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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of Washington Integrated Brain Project Resource Report Resource Website 1+ mentions |
University of Washington Integrated Brain Project (RRID:SCR_008075) | data or information resource, software resource, controlled vocabulary, ontology | The UW Integrated Brain Project is one project within the national Human Brain Project, a national multi-agency effort to develop informatics tools for managing the exploding amount of information that is accumulating about the human brain. The objective of the UW Integrated Brain Project effort is to organize and integrate distributed functional information about the brain around the structural information framework that is the long term goal of our work. This application therefore extends the utility of the Digital Anatomist Project by using it to organize non-structural information. The initial driving neuroscience problem that is being addressed is the management, visualization and analysis of cortical language mapping data. In recent years, advances in imaging technology such as PET and functional MRI have allowed researchers to observe areas of the cortex that are activated when the subject performs language tasks. These advances have greatly accelerated the amount of data available about human language, but have also emphasized the need to organize and integrate the sometimes contradictory sources of data, in order to develop theories about language organization. The hypothesis is that neuroanatomy is the common substrate on which the diverse kinds of data can be integrated. A result of the work done by this project is a set of software tools for generating a 3-D reconstruction of the patient''s own brain from MRI, for mapping functional data to this reconstruction, for normalizing individual anatomy by warping to a canonical brain atlas and by annotating data with terms from an anatomy ontology, for managing individual lab data in local laboratory information systems, for integrating and querying data across separate data management systems, and for visualizing the integrated results. Sponsors: This Human Brain Project research is funded jointly by the National Institute on Deafness and Other Communication Disorders, the National Institute of Mental Health, and the National Institute on Aging. | functional mri, anatomy, brain, imaging, neuroanatomy, neuroscience, open source license, pet, technology | Aging | nif-0000-10536 | SCR_008075 | UW Brain Project | 2026-08-09 09:04:57 | 1 | |||||||||
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SimTKCore Resource Report Resource Website |
SimTKCore (RRID:SCR_008268) | SimTKCore | simulation software, software application, software resource | SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications. | computational algorithm, high-performance, linear algebra, numerical integration, numerical method, optimization, monte carlo sampling, multibody dynamics, molecular force field evaluation, nonlinear root finding, optimizing, cpodes, simbody, ipopt, molmodel, mit license, linux, mac os x, windows |
is listed by: Biositemaps has parent organization: Stanford University; Stanford; California has parent organization: Simtk.org |
NIGMS U54 GM072970 | PMID:20107615 | nif-0000-23310 | SCR_008268 | 2026-08-09 09:04:58 | 0 | |||||||
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Ion Simulator Interface Resource Report Resource Website |
Ion Simulator Interface (RRID:SCR_008267) | ISIM | simulation software, software application, software resource | A simple Java graphical user interface for running the program ISIM. ISIM is a package that simulates the thermodynamic ensemble of ions around a macromolecule using a grand canonical Monte Carlo scheme and simple hard sphere ion models. It is meant to provide an alternative mechanism to mean field approaches to allow the calculation of ion distributions around a highly charged molecule using a simple model that takes into account ion-ion correlations and steric interactions. The original source was created in the McCammon group at UCSD but is no longer available. The version of ISIM used is available in the ISIM project on simtk.org. | grand canonical ensemble, monte carlo, Java, calculation, ion distribution |
is related to: Simtk.org has parent organization: University of California at San Diego; California; USA |
nif-0000-23306 | SCR_008267 | SimTK ISIM, SimTK Ion Simulator Interface | 2026-08-09 09:04:49 | 0 | ||||||||
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Hardy-Weinberg Equilibrium Calculator Resource Report Resource Website 100+ mentions |
Hardy-Weinberg Equilibrium Calculator (RRID:SCR_008371) | simulation software, software application, software resource | This portal leads to the Chi-sq Hardy-Weinberg equilibrium test calculator for biallelic markers (SNPs, indels etc), including analysis for ascertainment bias for dominant/recessive models (due to biological or technical causes.) The purpose of this web program is for estimating possible missingness and an approach to evaluating missingness under different genetic models. Mendelian randomization (MR) permits causal inference between exposures and a disease. It can be compared with randomized controlled trials. Whereas in a randomized controlled trial the randomization occurs at entry into the trial, in MR the randomization occurs during gamete formation and conception. Several factors, including time since conception and sampling variation, are relevant to the interpretation of an MR test. Particularly important is consideration of the missingness of genotypes that can be originated by chance, genotyping errors, or clinical ascertainment. Testing for Hardy-Weinberg equilibrium (HWE) is a genetic approach that permits evaluation of missingness. Through this tool, the authors demonstrate evidence of nonconformity with HWE in real data. They also perform simulations to characterize the sensitivity of HWE tests to missingness. Unresolved missingness could lead to a false rejection of causality in an MR investigation of trait-disease association. These results indicate that large-scale studies, very high quality genotyping data, and detailed knowledge of the life-course genetics of the alleles/genotypes studied will largely mitigate this risk. Sponsors: This resource is supported by an Intermediate Fellowship (grant FS/05/065/19497) from the British Heart Foundation. | gamete, genetic, allele, analysis, biallelic, biological, caluclator, conception, disease, dominant, genotype, hardy-weinberg equilibrium, marker, mendelian, model, randomization, recessive, snp, test, trait | nif-0000-25608 | SCR_008371 | HWE Calculator | 2026-08-09 09:04:58 | 103 | ||||||||||
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Discovery Studio Visualizer Resource Report Resource Website 1+ mentions |
Discovery Studio Visualizer (RRID:SCR_008398) | simulation software, software application, software resource | A life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Discovery Studio makes it easier to examine the properties of large and small molecules, study systems, identify leads and optimize candidates. Discovery Studio ADME Descriptors allow scientists to eliminate compounds with unfavorable ADME characteristics early in the discovery process and evaluate proposed structural refinements prior to synthesis. Applications of predictive ADME include pharmaceutical, cosmeceutical, and environmental sciences. | biomolecular, molecular, geometrics, alignment, metal, ion, informatics, workflow, absorption, drug discovery | nif-0000-30061 | SCR_008398 | Discovery Studio | 2026-08-09 09:04:59 | 7 | ||||||||||
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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 | |||||||||
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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 | ||||||||||
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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 | |||||||
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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 | |||||
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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 | ||||
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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 | ||||||||||
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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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Mass Spectrometry Ontology Resource Report Resource Website |
Mass Spectrometry Ontology (RRID:SCR_003579) | MS | data or information resource, controlled vocabulary, ontology | A structured controlled vocabulary for the annotation of mass spectrometry experiments. | obo |
is listed by: BioPortal has parent organization: HUPO Proteomics Standards Initiative |
nlx_157465 | SCR_003579 | 2026-08-09 09:03:50 | 0 | |||||||||
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Regulation of Gene Expression Ontolology Resource Report Resource Website |
Regulation of Gene Expression Ontolology (RRID:SCR_006124) | REXO | data or information resource, controlled vocabulary, ontology | An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations. | obo | is listed by: BioPortal | nlx_157572 | SCR_006124 | 2026-08-09 09:04:22 | 0 | |||||||||
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Student Health Record Ontology Resource Report Resource Website |
Student Health Record Ontology (RRID:SCR_005854) | SHR | data or information resource, controlled vocabulary, ontology | Ontology for the description of student health records. Student health records are created for entering college students in order to provide better health services will be formed. This file contains various sections such as history of disease, family history of disease, public examinations and ... . | owl | is listed by: BioPortal | nlx_157596 | SCR_005854 | SHR-Ontology | 2026-08-09 09:04:19 | 0 |
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