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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Indelible Resource Report Resource Website 10+ mentions |
Indelible (RRID:SCR_016163) | simulation software, software application, software resource | Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. | indel, insertion, deletion, biological, sequence, simulation, multi-partitioned, nucleotide, amio-acid, codon, data, set, insertion, deletion, substitution, continous, time, non-homogeneous, non-stationary, phylogeny, simulator, evolution |
is listed by: Debian is listed by: OMICtools |
BBSRC ; EPSRC/MRC Doctoral Training Centre studentship |
PMID:19423664 | Free, Available for download | OMICS_15369 | https://sources.debian.org/src/indelible/ | SCR_016163 | SciCrunch Registry | 2026-10-17 01:29:02 | 24 | ||||||
|
zUMIs Resource Report Resource Website 100+ mentions |
zUMIs (RRID:SCR_016139) | data analysis software, data processing software, software application, software resource | Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information. | single-cell, RNA-seq, UMI, Genomics, shell, r, perl, rna, cdna, cell, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/153940 | Open source, Free, Available for download | biotools:zumis | https://bio.tools/zumis | SCR_016139 | SciCrunch Registry | zumi | 2026-10-17 01:29:02 | 128 | ||||||
|
Microsoft Excel Resource Report Resource Website 10000+ mentions |
Microsoft Excel (RRID:SCR_016137) | data analysis software, data processing software, data visualization software, software application, software resource | Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data. | data, process, manage, analyze, spreadsheet, template, track, visualize, graph |
is related to: XLSTAT is related to: Statcel3 has plug in: OVAL has plug in: easyGV |
Microsoft | Commercially available, Trial available | SCR_016137 | SciCrunch Registry | , MS Excel | 2026-10-17 01:29:21 | 90742 | ||||||||
|
Fastml Resource Report Resource Website 100+ mentions |
Fastml (RRID:SCR_016092) | data access protocol, software resource, web application, web service | Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences. | ancestral, amino-acid, sequence, reconstruction, phylogenetic, relation, accurate, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Bioinformatics Center at Tel-Aviv University ; Israel Science Foundation 878/09 |
PMID:22661579 | Free, Freely available | biotools:fastml, OMICS_08650 | https://bio.tools/fastml, https://sources.debian.org/src/fastml/ | SCR_016092 | SciCrunch Registry | The FastML Server | 2026-10-17 01:29:08 | 111 | |||||
|
Gubbins Resource Report Resource Website 500+ mentions |
Gubbins (RRID:SCR_016131) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 098051 | PMID:25414349 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_14386 | https://sources.debian.org/src/gubbins/ | SCR_016131 | SciCrunch Registry | Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences | 2026-10-17 01:29:08 | 604 | |||||
|
MediBeacon Studio Software Resource Report Resource Website |
MediBeacon Studio Software (RRID:SCR_016252) | data analysis software, data processing software, software application, software resource | Software used to analyze glomerular filtration rate (GFR) measurement from MediBeacon GFR monitor. It is used with the Transdermal Continuous Renal Function Monitor. | nephrology, renal, kidney, gfr, glomerulus, transdermal, skin, measurement | has parent organization: MediBeacon | Commercially available, Comes with device purchase | SCR_016252 | SciCrunch Registry | Studio Software, MediBeacon Software, Preclinical Data Studio | 2026-10-17 01:29:05 | 0 | |||||||||
|
SciScore Resource Report Resource Website 10+ mentions |
SciScore (RRID:SCR_016251) | software application, software resource, text-mining software, web application | Text-mining software that reviews methods sections of scientific articles. It provides a numerical score to represent the "reproducibility" of the article's research. | mine, text, method, journal, paper, article, research, science, biomedicine, neuroscience, scicrunch, nif, ASWG | is related to: SciCrunch | PMID:35759334 PMID:33196023 |
Used by SciCrunch, Freely available, Available to the research community | http://sci-score.com | SCR_016251 | SciCrunch Registry | Sci Score, SciCrunch SciScore | 2026-10-17 01:29:10 | 13 | |||||||
