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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DISEASES Resource Report Resource Website 500+ mentions |
DISEASES (RRID:SCR_015664) | data or information resource, database | Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence. | disease, gene, disease-gene association, text-mining, , bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation Center for Protein Research NNF14CC0001; European Union Seventh Framework Programme n259348 |
PMID:25484339 | biotools:diseases | https://bio.tools/diseases | SCR_015664 | 2026-08-15 11:25:14 | 655 | |||||||
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TISSUES Resource Report Resource Website 10+ mentions |
TISSUES (RRID:SCR_015665) | data or information resource, database, web application, software resource | Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. | tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools |
uses: BRENDA Tissue and Enzyme Source Ontology is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation NNF14CC0001; NCI U54 CA189205-01; CSIRO’s OCE Science Leader program |
PMID:26157623 | Freely available, Free, Available for download | biotools:tissues | https://bio.tools/tissues | SCR_015665 | TISSUES: Tissue Expression Database, Tissue Expression Database | 2026-08-15 11:25:15 | 45 | |||||
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MIDAS Resource Report Resource Website 1+ mentions |
MIDAS (RRID:SCR_015704) | image analysis software, image processing software, data processing software, software application, software resource | Software for processing, display, and analysis of magnetic resonance spectroscopic imaging data. MIDAS supports a "whole-brain" MRSI acquisition method that has been implemented on MRI systems from three major manufacturers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mrsi, magnetic resonance spectroscopic imaging, processing software, brain imaging | NIBIB R01EB00822; NIBIB R01EB016064 |
PMID:16763967 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015704 | MIDAS Software, Metabolite Imaging and Data Analysis System, MIDAS: Metabolite Imaging and Data Analysis System | 2026-08-15 11:25:15 | 1 | ||||||||
|
Evolutionary Rate Covariation Resource Report Resource Website 1+ mentions |
Evolutionary Rate Covariation (RRID:SCR_015669) | ERC | data processing software, web application, software application, data analysis software, software resource | Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes. | statistical software, correlation, phylogeny, gene extraction, genetic evolutionary history, covariation, group analysis | PMID:25679399 PMID:24453993 PMID:22287101 |
Freely available, Free, Available for download | SCR_015669 | ERC: Evolutionary Rate Covariation, Evolutionary Rate Covariation (ERC) Analysis, Evolutionary Rate Covariation (ERC) | 2026-08-15 11:25:14 | 2 | ||||||||
|
Connectivity Map 02 Resource Report Resource Website 100+ mentions |
Connectivity Map 02 (RRID:SCR_015674) | cmap | data or information resource, database, web application, software resource | Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription, expression, gene, drug, disease pattern-matching algorithm, FASEB list |
has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
PMID:17008526 | THIS RESOURCE IS NO LONGER IN SERVICE | https://www.broadinstitute.org/cmap_build01 | SCR_015674 | Broad Institute Connectivity Map 02 Build, cmap | 2026-08-15 11:25:14 | 243 | ||||||
|
Mendeley Data Resource Report Resource Website 100+ mentions |
Mendeley Data (RRID:SCR_015671) | data or information resource, storage service resource, service resource, data repository | Cloud-based data repository for storing, publishing and accessing scientific data. Mendeley Data creates a permanent location and issues Force 11 compliant citations for uploaded data. | data repository, published data, citation, force 11, doi, dans, dans (data archiving and networking services) |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: Mendeley works with: DANS |
Free, Public, The research community can contribute to this resource, Account required | DOI:10.25504/FAIRsharing.3epmpp, DOI:10.17616/R3DD11, r3d100011868, DOI:10.17632 | https://doi.org/10.17616/R3DD11, https://doi.org/10.17616/r3dd11, https://doi.org/10.17632/, https://dx.doi.org/10.17632/, https://fairsharing.org/10.25504/FAIRsharing.3epmpp, https://doi.org/10.17616/R3DD11 | SCR_015671 | 2026-08-15 11:25:15 | 239 | ||||||||
|
TurboFIRE Resource Report Resource Website 1+ mentions |
TurboFIRE (RRID:SCR_015518) | data processing software, software application, data analysis software, software resource | Real-time task-based and resting-state fMRI analysis software. This software is developed and distributed to researchers by NeurInsight LLC. | fmri, fmri analysis, resting-state | Available to affiliated researchers | SCR_015518 | 2026-08-15 11:25:03 | 4 | |||||||||||
