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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
RNAstructure
 
Resource Report
Resource Website
10+ mentions
RNAstructure (RRID:SCR_017216) production service resource, web service, software application, analysis service resource, simulation software, data access protocol, service resource, software resource Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program. RNA, DNA, secondary, structure, prediction, analysis is listed by: SoftCite
has parent organization: University of Rochester; New York; USA
NIGMS R01 GM076485 PMID:23620284 Free, Freely available SCR_017216 2026-08-03 09:37:01 42
ClustalW
 
Resource Report
Resource Website
10000+ mentions
ClustalW (RRID:SCR_017277) ClustalW of DDBJ web service, data access protocol, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan. alignment, service, DNA, data, bank, Japan is listed by: SoftCite THIS RESOURCE IS NO LONGER IN SERVICE SCR_017277 ClustalW of DNA Data Bank of Japan 2026-08-03 09:36:34 10543
GRADEpro
 
Resource Report
Resource Website
100+ mentions
GRADEpro (RRID:SCR_021308) data management software, software resource, software application Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables. Summary of findings tables, cochrane systematic reviews, research evidence creating, research evidence management, research evidence sharing summaries, evidence profiles, is listed by: SoftCite Restricted https://cebgrade.mcmaster.ca/gradepro.html SCR_021308 Guideline Development Tool, GRADEpro GDT, GDT, GRADE Guideline Development Tool, G2DT 2026-08-03 09:37:19 376
Taverna
 
Resource Report
Resource Website
10+ mentions
Taverna (RRID:SCR_004437) Taverna workflow software, software resource, software application, data processing software An open source and domain independent Workflow Management System ����?? a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Taverna Workbench now has support for service sets, offline workflow editing, workflow validation, improved workflow run monitoring, and the pausing and canceling of workflow runs. The command line tool allows you to run workflows outside of the workbench and is available as a stand-alone download or bundled with the Taverna Workbench 2.2.0 download. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal. Taverna 2.2.0 includes * Copy/paste, shortcuts, undo/redo, drag and drop * Animated workflow diagram * Remembers added/removed services * Secure Web services support * Secure access to resources on the web * Up-to-date R support * Intermediate values during workflow runs * myExperiment integration * Excel and csv spreadsheet support * Command line tool is listed by: OMICtools
is listed by: SoftCite
is related to: myExperiment
is related to: U-Compare
is related to: Taverna Knowledge Blog
is related to: AIDA Toolkit
is related to: Knowledge Blog
has parent organization: University of Manchester; Manchester; United Kingdom
OMII-UK ;
EPSRC ;
BBSRC ;
Microsoft ;
ESRC ;
JISC
PMID:18337261
PMID:23640334
Open unspecified license nlx_43462, OMICS_01146 SCR_004437 2026-08-03 09:32:40 30
STAR
 
Resource Report
Resource Website
10000+ mentions
STAR (RRID:SCR_004463) image analysis software, software application, data processing software, alignment software, software resource Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools is used by: STARsolo
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
NHGRI U54 HG004557 PMID:23104886
DOI:10.1093/bioinformatics/bts635
biotools:star, OMICS_01254, SCR_015899 https://github.com/alexdobin/STAR, https://bio.tools/star, https://sources.debian.org/src/rna-star/ SCR_004463 Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner 2026-08-03 09:32:33 22809
Kepler
 
Resource Report
Resource Website
10+ mentions
Kepler (RRID:SCR_005252) Kepler workflow software, software resource, software application, data processing software Kepler is a software application for analyzing and modeling scientific data. Using Kepler''s graphical interface and components, scientists with little background in computer science can create executable models, called scientific workflows, for flexibly accessing scientific data (streaming sensor data, medical and satellite images, simulation output, observational data, etc.) and executing complex analyses on this data. Kepler is developed by a cross-project collaboration led by the Kepler/CORE team. The software builds upon the mature Ptolemy II framework, developed at the University of California, Berkeley. Ptolemy II is a software framework designed for modeling, design, and simulation of concurrent, real-time, embedded systems. The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scien��tists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging R scripts with compiled C code, or facilitating remote, distributed execution of models. Using Kepler''s graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a scientific workflowan executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and compo��nents developed by the scientific community to address common needs. Kepler is a java-based application that is maintained for the Windows, OSX, and Linux operating systems. The Kepler Project supports the official code-base for Kepler development, as well as provides materials and mechanisms for learning how to use Kepler, sharing experiences with other workflow developers, reporting bugs, suggesting enhancements, etc. The Kepler Project Leadership Team works to assure the long-term technical and financial viability of Kepler by making strategic decisions on behalf of the Kepler user community, as well as providing an official and durable point-of-contact to articulate and represent the interests of the Kepler Project and the Kepler software application. Details about how to get more involved with the Kepler Project can be found in the developer section of this website. software, workflow is listed by: SoftCite
is related to: bioKepler
has parent organization: University of California at Davis; California; USA
has parent organization: University of California at Santa Barbara; California; USA
has parent organization: University of California at San Diego; California; USA
NSF 0722079 nlx_144278 SCR_005252 Kepler Project 2026-08-03 09:32:49 47
MycoBank
 
