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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Brucellosis Ontology Resource Report Resource Website |
Brucellosis Ontology (RRID:SCR_006795) | IDOBRU | data or information resource, controlled vocabulary, ontology | A biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium. | owl | is listed by: BioPortal | Zoonotic disease brucellosis | nlx_157345 | http://www.phidias.us/bbp/idobru/index.php | SCR_006795 | 2026-08-09 09:04:32 | 0 | |||||||
|
SimSeq Resource Report Resource Website 10+ mentions |
SimSeq (RRID:SCR_006947) | SimSeq | simulation software, software application, software resource | An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free | biotools:simseq, OMICS_00258 | https://bio.tools/simseq | SCR_006947 | 2026-08-09 09:04:34 | 30 | |||||||
|
RNAProt Resource Report Resource Website 1+ mentions |
RNAProt (RRID:SCR_021218) | simulation software, software application, software resource | Software tool for modelling RNA binding protein binding preferences. Used to predict RPB binding sites. Computational RBP binding site prediction framework based on recurrent neural networks. Includes functionalities from dataset generation over model training to evaluation of binding preferences and binding site prediction. | RBP, RNA Binding Protein, RNA sequences, protein binding preferences, predict RPB binding sites, neural networks |
is related to: Conda is related to: BioConda |
Free, Available for download, Freely available | SCR_021218 | 2026-08-09 09:08:00 | 1 | ||||||||||
|
Evidence Graph Ontology Resource Report Resource Website |
Evidence Graph Ontology (RRID:SCR_021225) | EVI | data or information resource, controlled vocabulary, ontology | Evidence Graph Ontology extends core concepts from W3C Provenance Ontology PROV-O to describe evidence for correctness of findings in biomedical publications. Semantic data model in EVI is expressed using OWL2 Web Ontology Language. | Biomedical ontology, W3C Provenance Ontology concepts, PROV-O, evidence for correctness of findings, biomedical publications, OWL2 Web Ontology Language, semantic data model, EVI semantic model | has parent organization: University of Virginia; Virginia; USA | Free, Freely available | SCR_021225 | 2026-08-09 09:08:00 | 0 | |||||||||
|
Allen Mouse Reference Atlas Ontology Resource Report Resource Website 1+ mentions |
Allen Mouse Reference Atlas Ontology (RRID:SCR_021000) | data or information resource, controlled vocabulary, ontology | Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree. | structure ontology, brain structure, ontology, hierarchical partonomy, anatomical structures |
is used by: Allen Mouse Brain Common Coordinate Framework is used by: Early Postnatal Developmental Mouse Brain Atlas has parent organization: Allen Institute for Brain Science |
PMID:32386544 | Free, Freely available | SCR_021000 | 2026-08-09 09:07:55 | 5 | |||||||||
|
Sustainable Grazing System Pasture Model Resource Report Resource Website |
Sustainable Grazing System Pasture Model (RRID:SCR_021854) | simulation software, software application, software resource | Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output. | simulation model, livestock systems | Free, Available for download, Freely available | SCR_021854 | SGS Pasture Model | 2026-08-09 09:07:44 | 0 | ||||||||||
|
PlaForNEA Resource Report Resource Website |
PlaForNEA (RRID:SCR_022027) | simulation software, software application, software resource | Software allows estimating growth and production at stand level of main forest species implanted in Argentine Mesopotamia such as Pino taeda, Eucalyptus grandis, Pino elliottii and Araucaria angustifolia. Areas for which models were adjusted correspond to province of Misiones, northeast of Corrientes and Concordia in province of Entre Ríos. | estimating growth and production, forest species, Argentine Mesopotamia | Free, Available for download, Freely available | https://plafornea.software.informer.com/ | SCR_022027 | PLAFORNEA | 2026-08-09 09:08:09 | 0 | |||||||||
|
SimulaBeta Resource Report Resource Website 1+ mentions |
SimulaBeta (RRID:SCR_021900) | simulation software, software application, software resource | Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model. | Open source, insulin, glucose, simulation, modelling, model, beta cell, homeostasis |
