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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Arabidopsis thaliana Genome Database Resource Report Resource Website 10+ mentions |
Arabidopsis thaliana Genome Database (RRID:SCR_001901) | AtGDB | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing. | expressed sequence tag, est sequence, contig, gene structure, genome, arabidopsis thaliana, cdna, plant database, blast, annotation | has parent organization: Iowa State University; Iowa; USA | NSF IOS-0606909; NSF DBI-0110254; NSF DBI-0321600 |
PMID:16219921 PMID:14681433 PMID:12805580 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02582 | SCR_001901 | Arabidopsis thaliana Genome DB | 2026-08-05 10:43:29 | 10 | |||||
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OpenTopography Resource Report Resource Website 10+ mentions |
OpenTopography (RRID:SCR_002204) | OpenTopo | data or information resource, data repository, service resource, storage service resource | Accepts and provides access to high-resolution (meter to sub-meter scale) Earth science-oriented topography data (e.g. LiDAR) and bathymetric data, and related tools and resources. The OpenTopography Tool Registry provides a community populated clearinghouse of software, utilities, and tools oriented towards high-resolution topography data (e.g. collected with LiDAR technology) handling, processing, and analysis. Tools registered range from source code to full-featured software applications. Contributions to the registry via the Contribute a Tool page are welcome. OpenTopography also hosts a dataset catalog to which users can register datasets hosted elsewhere; these entries are discoverable by users alongside OpenTopography hosted datasets. Lidar point cloud data are available in LAS, LAZ and ASCII formats. Raster datasets and derived products can be downloaded in Arc ASCII, IMG, and GeoTIFF formats. Derived products and visualizations are available in Google Earth KML format. The OpenTopography user community and advisory committee provides feedback to define the scope of collaborations on data hosting and cyberinfrastructure development | topography, topographical surveying, cloud, earth sciences, aerial photography, topographic map, geography, bathymetric map, geological mapping, geographic information system, bathymetry |
is listed by: CINERGI is listed by: re3data.org is listed by: DataCite has parent organization: San Diego Supercomputer Center has parent organization: University of California; California; USA |
NSF 1948997; NSF 1948994; NSF 1948857 |
Free, Available for download, Freely available | nlx_154717, r3d100010655 | https://api.datacite.org/dois?prefix=10.5069, https://doi.org/10.17616/R3J616 | SCR_002204 | , OpenTopography Facility, Open Topography, NSF OpenTopography Facility | 2026-08-05 10:43:35 | 14 | |||||
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BCO-DMO Resource Report Resource Website 10+ mentions |
BCO-DMO (RRID:SCR_002191) | BCO-DMO | data or information resource, data repository, data set, storage service resource, service resource | Accepts and provides access to marine biogeochemical and ecological data sets from NSF-funded research programs. BCO-DMO is also the data repository for the US GLOBEC and JGOFS programs. | marine, biogeochemical, ecological, ocean, oceanographic, biology, polar |
is listed by: CINERGI has parent organization: Woods Hole Oceanographic Institution; Massachusetts; USA |
NSF | The community can contribute to this resource, For use by the academic and scientific community, Acknowledgement required, See terms of use, Non-commercial, Commercial with written permission | nlx_154701 | SCR_002191 | Biological and Chemical Oceanography Data Management Office, Biological & Chemical Oceanography Data Management Office | 2026-08-05 10:43:35 | 26 | ||||||
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National Center for Earth-Surface Dynamics Resource Report Resource Website |
National Center for Earth-Surface Dynamics (RRID:SCR_002195) | NCED | data or information resource, data repository, database, storage service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Field, laboratory, and model data related to earth-surface dynamics created or compiled by NCED-funded scientists. NCED is a Science and Technology Center developed to predict the coupled dynamics and co-evolution of landscapes and their ecosystems in order to transform management and restoration of the Earth-surface environment. | landscape, ecosystem, data set |
is listed by: CINERGI has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NSF | Free, Freely available | r3d100011295, nlx_154715 | https://doi.org/10.17616/R3XW6D | SCR_002195 | NCED Data Repository | 2026-08-05 10:43:35 | 0 | |||||
