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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NovoAlign Resource Report Resource Website 500+ mentions |
NovoAlign (RRID:SCR_014818) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software tool designed for mapping short reads onto a reference genome generated from Illumina, Ion Torrent, and 454 NGS platforms. Its features include paired end alignment, methylation status analysis, automatic base quality calibration, and in built adapter trimming and base quality trimming. | sequence analysis software, short read, map, genome, illumina, ion torrent, 454 ngs | Commercially available, Trial available by request | SCR_014818 | 2026-08-13 09:29:05 | 809 | |||||||||||
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EVidenceModeler Resource Report Resource Website 1000+ mentions |
EVidenceModeler (RRID:SCR_014659) | EVM | data analysis software, data processing software, software application, software resource, sequence analysis software | Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format). | sequence analysis software, framework, ab intio gene, gene prediction, protein alignment, transcript alignment, consensus gene structure | NIAID N01 AI30071; NLM R01 LM006845 |
PMID:18190707 | Free, Available for download, Freely available | SCR_017649 | SCR_014659 | 2026-08-13 09:29:13 | 1283 | |||||||
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PASA Resource Report Resource Website 1000+ mentions |
PASA (RRID:SCR_014656) | data analysis software, data processing software, software application, software resource, sequence analysis software | Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute. | gene structure, annotation, gene structure analysis tool, spliced alignment, transcript sequence, bio.tools |
is used by: BRO_annotation is listed by: Debian is listed by: bio.tools |
DOI:10.1093/nar/gkg770 | Available for download | biotools:PASA | https://bio.tools/PASA | SCR_014656 | Program to Assemble Spliced Alignments (PASA), Program to Assemble Spliced Alignments | 2026-08-13 09:29:13 | 1123 | ||||||
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Integrated Islet Distribution Program (IIDP) Resource Report Resource Website 100+ mentions Rating or validation data |
Integrated Islet Distribution Program (IIDP) (RRID:SCR_014387) | IIDP | data or information resource, organization portal, resource, portal | The goal of the Integrated Islet Distribution Program (IIDP) is to work with the leading islet isolation centers in the U.S. to distribute high quality human islets to the diabetes research community, in order to advance scientific discoveries and translational medicine. | program, islet, distribution, diabetes |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources |
Diabetes | NIDDK | http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx | SCR_014387 | Integrated Islet Distribution Program | 2026-08-13 09:29:02 | 323 | ||||||
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Fuzzy Logic Toolbox Resource Report Resource Website 1+ mentions |
Fuzzy Logic Toolbox (RRID:SCR_014268) | data analysis software, data processing software, simulation software, software application, software toolkit, software resource | A software toolbox which provides MATLAB functions, apps, and a Simulink block for analyzing, designing, and simulating fuzzy logic systems. Fuzzy Logic Toolbox allows users to model complex system behaviors using simple logic rules, and then implement these rules in a user-designed fuzzy inference system. Functions are provided for many common methods, including fuzzy clustering and adaptive neurofuzzy learning. The toolbox can be used as a stand-alone fuzzy inference engine or in connection with Simulink. Different versions of the software are available for specific fuzzy inference systems. | software toolkit, fuzzy logic, experimental design, data analysis, simulation system, model | Pay for Product, Account Required | SCR_014268 | 2026-08-13 09:28:59 | 2 | |||||||||||
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Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | workflow software, data processing software, software resource, software application | A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. | workflow, MD, molecular dynamics, simulation, software, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: bioKepler has parent organization: University of California at San Diego; California; USA |
NIGMS P41GM103426 | Requires Linux | biotools:ambergpumdsimulation | http://nbcr.ucsd.edu/data/downloads/workflows/, https://bio.tools/ambergpumdsimulation | SCR_014389 | Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation | 2026-08-13 09:29:10 | 1 | ||||||
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Biotium inc Resource Report Resource Website 10+ mentions |
Biotium inc (RRID:SCR_013538) | antibody supplier, commercial organization, material resource, reagent supplier | An Antibody supplier | nlx_152313 | SCR_013538 | 2026-08-13 09:28:52 | 13 | ||||||||||||
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BioToolBox Resource Report Resource Website 10+ mentions |
