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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Knowledge Engineering from Experimental Design Resource Report Resource Website 1+ mentions |
Knowledge Engineering from Experimental Design (RRID:SCR_001238) | KEfED | software application, software resource | Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable. | experimental design, observation, interpretation, reasoning, experimental data, observational assertion, knowledge engineering, java |
is listed by: FORCE11 is related to: Bioscholar has parent organization: Biomedical Informatics Research Network |
NIGMS R01-GM083871; NIMH 1R01MH079068-01A2; NCRR 1 U24 RR025736-01 |
PMID:21859449 | Free, Available for download, Freely available | nif-0000-07745 | https://wiki.birncommunity.org/display/NEWBIRNCC/Knowledge+Engineering+from+Experimental+Design+%28%27KEfED%27%29 | SCR_001238 | 2026-09-05 06:32:24 | 1 | |||||
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Resource Identification Portal Resource Report Resource Website 10+ mentions |
Resource Identification Portal (RRID:SCR_004098) | RII Portal | data or information resource, portal | Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource. | antibody, organism, service resource, software resource, database, resource, identifier, citation, biomedical, publication, research resource identifier, rrid, ASWG |
uses: Antibody Registry uses: SciCrunch Registry uses: Mouse Genome Informatics (MGI) uses: Zebrafish Information Network (ZFIN) uses: Rat Genome Database (RGD) uses: WormBase uses: FlyBase recommends: SciCrunch Registry recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: Rat Genome Database (RGD) is recommended by: Neuroscience Information Framework is recommended by: SciCrunch Registry is related to: NIF Data Federation has parent organization: SciCrunch |
NIGMS R24 GM144308 | The community can contribute to this resource | nlx_158572 | SCR_004098 | Resource Identification Initiative Portal | 2026-09-05 06:32:32 | 20 | ||||||
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NIGMS Inside Life Science Resource Report Resource Website |
NIGMS Inside Life Science (RRID:SCR_005852) | Inside Life Science | data or information resource, narrative resource | The NIGMS Inside Life Science series brings you inside the science of health. Each story shows how basic biomedical researchfrom the history of a field to the people doing cutting-edge work todaylays the foundation for advances in disease diagnosis, treatment and prevention. Through explorations of how the body works and highlights from recent studies, you''ll discover even more on what scientists have found and are finding about fundamental life processes. NIGMS supported all of the featured research. | science, health, biomedical research, disease, diagnosis, treatment, prevention | has parent organization: National Institute of General Medical Sciences | NIGMS | nlx_149383 | SCR_005852 | 2026-09-05 06:32:35 | 0 | ||||||||
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LONI MiND Resource Report Resource Website |
LONI MiND (RRID:SCR_004820) | MiND | service resource, software resource | The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework. | diffusion magnetic resonance imaging, metadata, dwi, dti, software interoperability, data sharing | has parent organization: David Geffen School of Medicine at UCLA; California; USA | NIH ; NCRR ; NIMH ; NCRR 1U54RR021813-01; NIGMS 5T32GM008042-25; NCRR P41 RR013642; NIMH R01 MH71940; NIBIB EB008432; NIBIB EB008281; NIBIB EB007813; NICHD HD050735 |
PMID:20206274 | nlx_143920 | http://mind.loni.ucla.edu/ | SCR_004820 | MiND: Metadata in NIfTI for DWI, Metadata in NIfTI for DWI | 2026-09-05 06:32:34 | 0 | |||||
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zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | biomaterial supply resource, material resource | Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NHGRI HG006431; NIDA DA14546; NIGMS GM63904 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-09-05 06:32:38 | 4 | ||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCRR KL2 RR029885; NIDDK P01 DK056492; NIDDK R01 DK088541; NIDDK RC4DK090860; NIGMS P50 GM071558; NLM RC2 LM010994 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-09-05 06:33:01 | 6 | ||||
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Conservation Resource Report Resource Website 1000+ mentions |
Conservation (RRID:SCR_016064) | software application, software resource, software toolkit | Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands. | scoring, protein, sequence, conservation, Jensen-Shannon, divergence, predict, catalytic, site, bound, ligands, clustal, fasta, concave | is related to: Princeton University; New Jersey; USA | NIGMS GM076275; NIH P50 GM071508; NIH T32 HG003284; NSF IIS-0612231; NSF PECASE MCB-0093399 |
PMID:17519246 | Free, Available for download | SCR_016064 | Conservation-code | 2026-09-05 06:33:01 | 1606 | |||||||
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SAINTexpress Resource Report Resource Website 10+ mentions |
SAINTexpress (RRID:SCR_018562) | software resource, software toolkit | Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments. | Probabilistic scoring, affinity purification, mass spectrometry data, mass spectrometry experiment data, assigning confidence score, protein-protein interaction, quantitative proteomic data | NCI R01 CA126239; NCRR R01 RR024031; NIGMS R01 GM094231 |
PMID:24513533 | Free, Freely available | SCR_018562 | Significance Analysis of INTeractome Express | 2026-09-05 06:33:04 | 16 | ||||||||
