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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
MUMmer
 
Resource Report
Resource Website
100+ mentions
MUMmer (RRID:SCR_018171) software resource, image analysis software, alignment software, data processing software, software application Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. Align, genome, DNA, protein, sequence, , bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
is listed by: SoftCite
is related to: MUMmerGPU
NLM R01 LM06845;
NSF IIS 9902923;
NIAID N01 AI15447
PMID:14759262 Free, Available for download, Freely available OMICS_14554, biotools:mummer https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ SCR_018171 MUMmer4, MUMmer 3.0 2026-08-06 09:29:20 480
GeneMarkS-T
 
Resource Report
Resource Website
100+ mentions
GeneMarkS-T (RRID:SCR_017648) data analysis software, software application, software resource, data processing software Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Georgia Institute of Technology; Georgia; USA
NHGRI HG000783 PMID:25870408 Restricted biotools:GeneMarkS-t https://bio.tools/GeneMarkS-T SCR_017648 2026-08-06 09:29:07 113
NetMHCpan Server
 
Resource Report
Resource Website
100+ mentions
NetMHCpan Server (RRID:SCR_018182) data access protocol, web service, software resource Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools is listed by: bio.tools
is listed by: Debian
Agencia Nacional de Promoción Científica y Tecnológica ;
Argentina ;
NIAID
PMID:19002680
PMID:28978689
Free, Available for download, Freely Available biotools:netmhcpan https://bio.tools/netmhcpan, https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ SCR_018182 NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan 2026-08-06 09:29:18 138
Mousebytes
 
Resource Report
Resource Website
1+ mentions
Mousebytes (RRID:SCR_017904) storage service resource, service resource, data repository, data or information resource, database Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available. Data, mouse, cognition, imaging, genomics, integration, bio.tools, OpenBehavior is listed by: Debian
is listed by: bio.tools
is listed by: OpenBehavior
has parent organization: Western University; Ontario; Canada
Weston Brain Institute (Canada) ;
Canadian Institute of Health Research ;
NSERC ;
Alzheimer’s Society of Canada ;
Canadian First Research Excellence Fund (BrainsCAN) ;
Brain Canada
PMID:31825307 Free, Freely available SCR_021549, SCR_021598, r3d100013886, biotools:Mousebytes https://bio.tools/MouseBytes, https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/, https://doi.org/10.17616/R31NJN7I SCR_017904 MouseBytes 2026-08-06 09:29:16 4
4See
 
Resource Report
Resource Website
1+ mentions
4See (RRID:SCR_018014) data visualization software, software application, software resource, data processing software Software tool to visualize 4C data. Visualize, 4C data, bio.tools is listed by: bio.tools
is listed by: Debian
DOI:10.3389/fgene.2019.01372 Free, Available for download, Freely available biotools:4see https://bio.tools/4see SCR_018014 2026-08-06 09:29:19 1
NeuroChaT
 
Resource Report
Resource Website
1+ mentions
NeuroChaT (RRID:SCR_018020) software resource, data analysis software, software toolkit, data processing software, software application Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools is listed by: Debian
is listed by: bio.tools
Wellcome Trust DOI:12688/wellcomeopenres.15533.1 Free, Available for download, Freely available biotools:NeuroChat https://bio.tools/NeuroChaT SCR_018020 Neuron Characterisation Toolbox 2026-08-06 09:29:19 2
Online Peri-Event Time Histogram for Open Ephys
 
Resource Report
Resource Website
1+ mentions
Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) OPETH data visualization software, software application, software resource, data processing software Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them. Open source, open ephys, optogenetics, behavior, electrophysiology data, neuroscience experiment, spike detection, behavior tagging, neuron, histogram, bio.tools is listed by: Debian
is listed by: bio.tools
Hungarian Academy of Sciences Lendület Program LP2015-2/2015;
European Research Council Starting Grant 715043;
Generalitat Valenciana Postdoctoral Fellowship Program APOSTD/2019/003
DOI:10.1101/783688 Free, Available for download, Freely available biotools:OPEtH https://bio.tools/OPETH SCR_018022 Online Peri-Event Time Histogram 2026-08-06 09:29:16 4
ΔG prediction server
 
Resource Report
Resource Website
10+ mentions
ΔG prediction server (RRID:SCR_018191) service resource, data access protocol, web service, software resource Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon. Amino acid sequence, putative transmembrane helix, free energy difference, sequence insertion, endoplasmic reticulum membrane, potential TM helix, predict energy difference, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Stockholm University; Stockholm; Sweden
Free, Freely available biotools:deltag_prediction http://dgpred.cbr.su.se/index.php?p=TMpred, https://bio.tools/deltag_prediction SCR_018191 ΔG prediction server v1.0 2026-08-06 09:29:21 12
BioNix
 
Resource Report
Resource Website
1+ mentions
BioNix (RRID:SCR_017662) software library, software toolkit, software resource Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language. Workflow, engine, package, manager, container, unify, bioinformatics, Nix, functional, bio.tools is listed by: Debian
is listed by: bio.tools
Free, Available for download, Freely available biotools:bioNix https://bio.tools/BioNix SCR_017662 2026-08-06 09:29:07 4
Multi-omics Visualization Platform
 
Resource Report
Resource Website
1+ mentions
Multi-omics Visualization Platform (RRID:SCR_018077) MVP software resource, data analysis software, data processing software, data visualization software, software application Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools is listed by: bio.tools
is listed by: Debian
NIH U24 CA199347 Free, Available for download, Freely available biotools:mvp_a http://galaxyp.org, https://bio.tools/mvp_a SCR_018077 Multi-omics Visualization Platform, Galaxy MVP 2026-08-06 09:29:19 1
PEMA
 