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National Snow and Ice Data Center Resource Report Resource Website 10+ mentions |
National Snow and Ice Data Center (RRID:SCR_002220) | NSIDC | data or information resource, data repository, image collection, database, storage service resource, service resource | National data center / repository for snow and ice data including snow, ice, glaciers, frozen ground, and climate interactions that make up Earth's cryosphere. The center manages and distributes scientific data, creates tools for data access, supports data users, performs scientific research, and educates the public about the cryosphere. Users may explore the Earth's frozen places in the collection of photographs and images. Photographs from field research trips, images captured by satellites of the changing cryosphere, and photos and images are available. Data sets are organized into the following groups: sea ice, frozen ground, snow cover, snow hydrology, glaciers and ice sheets, arctic people. | polar, snow, ice, climate, photo, visualization, sea ice, arctic, meteorology, frozen, antarctica, arctic region, sea ice, satellite, ice sheet, global warming, glacier, frozen ground, cryosphere, climatology, arctic people, snow cover, snow hydrology, catalog, data set, interaction, FASEB list |
is listed by: CINERGI is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: University of Colorado Boulder; Colorado; USA is parent organization of: Antarctic Glaciological Data Center is parent organization of: ACADIS Gateway |
NASA ; NSF ; NOAA |
PMID:32116128 | Public, Unless specifically stated that the information has limitations for its use, Acknowledgement requested, Free, Photos come from a variety of sources, And may have different copyright restrictions and credits. | DOI:10.7265, nlx_154742, DOI:10.25504/FAIRsharing.k9vqye, DOI:10.17616/R3HP4V, DOI:10.5067/ | https://doi.org/10.17616/R31NJMJB, https://doi.org/10.17616/r3HP4V, https://doi.org/10.7265/, https://dx.doi.org/10.7265/, https://fairsharing.org/10.25504/FAIRsharing.k9vqye, https://doi.org/10.5067/, https://dx.doi.org/10.5067/ | SCR_002220 | National Snow & Ice Data Center | 2026-08-05 10:43:36 | 48 | ||||
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RFMix Resource Report Resource Website 1+ mentions |
RFMix (RRID:SCR_027030) | software application, software resource | Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. | Discriminative Modeling, local ancestry and admixture inference, | NLM LM007033; NHGRI 2R01HG003229; NSF |
PMID:23910464 | Restricted | SCR_027030 | 2026-08-04 09:46:08 | 5 | |||||||||
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ReDU Resource Report Resource Website 1+ mentions |
ReDU (RRID:SCR_025105) | data access protocol, software resource, web service | Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE. | Mass Spectrometry data, find uniformly formatted public MS/MS data, formatted metadata, Global Natural Product Social Molecular Networking Platform, GNPS, find and re-analyze public Mass Spectrometry data, ReDU metadata standards, data validator, | has parent organization: University of California at San Diego; California; USA | NIGMS P41 GM103484; NCI R03 CA211211; NIGMS R01 GM107550; Sloan Foundation ; Gordon and Betty Moore Foundation ; American Society for Mass Spectrometry ; NSF ; Netherlands eScience Center ; FAPESP ; Krupp Endowed Fund ; US Office of Naval Research ; University of California ; San Diego Center for Microbiome Innovation SEED grants |
PMID:32807955 | Free, Freely available | SCR_025105 | Reanalysis of Data User | 2026-08-04 09:45:41 | 1 | |||||||
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SIMS Resource Report Resource Website 1+ mentions |
SIMS (RRID:SCR_025787) | software application, software resource | Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification. | label transfer, single-cell RNA sequencing analysis, single-cell RNA-seq data classification, | Schmidt Futures ; NHGRI 1RM1HG011543; NSF ; NIMH 1U24MH132628; University of California Office of the President ; QualcommInstitute |
PMID:38823397 | Free, Available for download, Freely available | SCR_025787 | scalable, interpretable machine learning for single cell | 2026-08-04 09:45:53 | 2 | ||||||||
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PAMGO Resource Report Resource Website 1+ mentions |