Resource Report
Resource Website
500+ mentions
MycoBank (RRID:SCR_004950) MycoBank data repository, data or information resource, database, storage service resource, service resource Database documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated and will also serve as Life Science Identifiers (LSIDs). Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural errors; however, no censorship whatsoever, (nomenclatural or taxonomic) will be exerted by MycoBank. Deposited names will remain -when desired- strictly confidential until after publication, and will then be accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases to realize a species bank that eventually will link all databases of life. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute to this new initiative. For the moment 2 search engines are available from the MycoBank website. The first one permits to search for fungal names (at any rank level), the authority or the MycoBank unique number. The second is dedicated to bibliographic queries related to fungal name''''s publications. MycoBank users willing to deposit their data will have to register so that they willbe able to contact the depositor for specific information (e.g. MycoBank number, possible points of attention regarding the name, actual publication, etc), and to avoid fake entries. yeast, aspergillus, penicillium, phaeoacremonium, russula, resupinate russulales, mycosphaerella, trichomycete, arthropod, hysteriaceae, mytilinidiaceae, mycology, nomenclature, life science identifier, bibliography, sequence alignment, polyphasic identification, image collection, FASEB list is listed by: SoftCite
is related to: Index Fungorum
PMID:24563843 nlx_91803, r3d100011222 https://doi.org/10.17616/R39D0Q SCR_004950 2026-08-03 09:32:45 743
PRISM (Stanford database)
 
Resource Report
Resource Website
10000+ mentions
PRISM (Stanford database) (RRID:SCR_005375) PRISM production service resource, data analysis service, service resource, database, analysis service resource, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. genomic, transcription factor, function, transcription factor binding site, transcription factor regulator, biological role, target gene, target genomic region, genome, FASEB list is listed by: OMICtools
is listed by: SoftCite
is related to: GREAT: Genomic Regions Enrichment of Annotations Tool
has parent organization: Stanford University School of Medicine; California; USA
PMID:23382538 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00489 SCR_005375 Predicting Regulatory Information from Single Motifs 2026-08-03 09:32:52 40813
Hmmer
 
Resource Report
Resource Website
5000+ mentions
Hmmer (RRID:SCR_005305) HMMER production service resource, data analysis service, software application, data processing software, data analysis software, analysis service resource, service resource, software resource Tool for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. homolog, protein sequence, source code, FASEB list is used by: Mantis
is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: Debian
is listed by: SoftCite
is related to: VectorBase
has parent organization: Janelia Research
Howard Hughes Medical Institute PMID:21593126
DOI:10.1093/bioinformatics/14.9.755
OMICS_00996, nlx_144358 https://sources.debian.org/src/hmmer/ SCR_005305 HMMER - biosequence analysis using profile hidden Markov models 2026-08-03 09:32:49 8774
Bowtie
 
Resource Report
Resource Website
10000+ mentions
Bowtie (RRID:SCR_005476) sequence analysis software, image analysis software, software application, data processing software, data analysis software, alignment software, software resource Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner. sequence, analysis, long, reference, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools is used by: deFuse
is used by: Short Read Sequence Typing for Bacterial Pathogens
is used by: TopHat
is used by: BS Seeker
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: Bowtie 2
has parent organization: Johns Hopkins University; Maryland; USA
is required by: RelocaTE
NHGRI R01 HG006102;
NIGMS R01 GM083873;
Amazon Web Services in Education Research
PMID:19261174
DOI:10.1186/gb-2009-10-3-r25
Free, Available for download, Freely available biotools:bowtie, OMICS_00653 https://github.com/BenLangmead/bowtie, https://bio.tools/bowtie, https://sources.debian.org/src/bowtie/ SCR_005476 2026-08-03 09:32:53 13226
InterProScan
 
