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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CellOrganizer Resource Report Resource Website 1+ mentions |
CellOrganizer (RRID:SCR_014828) | software application, data processing software, source code, software resource, image analysis software | Image analysis software that learns modular models of things such as cell shape, nuclear shape, vesicular organelle distribution and microtubule distribution directly from 2D or 3D images and can produce specific instances of cell geometries without the need to create them by hand or to segment microscope images. These geometries can be combined with biochemical models to perform spatially realistic cell simulations if used in conjunction with MCell. | image analysis, source code, model, modular model, cell shape, organelle, microtubule, distribution, 2d, 3d, cell geometry |
is related to: MCell has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Alexander von Humboldt Foundation ; Freiburg Institute for Advanced Studies ; NIGMS GM075205; NIGMS GM090033; NIGMS GM103712; NSF MCB1121919; NSF MCB1121793 |
Available for download | SCR_014828 | Cell Organizer | 2026-02-17 10:02:55 | 6 | ||||||||
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Ascidian Stock Center (ASC) Resource Report Resource Website 1+ mentions |
Ascidian Stock Center (ASC) (RRID:SCR_014949) | ASC | organism supplier, biomaterial supply resource, material resource | Supplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB). | ascidian, model organism, ciona, embryology, marine organism, culturing facility | is hosted by: University of California at Santa Barbara; California; USA | NIGMS R24GM07504 | Acknowledgement requested | SCR_014949 | Ascidian Stock Center | 2026-02-17 10:02:45 | 1 | |||||||
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Caenorhabditis elegans Natural Diversity Resource (CeNDR) Resource Report Resource Website 10+ mentions |
Caenorhabditis elegans Natural Diversity Resource (CeNDR) (RRID:SCR_014958) | CeNDR | organism supplier, biomaterial supply resource, material resource | Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery. | c. elegans, caenorhabditis elegans, strains, n2, roundworm, nematode, gene analysis, organism supplier, portal | has parent organization: Northwestern University; Illinois; USA | American Cancer Society Research Scholar Award ; Amazon Web Services Research Grant ; Weinberg College of Arts and Sciences starter innovation award ; Northwestern University Start-up Funds ; NIGMS R01GM107227; NSF DGE-1324585 |
PMID:27701074 | Available to the research community | SCR_014958 | Caenorhabditis elegans Natural Diversity Resource | 2026-02-17 10:02:59 | 22 | ||||||
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CRowd Extracted Expression of Differential Signatures Resource Report Resource Website 1+ mentions |
CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) | CREEDS | software application, web application, data or information resource, data processing software, database, software resource, data visualization software | Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures. | variant, disease expression, disease marker | NIGMS R01GM098316; NHLBI U54HL127624; NCI U54CA189201 |
PMID:27667448 | Freely available, Free, Available for download | SCR_015680 | CREEDS: CRowd Extracted Expression of Differential Signatures | 2026-02-17 10:03:18 | 3 | |||||||
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TFmodeller Resource Report Resource Website 1+ mentions |
TFmodeller (RRID:SCR_015715) | software application, web application, data processing software, data analysis software, software resource, sequence analysis software, data visualization software | Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs. | protein-dna complex, comparative model, modeling software, schematic interface diagram, interface alignment, dna motif, complex coordinate | NIGMS RO1-GM071962 | PMID:17459960 | Free for academic use, Freely available, Tutorial available | http://maya.ccg.unam.mx/~tfmodell/ | SCR_015715 | 2026-02-17 10:03:18 | 1 | ||||||||
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GEN3VA Resource Report Resource Website 1+ mentions |
GEN3VA (RRID:SCR_015682) | data analysis software, software application, data processing software, software resource | Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme. | GEO2Enrichr, gene expression signatures, enrichment analyses, multiple studies, biological theme, bio.tools |
is listed by: bio.tools is listed by: Debian works with: Gene Expression Omnibus (GEO) |
NHLBI U54 HL127624; NCI U54 CA189201; NIGMS R01 GM098316 |
PMID:27846806 | Free, Freely available | biotools:gen3va | https://github.com/MaayanLab/gen3va https://bio.tools/gen3va |
