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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-01 12:01:10 | 4 | |||||||
|
ART Resource Report Resource Website 1+ mentions |
ART (RRID:SCR_006538) | ART | software resource | A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina''''s Solexa, Roche''''s 454 and Applied Biosystems'''' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. | next-generation sequencing |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: National Institute of Environmental Health Sciences |
PMID:22199392 DOI:10.1093/bioinformatics/btr708 |
Free, Public | OMICS_00247 | https://sources.debian.org/src/augustus/ | SCR_006538 | ART - Set of Simulation Tools | 2026-08-01 12:03:14 | 9 | |||||
|
glmnet Resource Report Resource Website 100+ mentions |
glmnet (RRID:SCR_015505) | software toolkit, software resource | Procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. The algorithm uses cyclical coordinate descent in a path-wise fashion. | data regression, cyclical coordinate descent, linear model | is listed by: SoftCite | Free, Available for download | https://www.jstatsoft.org/article/view/v033i01 | SCR_015505 | Lasso and Elastic-Net Regularized Generalized Linear Models | 2026-08-02 09:06:56 | 464 | ||||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software toolkit, software resource | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-08-02 09:06:40 | 2839 | ||||||||
|
Metscape Resource Report Resource Website 100+ mentions |
Metscape (RRID:SCR_014687) | resource, software resource, source code | A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data. | metabolomics, metabolomics tool, visualization, expression profiling, gene, compound, metabolism, human |
is listed by: Metabolomics Workbench is listed by: SoftCite |
NIDDK U24 DK097153; NIDDK P30DK089503 |
PMID:22135418 | Freely available | SCR_014687 | 2026-08-03 09:35:35 | 145 | ||||||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | software toolkit, software resource, source code | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/, https://github.com/broadinstitute/picard, https://sources.debian.org/src/picard-tools/ | SCR_006525 | 2026-08-03 09:33:09 | 14139 | ||||||||
|
Clocklab Resource Report Resource Website 500+ mentions |
Clocklab (RRID:SCR_014309) | data processing software, data analysis software, standalone software, software resource, software application, data acquisition 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 | 2026-08-04 09:43:24 | 546 | ||||||||||
|
LabView Resource Report Resource Website 100+ mentions |
LabView (RRID:SCR_014325) | software development environment, software application, software resource, software development tool | 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 | 2026-08-04 09:43:24 | 244 | |||||||||
|
Mascot Resource Report Resource Website 5000+ mentions |
Mascot (RRID:SCR_014322) | data processing software, signal processing software, standalone software, software resource, software application | 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 | 2026-08-04 09:43:24 | 6896 | |||||||
|
ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | data processing software, data analysis software, software resource, software application, 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 | 2026-08-04 09:43:29 | 1981 | |||||||
|
IUPRED Resource Report Resource Website 100+ mentions |
IUPRED (RRID:SCR_014632) | data processing software, data analysis software, software resource, sequence analysis software, software application, 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) | 2026-08-04 09:43:30 | 295 | ||||||||
|
FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | web application, software resource | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-08-04 09:43:29 | 139 | |||||
|
FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | data processing software, data analysis software, data management software, software resource, software application | Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis. | quality control, sequence data, sequencing, analysis, data quality, pipeline, raw sequence data, modular set, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Open source, Available for download | biotools:fastqc, SCR_005539, OMICS_01043 | https://omictools.com/fastqc-tool, https://bio.tools/fastqc, https://sources.debian.org/src/fastqc/ | SCR_014583 | FastQC v0.11.5 | 2026-08-04 09:43:30 | 18745 | |||||||
|
Brain Extraction Tool Resource Report Resource Website 10+ mentions |
Brain Extraction Tool (RRID:SCR_014586) | BET2, BET | data processing software, software application, image processing software, software resource | Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces. | delete non-brain tissue from image, whole head, internal and external skull surfaces estimation, |
is listed by: SoftCite is a plug in for: FSL |
Free, Freely available | http://poc.vl-e.nl/distribution/manual/fsl-3.2/bet2/ | SCR_014586 | Brain Extraction Tool (BET), Brain Extraction Tool (BET2) | 2026-08-04 09:43:30 | 16 | |||||||
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | data processing software, alignment software, data analysis software, software resource, sequence analysis software, software application, image analysis software | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 | SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-08-04 09:43:30 | 1745 | |||||
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NVivo Resource Report Resource Website 10000+ mentions |
NVivo (RRID:SCR_014802) | data processing software, software application, software resource, data analysis software | Software suite for qualitative data analysis for text-based data and higher-order forms of data. Various packages are available and are dependent on the system used and the type of data analysis needed. | qualitative, data analysis, software, data solution | is listed by: SoftCite | SCR_014802 | 2026-08-04 09:43:31 | 11593 | |||||||||||
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PAUP Resource Report Resource Website 1000+ mentions |
PAUP (RRID:SCR_014931) | PAUP | data processing software, data analysis software, software resource, software application, data visualization software | Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis. | phylogenetic tree, phylogeny, evolutionary tree, molecular data, morphological data, behavioral data |
is listed by: SoftCite works with: PAML |
Free | http://people.sc.fsu.edu/~dswofford/paup_test/ | SCR_014931 | Phylogenetic Analysis Using Parsimony | 2026-08-04 09:43:33 | 2266 | |||||||
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Simulink Resource Report Resource Website 100+ mentions |
Simulink (RRID:SCR_014744) | simulation software, software application, software resource, software toolkit | Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems. | matlab, block diagram, multidomain simulation, simulation software, model based design, automatic code generation | is listed by: SoftCite | Commercially available, Free trial available | SCR_014744 | 2026-08-04 09:43:31 | 364 | ||||||||||
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Nexus Resource Report Resource Website 100+ mentions |
Nexus (RRID:SCR_015001) | data processing software, software application, software resource, data acquisition software | Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment. | biomechanics, motion capture |
is listed by: SoftCite works with: MATLAB works with: Bodybuilder |
Available for download | https://www.vicon.com/downloads/core-software/nexus | SCR_015001 | Nexus 2, Nexus 1.8.5, Nexus 2.5.0, Nexus 2.4.0 | 2026-08-04 09:43:33 | 373 | ||||||||
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WinWCP Resource Report Resource Website 100+ mentions |
WinWCP (RRID:SCR_014713) | data processing software, data analysis software, software resource, software application, data acquisition software | Windows software program for recording and analyzing signals from whole cell voltage and current clamp experiments. Its features include automatic waveform measurement, quantal content analysis, command voltage pulse generation, and spontaneous event detection. | data analysis software, whole cell, voltage, current, clamp experiments, neuron, neuroinformatics, single cell recording |
is listed by: SoftCite is affiliated with: Strathclyde Electrophysiology Suite |
Open source for academic and non-profit use, License available for purchase for commercial organizations | SCR_014713 | Windows Whole Cell Program | 2026-08-04 09:43:31 | 412 |
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