|
SpineML_2_BRAHMS Resource Report Resource Website 1+ mentions |
SpineML_2_BRAHMS (RRID:SCR_015640) | software application, software resource, simulation software, source code | Simulation software which can execute neural network models specified in the SpineML format (an extension of the INCF's NineML). It is used as the canonical simulator backend by SpineCreator and translates the SpineML specification of the model into object code and a SystemML specification of the network. | spineml, brahms, spinecreator, neural network, modeling software |
uses: SpineML uses: BRAHMS |
BIMPA EP/G015627/1 | PMID:24253973 | Free, Available for download | SCR_015640 | 2026-08-15 11:25:05 | 2 | ||||||||
|
Neurocare: Neuroconn DC-Stimulator Plus Resource Report Resource Website 1+ mentions |
Neurocare: Neuroconn DC-Stimulator Plus (RRID:SCR_015520) | tDCS | instrument resource | Device for administering transcranial electrical stimulation. It has applications in cranial electrotherapy that provides a weak direct current for non-invasive Interventional Neurophysiology. | commercial resource, material resource, hardware, transcranial electrical stimulation, cranial electrotherapy, tES, instrument, equipment, USEDit | PMID:26889687 | Commercially available, Available for purchase | https://drive.google.com/file/d/1SPn3_PCUego80oGB2-uPK7aUTmv62wry/view?usp=drivesdk | https://info.neurocaregroup.com/hubfs/neuroCare_May_2021/pdf/pb_dcsp_en.pdf | SCR_015520 | 2026-08-15 11:25:13 | 7 | |||||||
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DTI FiberTrak MR Clinical application Resource Report Resource Website |
DTI FiberTrak MR Clinical application (RRID:SCR_015521) | image analysis software, data processing software, software application, data analysis software, resource, software resource | Instrument and software tool used to visualize, trace, analyze, and process white matter fiber tracts of Diffusion Tensor Imaging (DTI) data in real-time. It supports pre-operative surgical planning, post-surgery evaluation, and general evaluation of fiber tracts around tumors and lesions in connection with functional areas. | white matter fiber tract, dti analysis, diffusion tensor imaging analysis, surgical preparation, surgical evaluation, hardware, instrument, equipment | Commercially available | SCR_015521 | Philips DTI FiberTrak, DTI FiberTrak | 2026-08-15 11:25:14 | 0 | ||||||||||
|
BRAHMS Resource Report Resource Website 10+ mentions |
BRAHMS (RRID:SCR_015642) | software resource | Simulation software that runs network simulations where the network is specified in its own format called SystemML. The components of the network can be implemented in C, C++, Python or Matlab and are used in SpineML_2_BRAHMS to provide a simulation back-end for SpineML models. | neural network, simulation, modeling software, spineml, systemml, c, c++, python, matlab | is used by: SpineML_2_BRAHMS | DOI:10.1016/j.aei.2009.08.002 | Free, Available for download | http://brahms.sourceforge.net/home/ | SCR_015642 | 2026-08-15 11:25:05 | 19 | ||||||||
|
Phobius Resource Report Resource Website 500+ mentions |
Phobius (RRID:SCR_015643) | production service resource, web service, data access protocol, software resource, service resource, analysis service resource | Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states. | Signal peptide prediction, whole genome annotation, transmembrane region, protein prediction, transmembrane topology, signal peptide, fasta, hidden markov model | is listed by: SoftCite | PMID:15111065 PMID:30976793 |
Freely Available, Free, Available for download | SCR_018767 | http://phobius.binf.ku.dk/, https://www.ebi.ac.uk/Tools/pfa/phobius/ | SCR_015643 | PHOBIUS | 2026-08-15 11:25:05 | 553 | ||||||
|
HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | data processing software, software application, data analysis software, source code, software resource, sequence analysis software | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2, https://bio.tools/hisat2, https://sources.debian.org/src/hisat2/ | SCR_015530 | HISAT | 2026-08-15 11:25:03 | 20753 | |||||
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Platanus Resource Report Resource Website 100+ mentions |
Platanus (RRID:SCR_015531) | data processing software, software application, data analysis software, software resource, sequence analysis software | De novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo sequence assembly, genomic sequence reconstruction, shotgun sequence data | DOI:10.1101/gr.170720.113 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015531 | PLATform for Assembling NUcleotide Sequences, Platanus - PLATform for Assembling NUcleotide Sequences, Platanus Genome Assembler | 2026-08-15 11:25:14 | 201 | |||||||||
