki package written in PHP. It is a powerful, scalable software deigned for high-traffic websites. MediaWiki uses PHP to process and display data stored in a database such as MySQL. When a user submits an edit to a page, MediaWiki writes it to the database without deleting the previous versions, allowing easy reversions. MediaWiki is able to manage image and multimedia files, as well, which are stored in the filesystem. | authoring tool, software, wiki, PHP, FASEB list |
is listed by: SoftCite is related to: WorkingWiki is parent organization of: Semantic MediaWiki |
Public, Free | SCR_014045 | SciCrunch Registry | 2026-10-24 12:47:12 | 49 | ||||||||||
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HomeCageScan Resource Report Resource Website 10+ mentions |
HomeCageScan (RRID:SCR_014253) | data acquisition software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software used for automatic high throughput analysis of unconstrained rodent behaviors in a home cage. HomeCageScan is ideal for longitudinal studies where several animals are studied and tested over long periods. Its features include twenty-four-hour recording capabilities, statistical analysis, automatic adaptation to environmental changes (including day and night changes), and a batch‐mode which allows user to run multiple videos successively without human intervention. The software can detect various behaviors ranging from feeding and urination to jumping and foraging. | automatic high throughput analysis, unconstrained rodent behavior, home cage, longitudinal study | is listed by: SoftCite | Available for purchase | SCR_014253 | SciCrunch Registry | 2026-10-24 12:47:14 | 30 | ||||||||||
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Adobe Photoshop Resource Report Resource Website 10000+ mentions |
Adobe Photoshop (RRID:SCR_014199) | data processing software, image analysis software, image processing software, software application, software resource | Software for image processing, analysis, and editing. The software includes features such as touch capabilities, a customizable toolbar, 2D and 3D image merging, and Cloud access and options. | image processing software, image analysis software, image editing, editing software, adobe |
is listed by: SoftCite is related to: Adobe Photoshop Lightroom |
SCR_014234, SCR_014298, SciRes_000161, SCR_002078 | http://www.adobe.com/products/cs6.html | SCR_014199 | SciCrunch Registry | Adobe Photoshop CC, Adobe Photoshop CS, Photoshop | 2026-10-24 12:47:14 | 26261 | ||||||||
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Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | data analysis software, data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing. | data, analysis, software, authoring, tool, scripting, graphing, statistical, publication |
is listed by: SoftCite is related to: OriginPro |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015636 | https://www.originlab.com/index.aspx?go=PRODUCTS&PID=1834 | SCR_014212 | SciCrunch Registry | OriginPro | 2026-10-24 12:47:14 | 13985 | |||||||
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Refmac Resource Report Resource Website 1000+ mentions |
Refmac (RRID:SCR_014225) | data analysis software, data processing software, sequence analysis software, software application, software resource | A molecular refinement program with two main modes: REVIEW, which checks and updates the input model to establish that the geometric restraints can be properly set up, and REFINE mode, which is the standard mode and documented in keywords. In REVIEW users can: check model coordinates and write an extended output set of coordinates, find disulphide bonds and other covalent links, cis-peptides, output the sequence and REMARK records. In REFINEMENT mode users can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. Also in REFINEMENT mode, Refmac produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps. The program is supported by CCP4. | molecular refinement, data analysis software, sequence analysis software |
is used by: PDB-REDO is listed by: SoftCite |
SCR_014225 | SciCrunch Registry | 2026-10-24 12:47:14 | 2011 | |||||||||||
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Phenix Resource Report Resource Website 10000+ mentions |
Phenix (RRID:SCR_014224) | data processing software, image analysis software, image reconstruction software, software application, software resource | A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab. | automation, molecular structure, xray crystallography, neutron crystallography, image reconstruction software |
is listed by: SoftCite is affiliated with: Phaser is related to: MolProbity has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at Berkeley; Berkeley; USA provides: Phenix.refine |
NIGMS | Available for download, Free for nonprofit work, Acknowledgement requested, For profit groups may access PHENIX through a Consortium agreement | https://www.phenix-online.org/documentation/ | SCR_014224 | SciCrunch Registry | Python-based Hierarchical ENvironment for Integrated Xtallography | 2026-10-24 12:47:16 | 11312 | |||||||
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MCODE Resource Report Resource Website 1000+ mentions |
MCODE (RRID:SCR_015828) | algorithm resource, data analysis software, data processing software, image analysis software, software application, software resource | Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks. | cluster, clustering, graph analysis, network, network topology, interconnectivity | is listed by: SoftCite | Canadian Institutes of Health Research (CIHR) ; MDS-Sciex ; Ontario Research and Development Challenge Fund |
PMID:12525261 PMID:25570063 |
Free, Available for download | http://baderlab.org/Software/MCODE | SCR_015828 | SciCrunch Registry | 2026-10-24 12:47:29 | 1254 | |||||||
