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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge https://bio.tools/centrifuge https://sources.debian.org/src/centrifuge/ |
SCR_016665 | 2026-02-16 09:49:05 | 9 | ||||||
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Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | data analysis service, analysis service resource, web application, software resource, production service resource, service resource | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/ https://bio.tools/pavian |
SCR_016679 | 2026-02-16 09:49:05 | 22 | ||||||
|
KnowEnG Resource Report Resource Website 1+ mentions |
KnowEnG (RRID:SCR_016875) | training resource, organization portal, software resource, portal, data or information resource | Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data. | center, excellence, big, data, computing, biomedical, analytics |
has parent organization: Mayo Clinic has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS U54 GM114838 | PMID:26205246 | https://github.com/BD2K/KnowEng | SCR_016875 | Knowledge Engine for Genomics, The Knowledge Engine for Genomics | 2026-02-16 09:49:06 | 1 | |||||||
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CheckMyMetal Resource Report Resource Website 1+ mentions |
CheckMyMetal (RRID:SCR_016887) | CMM | data access protocol, software resource, web service | Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal. | metal, binging, site, validation, server, systematic, inspection, macromolecular, structure, ion, charge, position, atom | NIGMS GM117325; NHGRI HG008424; NIAID HHSN272201200026C |
PMID:28291757 | Free, Freely available | SCR_016887 | 2026-02-16 09:49:07 | 5 | ||||||||
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exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | application programming interface, controlled vocabulary, organization portal, data analysis service, analysis service resource, data access protocol, atlas, ontology, data repository, software resource, database, storage service resource, expression atlas, consortium, portal, production service resource, service resource, data or information resource | Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. | Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset |
is recommended by: National Library of Medicine has parent organization: Baylor College of Medicine; Houston; Texas has parent organization: exRNA |
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage | NIDA U54 DA036134; NCI R01 CA163849; NIGMS R25 GM056929; NCATS UH3 TR000906; NCI U19 CA179512; NIDDK P30 DK63720; NHLBI K23 HL127099; NHLBI R01 HL136685; NIA R01 AG059729; NCATS UH3 TR000943; NCI R35 CA209904; NCI CA217685; NHLBI R01 HL122547; American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch |
PMID:30951672 | Restricted | SCR_017221 | 2026-02-16 09:49:11 | 24 | |||||||
|
RNAstructure Resource Report Resource Website 10+ mentions |
RNAstructure (RRID:SCR_017216) | software application, web service, data access protocol, analysis service resource, software resource, simulation software, production service resource, service 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 | 2026-02-16 09:49:11 | 42 | ||||||||
|
CCPN Data Model Resource Report Resource Website |
CCPN Data Model (RRID:SCR_016982) | software application, data processing software, data repository, database, storage service resource, software resource, data storage software, service resource, data or information resource | Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature. | data, macromolecular, NMR, spectroscopy, deposition, mining, interoperability, conversion |
is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Collaborative Computing Project for NMR works with: CCPN Analysis works with: CCPN Analysis |
EU ; BBSRC ; NLM P41 LM005799; NIGMS GM67965 |
PMID:15815974 PMID:15613391 PMID:21953355 |
Free, Public | SCR_016982 | The CCPN Data Model | 2026-02-16 09:49:08 | 0 | |||||||
|
eMERGE Network: electronic Medical Records and Genomics Resource Report Resource Website 1+ mentions |
eMERGE Network: electronic Medical Records and Genomics (RRID:SCR_007428) | eMERGE | data or information resource, topical portal, portal | A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community. | human, clinical, dna, alzheimer's disease, genome, genomics, gene, genetic, nervous system disease, nucleotide polymorphism, phenotype, bioinformatics, genomic medicine, privacy, community engagement, emr, electronic medical record |
is related to: PheKB is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: PheWAS Catalog has parent organization: Vanderbilt University; Tennessee; USA |
Aging | NIGMS ; NHGRI |
Available to the research community | nif-0000-00539 | SCR_007428 | eMERGE Network: electronic Medical Records & Genomics - A consortium of biorepositories linked to electronic medical records data for conducting genomics studies, eMERGE Network: electronic Medical Records Genomics, eMERGE Network: electronic Medical Records & Genomics, eMERGE Network, electronic Medical Records & Genomics, The eMERGE Network: electronic Medical Records & Genomics | 2026-02-16 09:46:58 | 2 | |||||
|
SimTKCore Resource Report Resource Website |