BioToolBox (RRID:SCR_015696) | software toolkit, software resource, software library | Tools for querying and analysis of genomic data. These libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them. Opening and saving common tab-delimited text formats Support for BED, GFF, VCF, narrowPeak files Scoring intervals with datasets from microarray and sequencing ChIPSeq, RNASeq, microarray expression Support for Bam, BigWig, BigBed, wig, and USeq data formats Intersection with other known annotation Works with any genomic annotation in GTF, GFF3, and UCSC formats The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized BioPerl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with any data format. | SCR_015696 | 2026-08-13 09:29:16 | 17 | |||||||||||||
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Ascidian Network for InSitu Expression and Embryological Data Resource Report Resource Website 50+ mentions |
Ascidian Network for InSitu Expression and Embryological Data (RRID:SCR_013030) | ANISEED | data or information resource, database, service resource, data repository, storage service resource, software resource |
Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata. This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories. ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website. |
embryology, embryo, gene, genome, anatomy, cis-regulatory, development, morphogenesis, morphology, protein, molecular neuroanatomy resource, cis-regulatory sequence, gene expression, protein annotation, cell, expression profile, function, regulation, blast, visualization, data analysis service, clone, FASEB list | CNRS ; French Ministry of Research ; Marseille-Nice Genopole ; ARC ; European Network QLK3-CT-2001-01890 |
PMID:20647237 | nif-0000-10155 | http://crfb.univ-mrs.fr/aniseed/index.php | SCR_013030 | Aniseed database | 2026-08-13 09:28:49 | 63 | ||||||
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Centers for Diabetes Translation Research Resource Report Resource Website 1+ mentions |
Centers for Diabetes Translation Research (RRID:SCR_015149) | topical portal, data or information resource, organization portal, disease-related portal, resource, portal | Centers that are part of an integrated program whose cores support and enhance diabetes type II translation research. The CDTRs aim to enhance the efficiency, productivity, effectiveness and multidisciplinary nature of diabetes translation research. | diabetes type ii, diabetes research, translation |
is listed by: NIDDK Information Network (dkNET) is affiliated with: Vanderbilt Center for Diabetes Translation Research is affiliated with: New York Regional Center for Diabetes Translation Research is affiliated with: Chicago Center for Diabetes Translation Research is affiliated with: Georgia Center for Diabetes Translation Research is affiliated with: Michigan Center for Diabetes Translational Research is affiliated with: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has organization facet: Chicago Center for Diabetes Translation Research has organization facet: New York Regional Center for Diabetes Translation Research has organization facet: Georgia Center for Diabetes Translation Research has organization facet: Health Delivery Systems Center for Diabetes Translational Research has organization facet: Michigan Center for Diabetes Translational Research has organization facet: Vanderbilt Center for Diabetes Translation Research has organization facet: Washington University Center for Diabetes Translation Research |
Diabetes | NIDDK P30RFA-DK15-003 | Available to the research community | SCR_015149 | 2026-08-13 09:29:08 | 1 | ||||||||
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Analyst®TF Software Resource Report Resource Website 10+ mentions |
Analyst®TF Software (RRID:SCR_015785) | data acquisition software, data processing software, software resource, software application | Acquisition software for mass spectrometry data from TripleTOF instrument(s). Analyst provides functionality for instrument control, data analysis, reporting, and audit trail. | mass spectrometry, ms acquisition, lc-ms acquisition, tripletof instrument, instrument control, data analysis, audit trail | Commercially available, Available for academic use, Available for purchase | SCR_015785 | Analyst Software, Analyst, Analyst TF, Analyst TF Software | 2026-08-13 09:29:28 | 39 | ||||||||||
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GeneMapper Resource Report Resource Website 5000+ mentions |
GeneMapper (RRID:SCR_014290) | data analysis software, data processing software, software application, software resource, sequence analysis software | Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment. | genotyping software, sequence analysis software, multiplication functionality, dna sizing, allele call, electrophoresis genotyping system | is listed by: SoftCite | Restricted | https://www.thermofisher.com/order/catalog/product/de/en/4370784, https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FLSG%2Fmanuals%2F4476603A.pdf, | https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600798&tab=DetailInfo | SCR_014290 | , GeneMapper Software 5, GeneMapper Software 6, GeneMapper Software | 2026-08-13 09:29:02 | 5354 | |||||||