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Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | SciCrunch Registry | 2026-10-24 12:47:29 | 83 | ||||||
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Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data analysis software, data processing software, simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | SciCrunch Registry | Autogrid toolkit, Autogrid: automated grid | 2026-10-24 12:47:30 | 1261 | ||||||
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Epik Resource Report Resource Website 1+ mentions |
Epik (RRID:SCR_016745) | simulation software, software application, software resource | Software program for pKa prediction and protonation state generation for drug like molecules. | predict, pKa, value, chemical, structure, drug, profile, protonation, state, molecule, Schrodinger |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger |
PMID:17899391 | Commercially available | SCR_016745 | SciCrunch Registry | 2026-10-24 12:47:40 | 6 | |||||||||
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Ligprep Resource Report Resource Website 50+ mentions |
Ligprep (RRID:SCR_016746) | Ligprep | simulation software, software application, software resource | Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures. | correct, optimize, ligand, protonation, stereochemistry, tautomer, conformation, energy, minimized, 3D, moleular, structure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Glide works with: Phase |
Commercially available | SCR_016746 | SciCrunch Registry | LigPrep, LigandPreparation, Ligand preparation | 2026-10-24 12:47:41 | 50 | ||||||||
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NetworkX Resource Report Resource Website 100+ mentions |
NetworkX (RRID:SCR_016864) | data analysis software, data processing software, network analysis software, software application, software resource | Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | create, analysis, structure, dynamic, function, complex, network, data | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/networkx/networkx | SCR_016864 | SciCrunch Registry | 2026-10-24 12:47:41 | 132 | |||||||||
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BRASS Resource Report Resource Website 10+ mentions |
BRASS (RRID:SCR_017091) | data analysis software, data processing software, software application, software resource | Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements. | analysis, BAM, file, paired, end, sequencing, determine, rearrangement, breakpoint, assemble |
is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | SCR_017091 | SciCrunch Registry | 2026-10-24 12:47:44 | 47 | ||||||||||
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Google Resource Report Resource Website 100+ mentions |
Google (RRID:SCR_017097) | commercial organization | American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook. | technology, company, internet, service, product, search, engine, cloud, computing, software, hardware, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is parent organization of: golang |
grid.420451.6, Crossref funder ID: 100006785, ISNI, Wikidata: Q95, biotools:Google | https://ror.org/00njsd438, https://bio.tools/Google | SCR_017097 | SciCrunch Registry | Google LLC | 2026-10-24 12:47:44 | 437 | ||||||||
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Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | SciCrunch Registry | 2026-10-24 12:48:05 | 56 | ||||||||
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Leica QWin Resource Report Resource Website 1+ mentions |
Leica QWin (RRID:SCR_018940) | data processing software, image analysis software, image processing software, software application, software resource | Software tool as image analysis and processing solution for quantitative microscopy which provides control of Leica microscopes and Leica digital cameras. Capability ranges from simple interactive image measurements to automatic, multi-parameter measurements. Available in editions including QWin Runner, QWin Lite, QWin Plus, QWin Standard and QWin Professional. | Leica, microscope, digital camera, image analysis, image processing, quantitative microscopy | is listed by: SoftCite | Restricted | http://www.mcbainsystems.com/pdf/Leica_QWin.pdf | SCR_018940 | SciCrunch Registry | 2026-10-24 12:48:05 | 5 | |||||||||
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PAST Resource Report Resource Website 100+ mentions |
PAST (RRID:SCR_019129) | data analysis software, data processing software, software application, software resource | Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy. | Paleontological statistics, data analysis, data manipulation function, data plotting, multivariate statistics, ecological analysis, spatial analysis, morphometrics, stratography | is listed by: SoftCite | Free, Available for download, Freely available | SCR_019129 | SciCrunch Registry | PAST 4.03, PAleontological STatistics | 2026-10-24 12:48:07 | 153 | |||||||||
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MSQuant Resource Report Resource Website 1+ mentions |
MSQuant (RRID:SCR_019206) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine. | Qantitative proteomics, mass spectrometry, spectra processes, LC runs, protein, peptide |
uses: Mascot is listed by: SoftCite |
Free, Available for download | http://msquant.alwaysdata.net/ | SCR_019206 | SciCrunch Registry | 2026-10-24 12:48:08 | 4 | |||||||||
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biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, data processing software, software application, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | SciCrunch Registry | biomaRt v 2.42.1 | 2026-10-24 12:48:08 | 2879 |
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