SCR_015682 | GENE Expression and Enrichment Vector Analyzer | 2026-02-17 10:03:07 | 5 | |||||
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NeuroExpresso Resource Report Resource Website 10+ mentions |
NeuroExpresso (RRID:SCR_015724) | data or information resource, database, web application, software resource | Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. | mouse brain, marker gene, tissue expression, microarray, gene expression, rna sequencing | NeuroDevNet ; CAMH ; NIMH MH077159; NIMH MH111099; NIGMS 719GM076990; NSERC Discovery Grant |
Freely available | https://github.com/oganm/neuroexpresso | SCR_015724 | 2026-02-17 10:03:18 | 24 | |||||||||
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microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | data access protocol, web service, software resource | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | NIDDK U24DK133658; NIA U19AG063744; NIGMS 1DP2GM137413; Korean Government ; Austrian Science Fund ; German Research Foundation ; Sao Paulo Research Foundation ; Mexican National Council of Science and Technology ; NIGMS R01GM107550; NSF ; Research Council of Norway ; NIAID R01AI167860; NIDDK T32DK007202; NIGMS 1R01GM132649; NIGMS R35GM142938; NIDDK U01DK119702; NIH Office of the Director S10 OD021750; NLM 1R01LM013115 |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-02-17 10:04:52 | 6 | ||||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | software application, data processing software, software resource | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-02-17 10:00:10 | 5 | |||||
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Ontodog: A Web-based Ontology View Generator Resource Report Resource Website 10+ mentions |
Ontodog: A Web-based Ontology View Generator (RRID:SCR_005061) | Ontodog | production service resource, source code, service resource, software resource | Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0. | ontology, interoperability | has parent organization: University of Michigan Medical School; Michigan; USA | Rackham Pilot Research ; NIAID R01AI081062; NIGMS 5R01GM93132-1 |
nlx_144053 | SCR_005061 | 2026-02-17 10:00:43 | 17 | ||||||||
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CellProfiler Image Analysis Software Resource Report Resource Website 1000+ mentions |
CellProfiler Image Analysis Software (RRID:SCR_007358) | image analysis software, software application, data processing software, software resource | Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types. | high-throughput, high content imaging, software, image, cell, phenotype, measurement, subcellular, intensity, size, shape, analysis, algorithm |
is listed by: Debian is related to: CellProfiler Analyst has parent organization: Broad Institute |
NIGMS R01 GM089652; NIGMS RC2 GM092519; NHGRI RL1 HG004671 |
PMID:21349861 PMID:17076895 PMID:19014601 PMID:19188593 |
Free, Available for download, Freely available | SCR_010649, nlx_66812, nif-0000-00280 | https://sources.debian.org/src/cellprofiler/ | SCR_007358 | Cell Profiler, CellProfiler - cell image analysis software | 2026-02-17 10:01:14 | 3265 | |||||
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Simbios Resource Report Resource Website 1+ mentions |
Simbios (RRID:SCR_004320) | organization portal, data or information resource, training resource, journal article, software resource, postdoctoral program resource, portal | Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers. |
is related to: Biomedical Computation Review is related to: National Centers for Biomedical Computing has parent organization: Stanford University; Stanford; California is parent organization of: Simtk.org is parent organization of: Biomedical Computation Review is parent organization of: BioSimulation Course |
NIGMS U54 GM072970 | PMID:22081222 PMID:20107615 |
nlx_33018 | SCR_004320 | Simbios - NIH Center for Biomedical Computation at Stanford, physics-based Simulation of Biological Structures | 2026-02-17 10:00:14 | 1 | ||||||||
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MOPED - Model Organism Protein Expression Database Resource Report Resource Website 1+ mentions |
MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) | MOPED | data or information resource, resource, production service resource, analysis service resource, database, service resource, data analysis service | An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. | protein expression, gene expression, model organism, gene, protein, pathway, proteomics, transcriptomics, data visualization, overlap plot, heatmap, dot plot, data sharing, protein localization, gene localization |
is related to: GeneCards is related to: UniProt is related to: KEGG is related to: Reactome |
Robert B McMillen Foundation ; NSF DBI0544757; NIGMS 5R01GM076680; NIDDK UO1DK072473; NIDDK 1U01DK089571 |