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Elastica2D Resource Report Resource Website 1+ mentions |
Elastica2D (RRID:SCR_015858) | data processing software, data or information resource, software application, model, software resource, data visualization software | Software for a 2D elastic beam model that can be used to model quasistatic bending of the vibrissa to compute forces and bending moments at the base. Elastica2D is part of the Digital Rat software project that that aims to enable morphologically and mechanically accurate modelling of the rat head and vibrissal (whisker) array. | matlab, quasistatic bending, vibrissa, 2d model, elastic, elastic beam, mechanical model | is used by: MATLAB | National Science Foundation 0446391; National Science Foundation 0818414; National Science Foundation 0846088 |
PMID:22298834 | Free, Available for download | SCR_015858 | 2026-08-15 11:25:18 | 1 | ||||||||
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Quantum Biology Institute Resource Report Resource Website |
Quantum Biology Institute (RRID:SCR_015855) | service resource, access service resource | Institute that provides resources and researches the concepts and mechanisms which underlie the complexities of biology. In particular, it incorporates concepts in physics and mathematics to resolve, unravel, and explain complex biological mechanisms and conditions. | physics, mathematics, quantum biology, biological mechanism | Available to the scientific community | http://www.nitrc.org/projects/foliations_2050/ | SCR_015855 | 2026-08-15 11:25:17 | 0 | ||||||||||
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Stanford Diabetes Research Center Resource Report Resource Website 1+ mentions |
Stanford Diabetes Research Center (RRID:SCR_015856) | service resource, access service resource | University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University. | stanford, diabetes, research center, niddk, service resource |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers has organization facet: Stanford Diabetes Research Center Diabetes Immune Monitoring Core has organization facet: Stanford Diabetes Research Center Stanford Islet Research Core has organization facet: Stanford Diabetes Research Center Diabetes Clinical and Translational Core has organization facet: Stanford Diabetes Research Center Diabetes Genomics Analysis Core is organization facet of: Diabetes Research Centers |
NIDDK P30 DK116074 | Available to the scientific community | SCR_015856 | 2026-08-15 11:25:09 | 1 | |||||||||
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Clinical Trials in Organ Transplantation (CTOT) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) | CTOT | project portal, portal, data or information resource, consortium, organization portal | Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients. | graft, graft patient, patient survival, clinical study, transplant, transplant recipient, mechanistic study |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers is related to: Clinical Trials in Organ Transplantation in Children (CTOT-C) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015859 | Clinical Trials in Organ Transplantation | 2026-08-15 11:25:17 | 1 | |||||||
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Clinical Trials in Organ Transplantation in Children (CTOT-C) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) | CTOT-C | project portal, portal, data or information resource, consortium, organization portal | Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients. | heart, kidney, lung, pediatric, cooperative research program, niaid, clinical study, mechanistic study, transplant |
is listed by: NIDDK Information Network (dkNET) is related to: Clinical Trials in Organ Transplantation (CTOT) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015860 | NIAID Clinical Trials in Organ Transplantation in Children, Clinical Trials in Organ Transplantation in Children, NIAID CTOT-C | 2026-08-15 11:25:09 | 1 | |||||||
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SpiCoDyn Resource Report Resource Website 1+ mentions |
SpiCoDyn (RRID:SCR_015744) | data processing software, software application, data analysis software, source code, software resource | Software for the analysis of multi-site neuronal spike signals. SPICODYN processes electrophysiological signals, focusing on spiking and bursting dynamics and functional-effective connectivity analysis. | spike signal, neuron, multi-site neuronal spike signal, eeg, electrophysiology, brain imaging | Open source, Available for download | SCR_015744 | 2026-08-15 11:25:15 | 2 |
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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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