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Pixelink Image Capture Software Resource Report Resource Website 1+ mentions |
Pixelink Image Capture Software (RRID:SCR_016197) | data processing software, software application, image acquisition software, data acquisition software, software resource | Software application for real-time, interactive, multi-camera recording. It is compatible with all Pixelink PL-B and PL-D line of cameras. | microscopy, microscope, image, camera, video, industrial | Commercially available, Account required | http://pixelink.com/wp-content/uploads/Pixelink-Capture-Jan-2018.pdf | SCR_016197 | Pixelink Capture, Image Capture Software | 2026-08-13 09:29:37 | 4 | |||||||||
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PsychoFit Resource Report Resource Website 10+ mentions |
PsychoFit (RRID:SCR_015381) | data analysis software, data processing software, software resource, software application | Software that fits s-shaped psychometric functions to psychophysical data using a maximum-likelihood technique. The psychometric functions available are logistic, Weibull, Gaussian integral, cumulative Poisson and step. PsychoFit produces, among other things, files with graphic information suitable for importing in a graphic program for plotting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | psychophysical data, psychometric, graphic program, s-shaped psychometric function | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015381 | 2026-08-13 09:29:23 | 16 | |||||||||||
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MyBioSource Resource Report Resource Website 100+ mentions |
MyBioSource (RRID:SCR_013493) | antibody supplier, commercial organization, material resource, reagent supplier | An Antibody supplier | nlx_152416 | SCR_013493 | MyBioSource Inc., MyBioSource.com, MyBioSource Inc | 2026-08-13 09:29:04 | 184 | |||||||||||
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Vocal Inventory Clustering Engine (VoICE) Resource Report Resource Website 1+ mentions |
Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) | VoICE | data analysis software, data processing software, software resource, software application | Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations. | bird, song, birdsong, vocal, audio, analysis, vocalization, spectral similarity, avian, matlab | uses: MATLAB | Autism Speaks 7657; UCLA ; 5T32HC00722834 ; NIMH RO1MH081754; NICHD P50 HD055784; NIMH R01 MH081754; NIMH R01 MH070712 |
Free, Available for download | SCR_016004 | VoICE (Vocal Inventory Clustering Engine), Vocal Inventory Clustering Engine (VoICE), VoICE: Vocal Inventory Clustering Engine, VoICE: A semi-automated pipeline for standardizing vocal analysis across models | 2026-08-13 09:29:20 | 2 | |||||||
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Cogent 2000 Resource Report Resource Website 100+ mentions |
Cogent 2000 (RRID:SCR_015672) | data processing software, software application, software toolkit, signal processing software, software resource | MATLAB Toolbox for presenting stimuli and recording responses with precise timing. It also provides additional utilities for the manipulation of sound, keyboard, mouse, joystick, serial port, parallel port, subject responses and physiological monitoring hardware. | matlab, timing, physiological monitoring, subject response, stimulus presenting, response recording | has parent organization: Wellcome Trust | Free, Available for download, Acknowledgment requested, Account required, Demo available | SCR_015672 | Cogent | 2026-08-13 09:29:16 | 224 | |||||||||
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Singularity Registry Resource Report Resource Website 1+ mentions |
Singularity Registry (RRID:SCR_016249) | sregistry | data distribution software, web application, data processing software, data access protocol, application programming interface, software application, data storage software, software resource | Web application and registry for institutional deployment of Singularity containers. | containers, singularity, containers, linux, python, django, storage | is related to: Singularity Hub | PMID:28494014 | Open source, Freely available | SCR_016249 | Singularity Registry Server | 2026-08-13 09:29:24 | 2 | |||||||
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AmplifX Resource Report Resource Website 50+ mentions |
AmplifX (RRID:SCR_014465) | data analysis software, data processing software, software resource, software application | A software for managing, testing, and drawing primers. The software can locate primers for target sequences, calculate the quality score, predict amplified fragments and dimers, and create graphic representations of the primers. | primer design, target sequences, amplification, graphic representation, data analysis software | SCR_014465 | 2026-08-13 09:29:11 | 96 | ||||||||||||
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Cytoskeleton Resource Report Resource Website 1000+ mentions |
Cytoskeleton (RRID:SCR_013532) | antibody supplier, commercial organization, material resource, reagent supplier | An Antibody supplier | nlx_152338 | SCR_013532 | Cytoskeleton inc. | 2026-08-13 09:28:50 | 2691 |
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