|
GraPhlAn Resource Report Resource Website 100+ mentions |
GraPhlAn (RRID:SCR_016130) | data processing software, data visualization software, software application, software resource | Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | circular, high, resolution, microbal, tree, taxonomy, annotation, phylogenetic, investigation |
is listed by: Debian is listed by: OMICtools has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11549 | https://huttenhower.sph.harvard.edu/graphlan, https://sources.debian.org/src/graphlan/ | SCR_016130 | SciCrunch Registry | Graphlan | 2026-10-17 01:29:01 | 186 | |||||||
|
BioPlex Resource Report Resource Website 1000+ mentions |
BioPlex (RRID:SCR_016144) | data or information resource, data repository, database, service resource, storage service resource | Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection. | cell, line, protein, immunopurification, mass, spectrometry, interaction, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
Canadian Institutes for Health Research ; NHGRI U41HG006673; NIDDK K01 DK098285 |
PMID:28514442 | biotools:bioplex_2.0 | https://bio.tools/bioplex_2.0 | SCR_016144 | SciCrunch Registry | BioPlex (biophysical interactions of ORFeome-based complexes), Harvard BioPlex, Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX) | 2026-10-17 01:29:02 | 1378 | ||||||
|
Virtual Digital Brain Resource Report Resource Website |
Virtual Digital Brain (RRID:SCR_016265) | VDB | software resource | Virtual resource for neuroscience. | brain, neuroscience, neuroimaging, cerebral | Free for academic use | SCR_016265 | SciCrunch Registry | 2026-10-17 01:29:03 | 0 | ||||||||||
|
mentha Resource Report Resource Website 100+ mentions |
mentha (RRID:SCR_016148) | data analysis software, data or information resource, data processing software, database, software application, software resource, web application | Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. | protein, ppi, imex, interactome, archival, bio.tools, FASEB list |
uses: PSICQUIC Registry is listed by: Debian is listed by: bio.tools is related to: IMEx - The International Molecular Exchange Consortium |
PMID:23900247 | biotools:mentha, r3d100011124 | https://bio.tools/mentha, https://doi.org/10.17616/R3SP8V | SCR_016148 | SciCrunch Registry | 2026-10-17 01:29:22 | 156 | ||||||||
|
easyGV Resource Report Resource Website 1+ mentions |
easyGV (RRID:SCR_016260) | data analysis software, data processing software, software application, software resource | Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface. | glycaemic, glycemia, variability, gv, glucose, diabetes, excel |
has parent organization: University of Oxford; Oxford; United Kingdom is a plug in for: Microsoft Excel |
PMID:21714681 | Free for academic use, Free for non-commercial use, Available for download | SCR_016260 | SciCrunch Registry | 2026-10-17 01:29:03 | 5 | |||||||||
|
Mass Univariate ERP Toolbox Resource Report Resource Website 1+ mentions |
Mass Univariate ERP Toolbox (RRID:SCR_016108) | data analysis software, data processing software, data visualization software, software application, software resource | Software toolkit of Matlab functions for analyzing and visualizing large numbers of t-tests performed on event-related potential data. The toolbox supports within-subject and between-subject t-tests with false discovery rate controls and control of the family-wise error rate via permutation tests. | matlab, analysis, t test, statistic, erp, event related potential, visualization, neuroimaging, erf, magnetic, resonance, imaging | requires: MATLAB | NIA AG08313; NICHD HD22614 |
PMID:21895683 | Free, Available for download | https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox | SCR_016108 | SciCrunch Registry | 2026-10-17 01:29:21 | 6 | |||||||
|
iELVis Resource Report Resource Website 10+ mentions |
iELVis (RRID:SCR_016109) | data processing software, data visualization software, software application, software resource | Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization. | electrode, stimulus, visualization, brain, neuroimaging, intracranial, localization, anatomy, functional, BRAIN Initiative | is recommended by: BRAIN Initiative | Natural Sciences and Engineering Research Council of Canada RGPIN-2014-04465; Page and Otto Marx Jr. Foundation ; Swiss National Science Foundation P300P3_148388; Swiss National Science Foundation PBGEP3_139829 |