PAMGO (RRID:SCR_000022) | PAMGO | data or information resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 10, 2016. A consortium that created universal descriptors to describe functionally similar gene products and their attributes across all organisms. In 2004, the PAMGO interest group joined the GO consortium to extend the GO to include terms describing various processes related to microbe-host interactions. The organization uses a controlled vocabulary to set a process in place to describe plant associated microbes and their interactions with their plant-hosts. These higher order terms can describe gene products of all types of symbionts (e.g. parasites, commensals, and mutualists), including prokaryotes and eukaryotes that associate with plant or animal hosts. This initiative is a multi-institutional collaborative effort to pool information and research in: the bacteria Dickeya dadantii, Pseudomonas syringae pv tomato and Agrobacterium tumefaciens, the fungus Magnaporthe grisea, the oomycetes Phytophthora sojae and Phytophthora ramorum, and the nematode Meloidogyne hapla. | ontology, plant ontology, microbe-host, controlled vocabulary, symbiosis, parasite, mutualist, commensal |
is affiliated with: Cornell University; New York; USA is affiliated with: North Carolina State University; North Carolina; USA is affiliated with: University of Wisconsin-Madison; Wisconsin; USA is affiliated with: Virginia Bioinformatics Institute has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
NSF 2005-35600-16370; NSF EF-0523736 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_92278 | SCR_000022 | Plant-Associated Microbe Gene Ontology, Plant Associated Microbe Gene Ontology, PAMGO - Plant-Associated Microbe Gene Ontology | 2026-08-05 10:43:05 | 5 | ||||||
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Sea Urchin Embryology Resource Report Resource Website |
Sea Urchin Embryology (RRID:SCR_000460) | Sea Urchin Embryology | data or information resource, training material, narrative resource, training resource | Laboratory modules designed for high school students covering sea urchin embryology including fertilization and development. | gamete, fertilization, development, experiment, sperm, high school | has parent organization: Stanford University; Stanford; California | NSF | nlx_156868 | SCR_000460 | 2026-08-05 10:43:10 | 0 | ||||||||
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bamova Resource Report Resource Website |
bamova (RRID:SCR_000510) | bamova | software resource, data processing software, software application, data analysis software | Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data). | mac os x, high throughput sequence |
is listed by: OMICtools has parent organization: University of Wyoming; Wyoming; USA |
NSF 701757 | PMID:21212231 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01532 | SCR_000510 | 2026-08-05 10:43:11 | 0 | ||||||
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Pathline Resource Report Resource Website |
Pathline (RRID:SCR_000635) | Pathline | data processing software, software application, data visualization software, data analysis software, software resource | Software visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species. The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species. | comparative functional genomics, functional data analysis, gene activity measurements, pathway data analysis, phylogenetic data analysis, ancestral relationships between species, |
has parent organization: University of Utah; Utah; USA has parent organization: Broad Institute |
NSF 0937060 | nlx_151898 | SCR_000635 | Pathline: A Tool For Comparative Genomics | 2026-08-05 10:43:12 | 0 | |||||||
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ZooBank Resource Report Resource Website 500+ mentions |
ZooBank (RRID:SCR_000901) | data or information resource, database, controlled vocabulary | A database of scientific names in zoology. ZooBank is an online, open-access, community-generated registry for zoological nomenclature. It serves as a service to taxonomists, biologists, and the global diversity informatics community. It is the Official Register of the International Commission on Zoological Nomenclature (ICZN). | zoo, bank, taxonomy, biology, global diversity, informatics, registry, zoology, iczn, official register of the international commission on zoological nomenclature, FASEB list | NSF DBI-1062441; NSF DBI-0956415 |
PMID:22977348 | nlx_156872 | SCR_000901 | 2026-08-05 10:43:16 | 551 | |||||||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | data processing software, software application, sequence analysis software, data analysis software, software toolkit, software resource | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Japan Society for the Promotion of Science ; NHGRI HG006039; NHGRI HG002096; Burroughs-Wellcome Fund ; NIGMS R01GM126567; NSF ABI 1661218; NIGMS R35GM139504 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-08-05 10:43:13 | 2763 | ||||