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PyRosetta Resource Report Resource Website 10+ mentions |
PyRosetta (RRID:SCR_018541) | software application, software resource, standalone software | Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions. | Molecular modeling, custom structure prediction, design algorithm, energy function, scoring function, bio.tools |
uses: Python Programming Language is listed by: bio.tools is listed by: Debian is related to: Rosetta has parent organization: Johns Hopkins University; Maryland; USA |
NIGMS R01 GM078221; NIGMS R01 GM73151; NSF 0846324 |
PMID:20061306 | Free, Freely available | biotools:pyrosetta | https://bio.tools/pyrosetta | SCR_018541 | Python Rosetta | 2026-09-05 06:33:04 | 25 | |||||
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ESRseq score Resource Report Resource Website 1+ mentions |
ESRseq score (RRID:SCR_022270) | software application, software resource | Software for comprehensive quantitative measure of splicing impact of complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts. | Splicing impact quantitative measure, set of RNA 6-mer sequences, deep sequencing, successfully spliced transcripts | NIGMS GM072740 | PMID:21659425 | SCR_022270 | 2026-09-05 06:33:10 | 2 | ||||||||||
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Coarse grained co-translational folding analysis Resource Report Resource Website 1+ mentions |
Coarse grained co-translational folding analysis (RRID:SCR_022271) | software application, software resource | Software for statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved, and also co-translational protein folding model. | statistical approach, identify loci within genes, significantly enriched in slowly translated codons, co-translational protein folding model evolutionarily conserved, | NIGMS F32GM116231; NIGMS R01GM124044 |
PMID:29073068 | Free, Freely available | SCR_022271 | Coarse-grained co-translational folding analysis | 2026-09-05 06:33:10 | 1 | ||||||||
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Sparse Inverse Covariance Estimation for Ecological Association Inference Resource Report Resource Website 10+ mentions |
Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) | SPIEC-EASI | software resource, software toolkit | Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets. | inverse covariance matrix estimation, sequencing data, microbial ecological networks inference, amplicon sequencing datasets microbial ecological networks, | NIAID T32AI007180; NIDDK R01 DK103358; NIGMS RO1 GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022646 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-09-05 06:33:11 | 12 | |||||||
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Bayesian Generalized Linear Regression Resource Report Resource Website 1+ mentions |
Bayesian Generalized Linear Regression (RRID:SCR_022522) | BGLR | software resource, software toolkit | Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures. | Bayesian regression models, parametric variable selection and shrinkage methods, semiparametric procedures |
is related to: CRAN is related to: R Project for Statistical Computing |
NIGMS R01GM099992; NIGMS R01GM101219 |
PMID:25009151 | Free, Available for download, Freely available | https://github.com/gdlc/BGLR-R | SCR_022522 | 2026-09-05 06:33:10 | 6 | ||||||
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MR-PRESSO Resource Report Resource Website 100+ mentions |
MR-PRESSO (RRID:SCR_023697) | software resource, software toolkit | Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing. | Mendelian randomization, identify horizontal pleiotropic outliers, multi instrument summary level MR testing, | American Heart Association Cardiovascular Genome Phenome Discovery ; AstraZeneca ; Goldfinch Bio ; NHGRI 5U01 HG009088; NHLBI R01 HL139865; NIGMS R35 GM124836; NIMH 1R01 MH094469; NIMH 1R01 MH107649 |
PMID:29686387 | Free, Available for download, Freely available | SCR_023697 | Mendelian Randomization Pleiotropy RESidual Sum and Outlier | 2026-09-05 06:33:15 | 100 | ||||||||
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BioMesh3D Resource Report Resource Website 1+ mentions |
BioMesh3D (RRID:SCR_009534) | BioMesh3D | software application, software resource | A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. | mesh, simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
PMID:23367171 | MIT License | nlx_155708 | http://www.nitrc.org/projects/biomesh3d | SCR_009534 | 2026-09-05 06:32:52 | 3 | |||||
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Brown University Transgenic and Gene Targeting Core Facility Resource Report Resource Website |
Brown University Transgenic and Gene Targeting Core Facility (RRID:SCR_017690) | MTGTF | access service resource, core facility, service resource | MTGTF is to support the investigators in using genetically modified mouse models in Brown University, affiliated hospitals and academic institutions in Rhode Island and other states. Provides services of molecular design and generation of transgenic and knock-out mouse models as well as general advice on use and management of such models. Conventional ES cell gene-targeting system is employed to serve as alternative or to fill the limitations of CRISPR/Cas9 system. Routine services include genotype analysis, sperm or embryo cryopreservation and storage, rederivation, in vitro fertilization (IVF). Other services, such as mouse vasectomy, embryo transfer, colony scale-up, intracytoplasmic sperm injection (ICSI) are also available. New services requiring MTGTF resources can be created through request. | Genetically, modified, mouse, model, support, molecular, design, transgenic, knock-out, ES, cell, targeting, system, CRISPR/Cas9, genotype, analysis, sperm, embryo, cryopreservation, storage, fertilization, vasectomy, service, core | NIGMS P30 GM103410 | Open | ABRF_79, SCR_017708 | SCR_017690 | Mouse Transgenic and Gene Targeting Facility | 2026-09-05 06:34:10 | 0 | |||||||