Resource Report
Resource Website
5000+ mentions
InterProScan (RRID:SCR_005829) production service resource, data analysis service, web service, software application, data processing software, data analysis software, analysis service resource, data access protocol, service resource, software resource Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools is listed by: Gene Ontology Tools
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: Gene Ontology
is related to: RARTF
is related to: InterPro
is related to: LegumeIP
is related to: UniProtKB
has parent organization: European Bioinformatics Institute
European Union ;
Biotechnology and Biological Sciences Research Council ;
EMBL
PMID:15980438
PMID:17202162
PMID:24451626
Free, Available for download, Freely available OMICS_01479, biotools:interproscan_4, nlx_149337 https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 SCR_005829 InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 2026-08-03 09:32:57 6936
FigTree
 
Resource Report
Resource Website
10000+ mentions
FigTree (RRID:SCR_008515) software resource, data visualization software, software application, data processing software A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST. data visualization software, graphical viewer, phylogenetic tree, annotate is listed by: Debian
is listed by: OMICtools
is listed by: SoftCite
has parent organization: University of Edinburgh; Scotland; United Kingdom
OMICS_04268, nif-0000-30567 https://sources.debian.org/src/figtree/ SCR_008515 FigTree 2026-08-03 09:34:04 11323
Augustus
 
Resource Report
Resource Website
1000+ mentions
Augustus (RRID:SCR_008417) sequence analysis software, software application, data processing software, web application, data analysis software, software resource Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. software, gene, prediction, eucaryotic, genomic, sequence is used by: BRAKER
is used by: BRO_annotation
is listed by: Debian
is listed by: OMICtools
is listed by: SoftCite
works with: Gsnap2Augustus
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;;
STA1009/6-1 ;
Institute for Mathematics and Computer Science ;
Ernst Moritz Arndt University of Greifswald
PMID:23700307
DOI:10.1093/bioinformatics/btw494
Free, Available for download, Freely available SCR_015981, OMICS_07777, nif-0000-30133 https://sources.debian.org/src/autodock-vina/ SCR_008417 Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] 2026-08-03 09:34:06 3542
Research Randomizer
 
Resource Report
Resource Website
1000+ mentions
Research Randomizer (RRID:SCR_008563) web service, data access protocol, software resource This site is designed for researchers and students who want a quick way to generate random numbers or assign participants to experimental conditions. Research Randomizer can be used in a wide variety of situations, including psychology experiments, medical trials, and survey research. The program uses a JavaScript random number generator to produce customized sets of random numbers. Since its release in 1997, Research Randomizer has been used to generate number sets over 10.7 million times. This service is part of Social Psychology Network and is fast, free, and runs with any recent web browser as long as JavaScript isn''t disabled. Research Randomizer is a free service offered to students and researchers interested in conducting random assignment and random sampling. By using this service, you agree to abide by the SPN User Policy and to hold Research Randomizer and its staff harmless in the event that you experience a problem with the program or its results. Although every effort has been made to develop a useful means of generating random numbers, Research Randomizer and its staff do not guarantee the quality or randomness of numbers generated. Any use to which these numbers are put remains the sole responsibility of the user who generated them. What are the system requirements needed to run Research Randomizer? This program works best with Firefox and other recent web browsers. If you''re using a browser that came with America Online, or older browsers made prior to 2003, you may experience some difficulties with Research Randomizer. You may also not be able to use Research Randomizer with some limited-function browsers that do not fully support JavaScript, such as the Opera broswer used on certain game consoles. We would suggest that you update to a fairly recent, fully- functional stand-alone browser. How do I know what browser I am using? The easiest way to find this out is to click Help on the pulldown menu at the top of the screen. One of the options should be About Mozilla Firefox, About Internet Explorer, About Netscape, or something similar. Selecting this option will open a window that displays the name, version number, and copyright date of your browser. How does Research Randomizer generate its numbers? Research Randomizer uses the Math.random method within the JavaScript programming language to generate its random numbers for all modern web browsers. If you are using an older version of Microsoft Internet Explorer or Netscape Navigator (that is prior to version 4.0 of either), Research Randomizer uses an adaptation of the Central Randomizer by Paul Houle. Note that Research Randomizer no longer supports much-older browsers by other vendors (e.g., Mosaic). Who designed Research Randomizer? The original idea and programming for Research Randomizer came from Geoffrey C. Urbaniak in 1997. Research Randomizer was then jointly developed with Scott Plous, webmaster of Social Psychology Network, and online tutorials were added to the main program. In 1999 the site was redesigned with the assistance of Mike Lestik, in 2003 Mike Lestik added the download function, and in 2007 Mike Lestik and Scott Plous redesigned the site and added new content. is listed by: SoftCite nif-0000-31448 SCR_008563 Research Randomizer 2026-08-03 09:34:07 2093
MODELLER
 