PMID:28192130 | Open source, Free, Available for download | https://github.com/iELVis/iELVis | SCR_016109 | SciCrunch Registry | iELVis (intracranial electrode visualization), Intracranial ELectrode VISualization | 2026-10-17 01:29:01 | 47 | ||||||
|
HIRN Consortium on Human Islet Biomimetics Resource Report Resource Website |
HIRN Consortium on Human Islet Biomimetics (RRID:SCR_016199) | HIRN-CHIB, CHIB | consortium, data or information resource, organization portal, portal | Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is combining advances in beta cell biology and cell biology with tissue engineering technologies to develop microdevices that support functional human islets. | beta, cell, biology, tissue, bioengineering, nanoengineering, human, stem | is organization facet of: Human Islet Research Network (HIRN) | NIDDK ; NIDDK U01 DK104162; NIDDK UC4 DK104165; NIDDK UC4 DK104196; NIDDK UC4 DK104202; NIDDK UC4 DK104208; NIDDK UC4 DK116283 |
SCR_016199 | SciCrunch Registry | Consortium on Human Islet Biomimetics (HIRN-CHIB) | 2026-10-17 01:29:23 | 0 | ||||||||
|
Mapping Population-based Structural Connectomes Resource Report Resource Website |
Mapping Population-based Structural Connectomes (RRID:SCR_016232) | data analysis software, data processing software, software application, software resource | Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis. | dwi, t1, tractography, algorithm, white matter, bundle, gray matter, shape, analysis, network, workflow | CPRIT RR150054; NIMH MH086633; NIMH MH092335; NSF DMS-1407655; NSF DMS1127914; NSF SES-1357666 |
Free for non-commercial use, Available for download | SCR_016232 | SciCrunch Registry | 2026-10-17 01:29:23 | 0 | ||||||||||
|
Garlic Resource Report Resource Website 10+ mentions |
Garlic (RRID:SCR_016118) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource | Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences. | visualization, editing, biomolecule, investigation, membrane, protein, analyze, sequence |
is listed by: Debian is listed by: OMICtools |
Open source, Free, Available for download | OMICS_21303 | https://sources.debian.org/src/garlic/ | SCR_016118 | SciCrunch Registry | 2026-10-17 01:29:21 | 38 | ||||||||
|
REmAb Resource Report Resource Website |
REmAb (RRID:SCR_016239) | analysis service resource, biomaterial analysis service, material analysis service, production service resource, service resource | Service for monoclonal antibody protein sequencing. It derives the sequences directly from the protein using mass spectrometry and without the need to access the cell line. | mass, spectrometry, monoclonal, anitbody, protein, sequencing, cell, line | Commercially available, Free consultation | SCR_016239 | SciCrunch Registry | Antibody Sequencing Service | 2026-10-17 01:29:23 | 0 | ||||||||||
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YAMP Resource Report Resource Website 1+ mentions |
YAMP (RRID:SCR_016236) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability. | metagenomics, reproducibility, workflow, containerization, sequencing, gene, rna, annotating, portable, data, process | Free, Available for download | SCR_016236 | SciCrunch Registry | YAMP: Yet Another Metagenomic Pipeline, Yet Another Metagenomic Pipeline (YAMP), Yet Another Metagenomic Pipeline | 2026-10-17 01:29:09 | 8 | ||||||||||
|
Gamgi Resource Report Resource Website |
Gamgi (RRID:SCR_016116) | GAMGI | data analysis software, data processing software, data visualization software, software application, software resource | Software application which provides a graphical interface to build, view and analyze atomic structures. It provides a graphical interface to study atomic structures, to prepare images for presentations, and teach the atomic structure of matter. | gui, graphical, interface, model, atom, atomic, structure |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Runs on Linux, Tutorial available | OMICS_21302 | https://sources.debian.org/src/gamgi/ | SCR_016116 | SciCrunch Registry | GAMGI: General Atomistic Modelling Graphic Interface, General Atomistic Modelling Graphic Interface | 2026-10-17 01:29:08 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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