uses: CyberUnits is related to: SPINA Carb is related to: SimThyr has parent organization: Ruhr University Bochum; North Rhine-Westphalia; Germany has parent organization: Ulm University; Baden-Wurttemberg; Germany |
Deutsche Forschungsgemeinschaft (DFG) GRK 1041; Open Access Publication Funds of the Ruhr-Universität Bochum ; Germany ; Ministry of Education (MOE) Singapore |
PMID:36271244 | Free, Available for download, Freely available | DOI:10.5281/zenodo.4922800 | https://doi.org/10.5281/zenodo.4922800 | SCR_021900 | 2026-08-09 09:08:06 | 2 | ||||||
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Mathematical Modelling Ontology Resource Report Resource Website |
Mathematical Modelling Ontology (RRID:SCR_000910) | MAMO | data or information resource, controlled vocabulary, ontology | Ontology that is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. | owl | is listed by: BioPortal | nlx_157467 | SCR_000910 | 2026-08-09 09:03:06 | 0 | |||||||||
|
Interactome Wiki Resource Report Resource Website |
Interactome Wiki (RRID:SCR_000750) | data or information resource, wiki, narrative resource | This Wiki page provides information about Interactome of various species. An interactome of a species provides an important clues on how to interpret metabolic pathways of constituent enzymes and global protein network, which facilitates in turn to understand the mechanism responsible for the cellular functions. | enzyme, function, animal, bacterial, cellular, interactome, mechanism, metabolic, pathway, plant, protein, species | nif-0000-10260 | SCR_000750 | Interactome | 2026-08-09 09:03:02 | 0 | ||||||||||
|
OpenSim Resource Report Resource Website 500+ mentions |
OpenSim (RRID:SCR_002683) | simulation software, software application, software resource | OpenSim is an open-source software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through multi-institutional collaboration. The underlying software is written in ANSI C++, and the graphical user interface (GUI) is written in Java. OpenSim technology makes it possible to develop customized controllers, analyses, contact models, and muscle models among other things. These plugins can be shared without the need to alter or compile source code. Users can analyze existing models and simulations and develop new models and simulations from within the GUI. | muscle-driven simulation, musculoskeletal biomechanics, neuromuscular simulation, modeling software, simulation software |
is related to: Simtk.org is related to: Neuromuscular Models Library has parent organization: Stanford University; Stanford; California |
Simbios ; NIGMS U54 GM072970; DARPA |
Public, Free, Acknowledgement requested | nif-0000-23308 | https://simtk.org/home/opensim, http://opensim.stanford.edu/support/index.html | SCR_002683 | 2026-08-09 09:03:34 | 612 | |||||||
|
Monte Carlo Simulation Software: tMCimg Resource Report Resource Website 1+ mentions |
Monte Carlo Simulation Software: tMCimg (RRID:SCR_002588) | tMCimg | simulation software, software application, software resource | Software application that uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available. | c, computed tomography, macos, microsoft, modeling, monte carlo, magnetic resonance, optical imaging, posix/unix-like, windows, mri, x-ray ct, ultrasound, photon | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:19424345 | Free, Available for download, Freely available | nlx_155993 | http://www.nitrc.org/projects/tmcimg | SCR_002588 | Monte Carlo Photon Transport | 2026-08-09 09:03:31 | 1 | |||||
|
Annotation Ontology Resource Report Resource Website 1+ mentions |
Annotation Ontology (RRID:SCR_002862) | AO | data or information resource, controlled vocabulary, ontology | Provides vocabulary for performing several types of annotation - comment, entities annotation (or semantic tags), textual annotation (classic tags), notes, examples, erratum... - on any kind of electronic document (text, images, audio, tables...) and document parts. AO is not providing any domain ontology but it is fostering the reuse of the existing ones for not breaking the principle of scalability of the Semantic Web. | annotation, semantic tag, text mining, semantic web, standard |
is listed by: FORCE11 is related to: Annotea is related to: W3C Open Annotation Community Group is related to: DOMEO has parent organization: Harvard Medical School; Massachusetts; USA |
EMD Serono ; Inc. ; Eli Lilly and Company |