Resource Report
Resource Website
5000+ mentions
MODELLER (RRID:SCR_008395) portal, software application, topical portal, simulation software, data or information resource, software resource Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms. comparative, protein, structure, modelling, satisfaction, spatial, restrain, homology, 3D, alignment, sequence, hydrogen, atom, cluster is listed by: SoftCite
has parent organization: University of California at San Francisco; California; USA
Sandler Family Supporting Foundation ;
NIGMS R01 GM54762;
NIGMS P01 GM71790;
NIH P01 A135707;
NIGMS U54 GM62529;
IBM ;
Intel
Restricted nif-0000-30054 SCR_008395 2026-08-03 09:34:02 5736
MACH
 
Resource Report
Resource Website
500+ mentions
MACH (RRID:SCR_009621) software resource, data processing software, software application, data analysis software QTL analysis based on imputed dosages/posterior_probabilities. genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
has parent organization: University of Michigan; Ann Arbor; USA
PMID:21058334
PMID:19715440
DOI:10.1002/gepi.20533
Free, Non-commercial, Acknowledgement requested nlx_155856, biotools:mach http://www.nitrc.org/projects/mach, https://bio.tools/mach https://sources.debian.org/src/mach-haplotyper/ SCR_009621 mach2qtl, MaCH 2026-08-03 09:34:26 925
WEBLOGO
 
Resource Report
Resource Website
1000+ mentions
WEBLOGO (RRID:SCR_010236) web service, data access protocol, service resource, software resource Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator. Generate sequence logo, pattern graphical representation, multiple sequence alignment, sequence logo generator, amino acid sequence alignment, nucleic acid sequence alignment, sequence alignment representation, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
has parent organization: University of California at Berkeley; Berkeley; USA
NHGRI K22 HG00056;
Searle Scholars program ;
NIGMS P50 GM62412
PMID:15173120 Free, Available for download, Freely available nlx_156853, biotools:weblogo_3 http://weblogo.threeplusone.com/, https://bio.tools/weblogo_3 SCR_010236 WebLogo Version 2.8.2, WebLogo3, WebLogo 2026-08-03 09:34:33 3653
Geneious
 
Resource Report
Resource Website
10000+ mentions
Geneious (RRID:SCR_010519) sequence analysis software, data management software, software toolkit, software application, data processing software, data analysis software, software resource Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools. Sequence alignment software, data management software, analysis software, Geneious Biologics, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is parent organization of: Geneious Microsatellite Plugin
PMID:22543367 Restricted OMICS_00016, biotools:geneious http://nebc.nerc.ac.uk/news/geneiousonbl, https://bio.tools/geneious SCR_010519 Geneious Prime, Geneious 11.0, Geneious 11.1.2, Geneious 8.1, Geneious Basic 2026-08-03 09:34:51 12252
ABySS
 
Resource Report
Resource Website
500+ mentions
ABySS (RRID:SCR_010709) ABySS sequence analysis software, software application, data processing software, data analysis software, software resource Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements. paired-end sequence assembler, short reads, assembling human genome, large genomes, bloom filter, is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
Genome Canada ;
Genome British Columbia ;
British Columbia Cancer Foundation ;
NHGRI R01HG007182
PMID:19251739
DOI:10.1101/068338
DOI:10.1101/gr.214346.116
Free, Available for download, Freely available biotools:abyss, OMICS_00006 https://github.com/bcgsc/abyss, https://sources.debian.org/src/abyss/, https://bio.tools/abyss, SCR_010709 ABySS 1.0, ABySS 2.0 2026-08-03 09:34:48 761
Image Pro Plus
 
Resource Report
Resource Website
10000+ mentions
Image Pro Plus (RRID:SCR_007369) image acquisition software, data acquisition software, software toolkit, software application, data processing software, image analysis software, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data. morphometric, image analysis, image acquisition, automation, classification, microscope control is listed by: SoftCite nif-0000-00313, SCR_015803, SCR_016879 SCR_007369 Image-Pro Plus, Image-Pro Plus Morphometric Analysis Software 2026-08-03 09:33:21 18240

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