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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-02-13 10:57:50 | 5 | ||||||||
|
BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data analysis software, software resource, data processing software, software application | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download https://bio.tools/binpacker |
SCR_017038 | 2026-02-13 10:57:50 | 10 | ||||||
|
CCPN Data Model Resource Report Resource Website |
CCPN Data Model (RRID:SCR_016982) | data repository, storage service resource, data processing software, data storage software, data or information resource, service resource, software application, software resource, database | 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 | 2026-02-13 10:57:54 | 0 | |||||||
|
exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | ontology, data repository, storage service resource, application programming interface, data analysis service, expression atlas, portal, analysis service resource, consortium, data or information resource, production service resource, organization portal, service resource, controlled vocabulary, atlas, data access protocol, software resource, database | 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 | 2026-02-13 10:57:55 | 24 | |||||||
|
RNAstructure Resource Report Resource Website 10+ mentions |
RNAstructure (RRID:SCR_017216) | web service, analysis service resource, production service resource, service resource, software application, data access protocol, software resource, simulation software | 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 | 2026-02-13 10:57:53 | 42 | ||||||||
|
SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | software resource, data processing software, data acquisition software, software application | 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 | 2026-02-13 10:57:55 | 213 | |||||||||
|
Protomo Resource Report Resource Website 1+ mentions |
Protomo (RRID:SCR_017296) | image processing software, software resource, data processing software, software application | 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 | 2026-02-13 10:57:54 | 4 | |||||||||
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data analysis software, software resource, data processing software, software application | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-02-13 10:57:22 | 3702 | |||||
|
libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | software resource, simulation software, software application | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | 2026-02-13 10:57:20 | 11 | ||||||
|
NMRbox Resource Report Resource Website 50+ mentions |
NMRbox (RRID:SCR_014827) | software resource, software toolkit, web application | Computing platform for biomolecular NMR available to not-for-profit or government users. It consists of a virtual machine (VM) provisioned with dozens of widely-used NMR software packages, and is available as a cloud-based Platform-as-a-Service (PaaS) or as a downloadable VM for local execution. | Nuclear Magnetic Resonance, nmr, spectra, computing platform, platform, virtual machine, cloud, software toolbox | NIGMS P41GM111135 | Account required | SCR_014827 | , Nuclear Magnetic Resonance box, NMRbox.org | 2026-02-13 10:57:25 | 78 | |||||||||
|
Track-A-Worm Resource Report Resource Website 1+ mentions |
Track-A-Worm (RRID:SCR_018299) | data analysis software, software resource, data processing software, software application | Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification. | Quantitative assessment, C.Elegans locomotory, bending behavior, behavioral analysis, gene, moving worm position, body shape, automated recording | is related to: University of Connecticut; Connecticut; USA | NIGMS R01 GM083049; NIMH R01 MH085927 |
PMID:23922769 | Free, Available for download, Freely available | SCR_018299 | Tracker-A-Worm version 1.0, Tracker-A-Worm version 2.0 | 2026-02-13 10:58:10 | 3 | |||||||
|
RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | web service, software application, 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 | 2026-02-13 10:58:17 | 149 | ||||||
|
UltraScan Resource Report Resource Website 10+ mentions |
UltraScan (RRID:SCR_018126) | data analysis software, software resource, data processing software, software application | Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. | Hydrodynamic data, analytical ultracentrifugation experiment, data editing, analysis, sedimentation velocity experiment, spectrum analysis, genetic algorithm, Monte Carlo analysis | NSF DBI 9724273; NSF DBI 9974819; NSF ANI 228927; NSF TG-MCB 060019T; NSF TG-MCB 070038; NSF TG-MCB 070039; NSF TG-MCB 070040; NSF OCI 1032742; NSF ACI 1339649; NCRR RR022200; NCRR RR 022200 03S1; NIGMS GM120600; San Antonio Life Science Institute ; Howard Hughes Medical Institute ; Robert J. Kleberg Jr. and Helen C. Kleberg Foundation |
Free, Available for download, Freely available | SCR_018126 | 2026-02-13 10:58:09 | 20 | ||||||||||
|
TimeZone Resource Report Resource Website 1+ mentions |
TimeZone (RRID:SCR_018564) | data analysis software, software resource, data processing software, software application | Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes. | Detect footprint, positive selection, functionally adaptive, point mutation, microbial genome | NIGMS R01 GM084318; NIAID RC4 AI092828 |
PMID:23471110 | Free, Available for download, Freely available | SCR_018564 | 2026-02-13 10:58:15 | 1 | |||||||||
|
Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | data processing software, data analysis software, software toolkit, software application, 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 | 2026-02-13 10:58:16 | 270 | ||||||
|
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 | 2026-02-13 10:58:14 | 0 | ||||||
|
ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data processing software, data management software, software toolkit, software application, 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 | 2026-02-13 10:58:14 | 0 | |||||||
|
PhyDyn Resource Report Resource Website 10+ mentions |
PhyDyn (RRID:SCR_018544) | software resource, simulation software, software application | 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 | 2026-02-13 10:58:13 | 10 | ||||||||
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MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, software resource, web service, service resource | 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 | 2026-02-13 10:58:16 | 20 | ||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | web service, analysis service resource, production service resource, service resource, data access protocol, software 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 | 2026-02-13 10:58:22 | 4 |
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