PMID:24350770 PMID:22139914 |
nlx_151470 | SCR_006065 | Multi-Omics Profiling Expression Database | 2026-02-17 10:00:51 | 2 | ||||||
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EcoliWiki Resource Report Resource Website 1+ mentions |
EcoliWiki (RRID:SCR_010656) | EcoliWiki | narrative resource, data access protocol, data or information resource, software resource, web service, wiki | A component of EcoliHub, EcoliWiki is a wiki-based system for finding, editing, and adding information about E. coli K-12 and other model organism strains of E. coli. EcoliWiki is being constructed to include information about bacteriophage, plasmids, and mobile genetic elements. Information should be easily accessible and correct, and users have the right to edit any information they feel is incorrect. Most of the E. coli information was initially seeded with a subset of information from parsing EcoCyc data dumps. For phage gamma and the F plasmid, Genbank accessions were converted to GFF, which was parsed into the appropriate tables. Other sources of content include: * user additions * monthly addition of annotations from EcoCyc * structural data from the PDB * domains and motif information from InterPro * various databases including EcoGene, RegulonDB, Genbank, GenoBase, ASAP * many many scientific papers EcoliWiki participates in the RefGenome project. EcoliWiki provides REST web services as part of the EcoliHub Web Services infrastructure project. | phantom gene, genome sequence, bacteriophage, escherichia coli, e. coli, prokaryotic, gene, model organism, annotation | NIGMS U24GM088849 | nlx_68806 | SCR_010656 | 2026-02-17 10:01:50 | 4 | |||||||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie https://bio.tools/stringtie https://sources.debian.org/src/stringtie/ |
SCR_016323 | 2026-02-17 10:03:23 | 4072 | ||||||
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BioDepot-workflow-builder Resource Report Resource Website 1+ mentions |
BioDepot-workflow-builder (RRID:SCR_017402) | Bwb | software application, data processing software, software resource, workflow software | Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results. | bioinformatics, big, data, workflow, reproducible, Docker | NIGMS R01 GM126019; NHLBI U54 HL127624; NHGRI U24HG012674; NIAID R03AI159286 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-02-17 10:03:13 | 1 | ||||||||
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R/qtl2 Resource Report Resource Website 10+ mentions |
R/qtl2 (RRID:SCR_018181) | data analysis software, software application, data processing software, software resource | Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. | High density genotyping data, molecular phenotype, gene expression, proteomics, mapping trait loci, diversity outbred mice, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM074244; NIGMS R01 GM070683; NIGMS R01 GM123489 |
PMID:30591514 | Free, Available for download, Freely available | biotools:R_qtl2, SCR_020965 | https://bio.tools/R_qtl2 https://kbroman.org/qtl2 https://github.com/rqtl/qtl2 |
SCR_018181 | QTL, R/quantitative trait loci, QTL2, Quantitative Trait Locus 2, quantitative trait loci 2, R/qtl, qtl2 | 2026-02-17 10:03:02 | 13 | |||||
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ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, service resource, web service, software resource | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R35 GM118078; NIGMS R01 GM061867 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-02-17 10:03:02 | 858 | |||||||
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ConnecTF Resource Report Resource Website 1+ mentions |
ConnecTF (RRID:SCR_022577) | data access protocol, web service, software resource | Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation. | integrate transcription factor gene interactions, validate regulatory networks, gene regulatory network validation | NIGMS RO1-GM121753; NSF PGRP IOS-1339362; NSF PGRP IOS-1840761; NIGMS F32GM116347 |
PMID:33631799 | Free, Available for download, Freely available | https://github.com/coruzzilab/connectf_server | SCR_022577 | 2026-02-17 10:04:07 | 3 | ||||||||
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | image processing software, software application, data processing software, software resource | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; NIAID R01AI130303; NSF NSF-1707316; NIMH R01MH110932; NIGMS F31GM116517; NINDS R01NS095367; NIMH P50MH09427; NIH Office of the Director DP2OD006514; NINDS R01NS076467; NINDS U01NS090449; NIGMS P41GM10371; Multidisciplinary University Research Initiative Army Research Office |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-02-17 10:04:29 | 0 |
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