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Kansas University at Lawrence High Throughput Screening Laboratory Core Facility Resource Report Resource Website 1+ mentions |
Kansas University at Lawrence High Throughput Screening Laboratory Core Facility (RRID:SCR_017752) | KU-HTSL | access service resource, core facility, service resource | Core offers high throughput screening of large chemical libraries of compounds to identify novel chemical entities that target biological system of interest.Provides target identification and validation, assay development, high throughput screening, hit confirmation, data mining and medicinal chemistry to facilitate hit to lead development. | Screening, large, chemical, library, compound, novel, entity, target, identification, validation, assay, development, data, mining, medicinal, chemistry, service, core | NIGMS P30 GM103495; State of Kansas ; University of Kansas |
Open | ABRF_254 | SCR_017752 | High Throughput Screening Laboratory at KU | 2026-09-05 06:34:11 | 1 | |||||||
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University of New England In Vivo Behavior Core Facility Resource Report Resource Website 1+ mentions |
University of New England In Vivo Behavior Core Facility (RRID:SCR_017883) | access service resource, core facility, service resource | Core provides technical expertise, training, instrumentation and related services for assessing behavior in animals to help to gain insight into function of nervous system and mechanisms of acute and chronic pain. Services include Behavioral Testing; General Behavioral Phenotyping: Observational Screens, Motor Function; Pain/Sensory Testing: Thermal, Mechanical, Chemical; Additional Neurobehavioral Tests: Psychiatric, Addiction, Learning and Memory;Miscellaneous Systems: GI Transit, Cardiovascular and Respiration. Other Services: Assistance choosing behavioral test and statistical tests for assessing results; Training in surgical techniques for small animal surgeries; Staff expertise includes surgical methods for producing pain models; dosing of drugs/anesthetics including central, systemic and localized administration; and tissue extractions. | in vivo, behavior, pain, sensory testing, training, function, addiction, neuropathic, CIPN, , system, acute, chronic, mechanism, motor, learning, memory, neurobehavioral |
is listed by: ABRF CoreMarketplace has parent organization: University of New England; Biddeford; USA |
NIGMS P30GM145497 | Open | https://coremarketplace.org/?FacilityID=758 | SCR_017883 | In Vivo Behavior Core | 2026-09-05 06:34:14 | 1 | |||||||
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Nemours/A.I.duPont Hospital for Children Cell Science Core Facility Resource Report Resource Website |
Nemours/A.I.duPont Hospital for Children Cell Science Core Facility (RRID:SCR_017854) | CSC | access service resource, core facility, service resource | Core specializes in cell, protein, and small molecules analysis as well as cell culture techniques. Services include:2-D gel electrophoresis, 2-D DIGE, LC-MS/MS, HPLC, flow cytometry, fluorescence-activated cell sorting (FACS), cell and tissue culture, and immortalization of cell lines. Our staff works closely with investigators to help design, perform, and analyze experiments.Offers training and assistance in flow cytometry, tissue culture, and operation many of our walk-up instruments.Instruments:Cell Sorter: FACS Aria III, BD Biosciences;Flow Cytometers, analyzers:C6, Accuri/BD Biosciences;Novocyte 3000, ACEA Biosciences;software for analysis: FSC Express, DeNovo software;LC-MS/MS: 6460 Triple Quadrupole, Agilent;Typhoon Trio Scanner, GE Lifesciences;Blood Analyzer: Hemavet 950, Drew Scientific.Plate Readers:;Victor Nivo 5F, Perkin Elmer;Luminometer: Centro XS, Berthold.Services:Cell Sorting (FACS);2-D gel electrophoresis/2D-DIGE;LC-MS/MS analysis of compounds; Cell immortilization. | Cell, protein, small, molecules, analysis, culture, electrophoresis, 2D DIGE, LC-MS/MS, HPLC, FACS, immortalization, flow, cytometry, sorting, training, service, core, | NIGMS P30 GM114736 | Open | ABRF_662 | SCR_017854 | Cell Science Core | 2026-09-05 06:34:14 | 0 | |||||||
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University of Nebraska Medical Center Animal Behavior Core Facility Resource Report Resource Website 1+ mentions |
University of Nebraska Medical Center Animal Behavior Core Facility (RRID:SCR_018830) | access service resource, core facility, service resource | Provides investigators with expertise, equipment, and space that is required to conduct innovative acoustic, behavioral, and cognitive research with focus on rigor, reproducibility, and maintaining the highest standards of animal welfare. | USEDit, acoustic, behavioral, cognitive, expertise, equipment, space service, ABRF, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Nebraska; Nebraska; USA |
NIGMS 1P20GM130447 | Restricted | ABRF_1021 | https://coremarketplace.org/?FacilityID=1021 | SCR_018830 | UNMC Animal Behavior Core, University of Nebraska Medical Center UNMC Animal Behavior Core, Animal Behavior Core | 2026-09-05 06:34:17 | 7 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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