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3DVC Resource Report Resource Website |
3DVC (RRID:SCR_001377) | 3DVC | community building portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content. | cell, model, biological structure, molecule |
lists: Albinism database lists: ButterflyBase lists: G2P Knowledge Centre lists: Bio-Job.org lists: RettBASE: IRSF MECP2 Variation Database lists: Resource for Biocomputing Visualization and Informatics lists: National Center for Integrative Biomedical Informatics lists: Genome Network Platform lists: NeuroExplorer lists: Open Provenance Model lists: BarleyBase lists: BioModels lists: Arabidopsis Reactome lists: MEDLINE lists: bioDBcore lists: GermOnline lists: GlycoMapsDB lists: SNPHunter lists: Allen Institute for Brain Science Sleep Study lists: Coddle-Codons Optimized to Discover Deleterious LEsions lists: MicroArray and Gene Expression Markup Language lists: Fungal Genome Initiative lists: EMDataResource.org lists: University of Southern California LONI Software lists: Ontology Development and Information Extraction lists: Software Distribution Sets lists: L-Measure lists: UCSF Chimera lists: Zebrafish Neurophenome Project Database lists: Standards-based Infrastructure with Distributed Resources lists: HapMap 3 and ENCODE 3 lists: NCBI BioProject lists: SEQanswers Wiki lists: NIF Data Federation lists: SMD lists: SoyBase lists: modelcrop.org lists: BiGG Database lists: FSST - Functional Similarity Search Tool lists: LHP LHDL lists: Open Provenance Model Vocabulary lists: DiseaseMeth lists: neuroVIISAS lists: Predictive Networks lists: SitEx lists: NRCAM lists: DisGeNET lists: MCMBB lists: BARD lists: Mouse Genome Informatics (MGI) lists: European Nucleotide Archive (ENA) lists: Comparative Toxicogenomics Database (CTD) lists: PomBase lists: Stanford University HIV Drug Resistance Database lists: Database of Chemical Compounds and Reactions in Biological Pathways lists: UCSD-Nature Signaling Gateway Molecule Pages lists: IntAct lists: The WWW Virtual Library: Model Organisms lists: Helicobacter Pylori Database of Protein Interactomes lists: Genes to Cognition: Neuroscience Research Programme lists: neuroConstruct lists: ModelDB lists: 3DViewnix lists: TMRPres2D lists: Ikaros Project lists: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING lists: Interagency Modeling and Analysis Group lists: Annozilla (Annotea on Mozilla) lists: Artificial Selected Proteins/Peptides Database lists: Cancer Chromosomes lists: CATMA - Complete Arabidopsis Transcriptome MicroArray lists: Combinatorial Extension (CE) lists: ChemDB: The UC Irvine ChemDB lists: CluSTr lists: CTDatabase lists: DRC - Database of Ribosomal Crosslinks lists: Gene Expression in Tooth Database lists: GenoBase lists: GPX-Macrophage lists: Hetero-compound Information Centre- Uppsala lists: IMG lists: InSatDb lists: InterDom lists: IPD-HPA - Human Platelet Antigens lists: Max Planck Unified Proteome Database lists: Molecular Modelling DataBase lists: MegaMotifbase lists: Metalloprotein Site Database lists: MitoDat - Mendelian Inheritance and the Mitochondrion lists: Madison Metabolomics Consortium Database lists: Olfactory Receptor DataBase lists: SUPERFAMILY lists: EyeBrowse lists: Allen Institute Mouse Diversity Study lists: BIRD - Bio Info R and D lists: Bioinformatics Links Directory lists: Electroencephalogram Database: Prediction of Epileptic Seizures lists: Human Protein-Protein Interaction Mining Tool lists: Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki lists: Systems Biology Workbench lists: CellML lists: MathML lists: AraCyc lists: Biochemical Pathways database lists: CellML Model Repository lists: Cytokine Family Database lists: Bacterial Genomes lists: U.S. Pig Genome Project lists: ComBase: A Combined Database For Predictive Microbiology lists: GeneWindow lists: Comprehensive Systems-Biology Database lists: Candidate Genes to Inherited Diseases lists: MeGX lists: Mammalian Phosphorylation Resource lists: Efficient Mixed-Model Association lists: Proteome Analyst PA-GOSUB lists: PubCrawler lists: Conical: The Computational Neuroscience Class Library lists: Gene Expression Profile Analysis Suite lists: Adaptive Poisson-Boltzmann Solver lists: Aggrescan: The Hot Spot Finder lists: Distributed Annotation System lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: DNAWorks at Helix Systems lists: Microarray DB lists: Gene Relationships Across Implicated Loci lists: SEQtools lists: DeRisi Lab lists: Protein Subcellular Location Image Database lists: Open Information Integration lists: Metagenomics Program at JGI lists: BrainPeps lists: EGAN: Exploratory Gene Association Networks lists: CBioC