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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | data or information resource, narrative resource, software repository, software resource, software toolkit, source code, wiki | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl, https://sources.debian.org/src/bioperl/ | SCR_002989 | 2026-09-12 12:55:49 | 408 | |||||
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arrayQualityMetrics Resource Report Resource Website 100+ mentions |
arrayQualityMetrics (RRID:SCR_001335) | arrayQualityMetrics | software resource | Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported. | microarray, quality control, report writing |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
PMID:19106121 | Free, Available for download, Freely available | OMICS_02005 | SCR_001335 | Quality metrics on microarray data sets | 2026-09-12 12:55:24 | 183 | ||||||
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PeptideProphet Resource Report Resource Website 1+ mentions |
PeptideProphet (RRID:SCR_000274) | software resource | Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:12403597 | Free, Available for download, Freely available | OMICS_02520, biotools:peptideprophet | https://bio.tools/peptideprophet | SCR_000274 | 2026-09-12 12:55:06 | 4 | |||||||
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PyMOL Resource Report Resource Website 1000+ mentions |
PyMOL (RRID:SCR_000305) | 3d visualization software, data processing software, data visualization software, software application, software resource | A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures. | visualization, molecule, 3d, molecular structure visualization, molecular visualization system, |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Restricted | nlx_156834, OMICS_03802 | https://sources.debian.org/src/pymol/ | SCR_000305 | 2026-09-12 12:55:06 | 3493 | ||||||||
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MuTect Resource Report Resource Website 100+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | Mutect | 2026-09-12 12:55:11 | 102 | ||||
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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 | 2026-09-12 12:58:11 | 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 | 2026-09-12 12:58:14 | 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 | Adobe Photoshop CC, Adobe Photoshop CS, Photoshop | 2026-09-12 12:58:13 | 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 | OriginPro | 2026-09-12 12:58:13 | 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 | 2026-09-12 12:58:14 | 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 | Python-based Hierarchical ENvironment for Integrated Xtallography | 2026-09-12 12:58:14 | 11312 | |||||||
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SlideBook Resource Report Resource Website 500+ mentions |
SlideBook (RRID:SCR_014300) | data analysis software, data processing software, image processing software, software application, software resource | Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton. | digital microscopy software, research microscopy, image processing software, data analysis software | is listed by: SoftCite | Available for download, Free, Compatible with Windows 7 and Windows XP | SCR_014300 | SlideBook 6 | 2026-09-12 12:58:15 | 982 | |||||||||
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Proteome Discoverer Resource Report Resource Website 1000+ mentions |
Proteome Discoverer (RRID:SCR_014477) | data analysis software, data processing software, software application, software resource, workflow software | Software for identifying, characterizing, and quantifying proteins in biological samples. Can be used for range of proteomics workflows such as protein and peptide identification, PTM analysis, and isobaric mass tagging for quantification. Supports multiple database search algorithms and multiple dissociation techniques., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis, workflow software, proteomics, database search, FASEB list |
is used by: thermo-msf-parser is listed by: SoftCite works with: Peakjuggler works with: pepwheel |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014477 | 2026-09-12 12:58:17 | 1521 | ||||||||||
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MaxQuant Resource Report Resource Website 10000+ mentions |
MaxQuant (RRID:SCR_014485) | data analysis software, data processing software, software application, software resource | A quantitative proteomics software package for analyzing large-scale mass-spectrometric data sets. It is a set of algorithms that include peak detection and scoring of peptides, mass calibration, database searches for protein identification, protein quantification, and provides summary statistics. | mass spectrometry analysis software, proteomics software, mass calibration, protein identification, protein quantification, FASEB list | is listed by: SoftCite | PMID:19029910 PMID:25059623 |
SCR_014485 | 2026-09-12 12:58:17 | 13452 | ||||||||||
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Multi Gauge Resource Report Resource Website 10+ mentions |
Multi Gauge (RRID:SCR_014299) | data analysis software, data processing software, software application, software resource | A software application for one-dimensional electrophoretic analysis of multi-labeled fluorophores. It was designed to analyze multi-channel fluorescence data from Fujifilm FLA-5000 and FLA-8000 scanning systems. The software also works with other scanners in the BAS/FLA series and with the LAS series. | data analysis software, one dimensional electrophoretic analysis, fluorophore, multi channel fluorescence data | is listed by: SoftCite | http://www.scienceimaging.se/application-info/55.html | SCR_014299 | MultiGuage | 2026-09-12 12:58:15 | 37 | |||||||||
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Clocklab Resource Report Resource Website 500+ mentions |
Clocklab (RRID:SCR_014309) | data acquisition software, data analysis software, data processing software, software application, software resource, standalone software | Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program. | circadian activity data, interactive, data analysis software, data acquisition software, standalone software | is listed by: SoftCite | Pay for product, Users can order different components of ClockLab separately | SCR_014309 | 2026-09-12 12:58:15 | 573 | ||||||||||
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LabView Resource Report Resource Website 100+ mentions |
LabView (RRID:SCR_014325) | software application, software development environment, software development tool, software resource | A development environment for engineers and scientists to visualize, create, and code engineering systems. The system design software is integrated with all measurement hardware and contains signal processing IP. Other features include multithreaded execution, software deployment to hardware, and program integration into a single environment. | development environment, system design software, software development tool |
is used by: Demon Voltammetry and Analysis Software is listed by: SoftCite is related to: ZebEyeTrack is related to: ActiView |
Pay for product, Free trail is available | SCR_014325 | LabVIEW System Design Software, NI LabVIEW software, LabView System Design Software, LabVIEW | 2026-09-12 12:58:15 | 261 | |||||||||
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Mascot Resource Report Resource Website 5000+ mentions |
Mascot (RRID:SCR_014322) | data processing software, signal processing software, software application, software resource, standalone software | A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters. | server, software package, mass spectrometry, protein, identify, characterize, bio.tools |
is used by: MSQuant is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MascotScan |
Free, Can be licensed for in-house use, Available for download | biotools:MASCOT | http://www.matrixscience.com/search_intro.html, https://bio.tools/MASCOT | SCR_014322 | Mascot Server | 2026-09-12 12:58:15 | 7141 | |||||||
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ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | data analysis software, data processing software, software application, software resource, web application | Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, model, best fit model, protein evolution, amino acid replacement, server, bio.tools |
uses: PhyML is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is hosted by: GitHub |
PMID:15647292 DOI:10.1093/bioinformatics/btr088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11547, biotools:prottest | https://github.com/ddarriba/prottest3, https://bio.tools/prottest, https://sources.debian.org/src/prottest/ | SCR_014628 | 2026-09-12 12:58:19 | 1984 | |||||||
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IUPRED Resource Report Resource Website 100+ mentions |
IUPRED (RRID:SCR_014632) | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | A web server which recognizes tertiary structures from an amino acid sequence based on estimated pairwise energy content. Users can input SWISS-PROT/TrEMBL identifier or accession number, or paste the amino acid sequence. | web application, sequence analysis, web server, territory structure, amino acid sequence, swiss prot, trembl | is listed by: SoftCite | PMID:15955779 | Available to academic users, Available for download, Commercial users must enquire | SCR_014632 | Prediction of Intrinsically Unstructured Proteins, Prediction of Intrinsically Unstructured Proteins (IUPRED) | 2026-09-12 12:58:20 | 306 |
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