SimTKCore (RRID:SCR_008268) | SimTKCore | software application, software resource, simulation software | SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications. | computational algorithm, high-performance, linear algebra, numerical integration, numerical method, optimization, monte carlo sampling, multibody dynamics, molecular force field evaluation, nonlinear root finding, optimizing, cpodes, simbody, ipopt, molmodel, mit license, linux, mac os x, windows |
is listed by: Biositemaps has parent organization: Stanford University; Stanford; California has parent organization: Simtk.org |
NIGMS U54 GM072970 | PMID:20107615 | nif-0000-23310 | SCR_008268 | 2026-02-16 09:47:08 | 0 | |||||||
|
Hippocampal Slice Wave Animations Resource Report Resource Website |
Hippocampal Slice Wave Animations (RRID:SCR_008372) | software application, data processing software, data visualization software, simulation software, resource, software resource, topical portal, animation software, portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest. | animation, hippocampal, hippocampus, mitochondrial, movie, neuroscience, rat, slice, wave | MRC of Canada MT10520; NIDA DA02575; NIDA DA02121; NIMH MH40165; NIDDK DK42086; NIDDK DK44840; NINDS NS-33502; NIGMS 5T32GM07151-22; NICHD HD07009 |
PMID:9614233 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25609 | SCR_008372 | GIF Animations | 2026-02-16 09:47:10 | 0 | |||||||
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MODELLER Resource Report Resource Website 5000+ mentions |
MODELLER (RRID:SCR_008395) | software application, portal, software resource, topical portal, simulation software, data or information 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 | 2026-02-16 09:47:10 | 5736 | ||||||||
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SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | data acquisition software, software application, data processing software, software resource | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | 2026-02-16 09:49:12 | 213 | |||||||||
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Protomo Resource Report Resource Website 1+ mentions |
Protomo (RRID:SCR_017296) | data processing software, software application, software resource, image processing software | Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler. | electron, tomography, 3D, image, processing | NIGMS GM30598; NIGMS GM64346 |
PMID:16973379 | Restricted | SCR_017296 | 2026-02-16 09:49:12 | 4 | |||||||||
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RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | software application, web service, data access protocol, software resource, simulation software | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | 2026-02-16 09:49:26 | 149 | ||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-02-16 09:49:33 | 4 | ||||||||
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Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | software application, data processing software, software toolkit, data analysis software, software resource | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NIH Office of the Director DP2 OD00667; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NHGRI P50 HG006193; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | Monocle, Monocle 3 | 2026-02-16 09:49:31 | 270 | ||||||
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BpForms Resource Report Resource Website |
BpForms (RRID:SCR_018653) | data access protocol, software resource, web service, software toolkit | Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. | Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools |
uses: BcForms is used by: ObjTables is used by: Datanator is listed by: Debian is listed by: bio.tools is related to: BcForms is related to: ObjTables |
NIBIB P41 EB023912; NSF 1649014; NIGMS R35 GM119771 |
PMID:32423472 | Free, Freely available | biotools:bpforms | https://bio.tools/bpforms | SCR_018653 | 2026-02-16 09:49:30 | 0 | ||||||
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ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | software application, data processing software, software toolkit, data management software, software resource | Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. | Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools |
uses: BpForms uses: BcForms is listed by: bio.tools is listed by: Debian is related to: BpForms |
NIBIB P41 EB023912; NSF 1649014; NIGMS R35 GM119771 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | 2026-02-16 09:49:33 | 0 | |||||||
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PhyDyn Resource Report Resource Website 10+ mentions |
PhyDyn (RRID:SCR_018544) | software application, software resource, simulation software | Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST. | Bayesian phylogenetic inference, epidemiological modelling, epidemiological parameter estimation, pathogen phylogeny estimation |
is related to: BEAST2 is related to: BEAST |
NIGMS U01 GM110749; MRC Centre for Global Infectious Disease Analysis |
PMID:30422979 | Free, Available for download, Freely available | SCR_018544 | 2026-02-16 09:49:31 | 10 | ||||||||
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MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | service resource, data access protocol, software resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; NHGRI U01 HG006476; NCI K22 CA188163; NCATS UL1 TR001114; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info https://bio.tools/mygene.info https://bio.tools/mygene.info |
SCR_018660 | 2026-02-16 09:49:30 | 20 |
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