Resource Report
Resource Website
1+ mentions
PEMA (RRID:SCR_017676) software resource, data analysis software, software toolkit, data processing software, software application Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution. Environmental, DNA, metabarcoding, analysis, ASVs, OTUs, 16S rRNA, COI, ITS, marker, gene, clustering, taxonomy, bio.tools is listed by: bio.tools
is listed by: Debian
DOI:10.1101/709113 Free, Freely available biotools:PEMA https://docs.google.com/presentation/d/1lVH23DPa2NDNBhVvOTRoip8mraw8zfw8VQwbK4vkB1U/edit?fbclid=IwAR14PpWfPtxB8lLBBnoxs7UbG3IJfkArrJBS5f2kRA__kvGDUb8wiJ2Cy_s#slide=id.g57f092f54d_1_21, https://bio.tools/PEMA SCR_017676 Pipeline for Environmental DNA Metabarcoding Analysis 2026-08-06 09:29:07 1
DichroWeb
 
Resource Report
Resource Website
50+ mentions
DichroWeb (RRID:SCR_018125) software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: University of London; London; United Kingdom
BBSRC PMID:17896349
PMID:15215473
Restricted biotools:dichroweb https://bio.tools/dichroweb SCR_018125 2026-08-06 09:29:14 62
ProtParam Tool
 
Resource Report
Resource Website
5000+ mentions
ProtParam Tool (RRID:SCR_018087) sequence analysis software, software resource, service resource, production service resource, data analysis software, data processing software, software application, analysis service resource Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: ExPASy Bioinformatics Resource Portal
NHGRI U01 HG02712;
Swiss Federal Government through Federal Office of Education and Science
PMID:10027275 Free, Freely available biotools:protparam https://bio.tools/protparam SCR_018087 ProtParam 2026-08-06 09:29:19 5406
biospytial
 
Resource Report
Resource Website
1+ mentions
biospytial (RRID:SCR_018226) software resource, data analysis software, data management software, software toolkit, data processing software, data visualization software, software application Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system. spatial data infrastructure, biodiversity informatics, ecological knowledge engine, ecological data analysis, biodiversity, taxonomic classification, bio.tools is listed by: Debian
is listed by: bio.tools
CONACyT ;
GBIF ;
Lancaster University
DOI:10.5524/100723 Free, Available for download, Freely available biotools:biospytial https://bio.tools/biospytial SCR_018226 2026-08-06 09:29:22 2
Plant Co-expression Annotation Resource
 
Resource Report
Resource Website
1+ mentions
Plant Co-expression Annotation Resource (RRID:SCR_018429) Plantannot software resource, service resource, data access protocol, web service, data or information resource Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard. Omics, plant, annotation, function, breeding, genetically modified crops, abiotic stress in plant, plant genome, plant genomic data, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: Phytozome
is related to: NCBI
is related to: Machado
Embrapa DOI:10.1101/2020.05.22.110510 Free, Freely available biotools:plantannot https://www.machado.cnptia.embrapa.br/plantannot2, https://bio.tools/plantannot SCR_018429 Plantannot v2 2026-08-06 09:29:19 1
pepwheel
 
Resource Report
Resource Website
1+ mentions
pepwheel (RRID:SCR_018398) service resource, data access protocol, web service, software resource Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation. Computational proteomics, data analysis pipeline, label free quantification, mass spectrometry, quantitative proteomics, visualise protein sequence, helical wheel diagram, peptice sequence display, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: EMBOSS
works with: Proteome Discoverer
Free, Freely available biotools:pepwheel https://bio.tools/pepwheel SCR_018398 2026-08-06 09:29:19 1
TDimpute
 
Resource Report
Resource Website
1+ mentions
TDimpute (RRID:SCR_018306) data analysis software, software application, software resource, data processing software Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data. Transfer learning; gene expression prediction; DNA methylation; TCGA, neural network, missing gene expression, data, bio.tools is listed by: Debian
is listed by: bio.tools
DOI:10.1101/803692 Free, Available for download, Freely available biotools:tDimpute, BioTools:TDimpute https://bio.tools/TDimpute, https://bio.tools/TDimpute, https://bio.tools/TDimpute SCR_018306 2026-08-06 09:29:23 1
betaVAEImputation
 
Resource Report
Resource Website
1+ mentions
betaVAEImputation (RRID:SCR_018730) data analysis software, software application, software resource, data processing software Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis. Genomic data, handling missing data, deep learning framework, variational autoencoder, imputing missing values, transcriptome, methylome, data analysis, bio.tools is listed by: bio.tools
is listed by: Debian
Free, Available for download, Freely available biotools:betavaeimputation https://bio.tools/betavaeimputation SCR_018730 2026-08-06 09:29:21 2
Protein Interactions Calculator
 
Resource Report
Resource Website
10+ mentions
Protein Interactions Calculator (RRID:SCR_018574) software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex. Protein interaction, interaction calculation, single site, accessible surface are, residue depth, protein surface, residue distance, residue interaction, protein complex, bio.tools is listed by: Debian
is listed by: bio.tools
Department of Biotechnology Government of India PMID:17584791 Free, Freely available biotools:pic https://bio.tools/pic http://crick.mbu.iisc.ernet.in/~PIC SCR_018574 2026-08-06 09:29:20 27
LRPath
 
Resource Report
Resource Website
1+ mentions
LRPath (RRID:SCR_018572) software resource, data access protocol, service resource, production service resource, web service, analysis service resource Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools is listed by: bio.tools
is listed by: Debian
NIEHS P30 ES06096;
NIEHS U01 ES015675;
NHGRI R01 HG003749;
NLM R01 LM008106;
NIDA U54 DA021519
PMID:19038984 Free, Freely available biotools:lrpath https://bio.tools/lrpath SCR_018572 2026-08-06 09:29:28 4

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