lists: OrChem lists: Generic GO Term Finder lists: G-node portal electrophysiology data sharing lists: LegumeIP lists: Roadmap Epigenomics Project lists: TrakEM2 lists: ATID: Alternative Translational Initiation Database lists: linked life data - a semantic data integration platform for the biomedical domain lists: Crux tandem mass spectrometry analysis software lists: CellProfiler Analyst lists: Scirus - for scientific information only lists: SRS lists: KEGG lists: Antibodypedia lists: SWISS-MODEL Repository lists: BTKbase lists: ExTopoDB lists: MINAS - Metal Ions in Nucleic AcidS lists: Tripod lists: NIH electronic Research Materials catalogue lists: Alliance for Cellular Signaling Molecule Pages Database lists: Death Domain database lists: Cube-DB lists: OntoQuest lists: EASE: the Expression Analysis Systematic Explorer lists: Greglist lists: Chloroplast Genome Database lists: Montage RTS2000 lists: BGI-RISe - Beijing Genomics Institute Rice Information System lists: ApiDB CryptoDB lists: Chilibot: Gene and Protein relationships from MEDLINE lists: AutDB lists: DAVID lists: Dataverse Network Project lists: Binding MOAD lists: Biological Magnetic Resonance Data Bank (BMRB) lists: RNAhybrid lists: RegulonDB lists: Artemis: Genome Browser and Annotation Tool lists: Genomedata lists: CATSS - Child and Adolescent Twin Study in Sweden lists: Viking Viewer for Connectomics lists: SpliceDB lists: Galaxy lists: SPM lists: Hyper Cell Line Database lists: MeGX has parent organization: University of California at San Diego; California; USA |
NSF 1216893 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152536 | http://www.3dvcell.org/conference-toward-3d-virtual-cell | SCR_001377 | 3D Virtual Cell | 2026-08-05 10:43:21 | 0 | |||||
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FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | software resource, web application | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-08-05 10:46:11 | 139 | |||||
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CellOrganizer Resource Report Resource Website 1+ mentions |
CellOrganizer (RRID:SCR_014828) | data processing software, source code, image analysis software, software application, software resource | 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 | 2026-08-05 10:46:12 | 6 | ||||||||
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NeuroManager Resource Report Resource Website 1+ mentions |
NeuroManager (RRID:SCR_015559) | software resource, software application, simulation software, source code | Simulation submission manager for computational neuroscience. It manages simulation processing, file transfers, and job submission for a heterogeneous mixture of standalone server, cluster, and cloud servers. | computational neuroscience, simulation manager, simulation management |
has parent organization: University of Texas at San Antonio; Texas; USA is hosted by: GitHub |
NSF EF 1137897; NSF DBI 1451032; NIMHD G12MD007591; Texas Advanced Computing Center |
PMID:26528175 | Open source | http://journal.frontiersin.org/article/10.3389/fninf.2015.00024/abstract | SCR_015559 | 2026-08-05 10:46:25 | 1 | |||||||
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Rosetta Resource Report Resource Website 100+ mentions |
Rosetta (RRID:SCR_015701) | software toolkit, software application, simulation software, software resource | Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. | Molecular modeling, structure prediction, computational modeling, protein analysis, enzyme design, macromolecular complexes |
is used by: trRosetta is related to: PyRosetta works with: ROSIE |
Hertz Foundation Fellowship ; NSF Graduate Research Fellowship ; Simons Foundation ; NIGMS GM078221; NIGMS GM73141; NIGMS GM114961; NIGMS GM084453; NIGMS GM111819; NSF BMAT 1507736; NCI F32 CA189246; NIGMS GM092802; NIGMS GM110089; NIGMS GM117189 |
PMID:28430426 PMID:21829626 PMID:18442991 |
Restricted | SCR_015701 | Rosetta modeling software | 2026-08-05 10:46:29 | 212 | |||||||
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AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | data processing software, source code, image analysis software, software application, alignment software, software resource | Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. | software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NSF EF 03-31494; NHGRI R01 HG2362; NSF CCF0347992 |
PMID:17237099 DOI:10.1093/bioinformatics/btl311 |
Free, Available for download | OMICS_19787 | http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ | https://sources.debian.org/src/amos-assembler/ | SCR_015969 | amap-align | 2026-08-05 10:46:31 | 388 |
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