PMID:21624159 | Free, Freely available, Available for download | nif-0000-02943 | https://www.force11.org/node/4718 | SCR_002862 | AO - Annotation Ontology, annotation-ontology | 2026-08-09 09:03:38 | 1 | ||||
|
TumorSim Resource Report Resource Website 1+ mentions |
TumorSim (RRID:SCR_002604) | simulation software, software application, software resource | Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images. | clinical neuroinformatics, magnetic resonance, mri, brain, segmentation, simulation, tumor, ground truth |
uses: BrainWeb - Simulated Brain Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
Cancer | NIBIB R01 EB000219 | PMID:19119055 | Free, Available for download, Freely available | nlx_156007 | SCR_002604 | 2026-08-09 09:03:32 | 1 | ||||||
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ChemChaste Resource Report Resource Website 1+ mentions |
ChemChaste (RRID:SCR_022208) | simulation software, software application, software resource | Software tool for simulating spatially inhomogenous biochemical reaction diffusion systems for modelling cell environment feedbacks. Simulation software for spatially organised biochemical systems. | spatially organised, biochemical systems, simulating biochemical systems, spatially inhomogenous biochemical reaction diffusion systems, modelling cell environment feedbacks | DOI:10.1101/2021.10.21.465304 | Free, Available for download, Freely available | SCR_022208 | 2026-08-09 09:08:12 | 1 | ||||||||||
|
PBSIM Resource Report Resource Website 10+ mentions |
PBSIM (RRID:SCR_002512) | simulation software, software application, software resource | Software that simulates PacBio reads by using either a model-based or sampling-based simulation. | pacbio simulation, model-based simulation, sampling-based simulation |
is listed by: OMICtools is listed by: Debian |
PMID:23129296 DOI:10.1093/bioinformatics/bts649 |
Free, Available for download, Freely available | OMICS_00253 | https://sources.debian.org/src/pbsim/ | SCR_002512 | PacBio reads simulator | 2026-08-09 09:03:27 | 11 | ||||||
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Biologic Stylus Resource Report Resource Website |
Biologic Stylus (RRID:SCR_002991) | Biologic Stylus | simulation software, software application, source code, software resource | Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python | bioinformatics, simulation | has parent organization: SourceForge | Free, Available for download, Freely available | nif-0000-30198 | SCR_002991 | biologicstylus | 2026-08-09 09:03:40 | 0 | |||||||
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Biomedical Resource Ontology Resource Report Resource Website 1+ mentions |
Biomedical Resource Ontology (RRID:SCR_004443) | BRO | data or information resource, controlled vocabulary, ontology | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The biositemaps site is no longer available but the biomedical resource ontology is still available via bioportal Biomedical Resource Ontology (BRO). | sitemap, resource type, owl, resource |
is listed by: BioPortal is listed by: Biositemaps is related to: Biositemaps is related to: iBIOFind is related to: bioDBcore has parent organization: National Centers for Biomedical Computing |
NIH | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143813 | http://bioportal.bioontology.org/ontologies/1104, https://bioportal.bioontology.org/ontologies/BRO | SCR_004443 | 2026-08-09 09:04:06 | 4 | ||||||
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Hymenoptera Anatomy Ontology Resource Report Resource Website 1+ mentions |
Hymenoptera Anatomy Ontology (RRID:SCR_003340) | HAO | data or information resource, controlled vocabulary, ontology | A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants) | owl, anatomy, organismal |
is listed by: BioPortal is listed by: OBO |
NSF DBI 0850223 | Free, Freely available | nlx_157435 | http://purl.bioontology.org/ontology/HAO, http://purl.obolibrary.org/obo/hao.owl | SCR_003340 | 2026-08-09 09:03:43 | 3 | ||||||
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NIF Cell Ontology Resource Report Resource Website |
NIF Cell Ontology (RRID:SCR_003977) | NIFCELL | data or information resource, controlled vocabulary, ontology | Ontology for cell types from NIFSTD | owl |
is listed by: BioPortal has parent organization: NIFSTD |
nlx_157492 | SCR_003977 | Neuroscience Information Framework (NIF) Cell Ontology, Neuroscience Information Framework Cell Ontology | 2026-08-09 09:03:49 | 0 |
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