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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Simmune Resource Report Resource Website 1+ mentions |
Simmune (RRID:SCR_016618) | Simmune | software application, data processing software, data analysis software, software resource, software toolkit | Software package to define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator. | interaction, analysis, molecule, network, cell, response, external, signal |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | SCR_016618 | simulate immunological phenomena | 2026-02-17 10:02:44 | 1 | ||||||||
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McGill Cell Imaging and Analysis Network Core Facility Resource Report Resource Website 1+ mentions |
McGill Cell Imaging and Analysis Network Core Facility (RRID:SCR_012623) | McGill CIAN | service resource, access service resource, core facility | Core facility at Biology Department in McGill Faculty of Science. Expertise in Light Microscopy and Image Analysis. Provides light microscopes, ranging from Point Scanning and Spinning Disc Confocals to Multi-Photon, TIRF, Light Sheet and Super-Resolution microscopes. Provides services in Automation/High throughput screening (liquid handler, pinning robot), Protein expression and antibody production. Users get training. | Light, microscopy, image, analysis, service, automation, high, throughput, screening, protein, expression, antibody, production, training |
is listed by: ScienceExchange is related to: McGill University Labs and Facilities has parent organization: McGill University; Montreal; Canada |
Restricted | SciEx_569 | http://www.scienceexchange.com/facilities/cell-imaging-and-analysis-network-cian | SCR_012623 | McGill University Cell Imaging and Analysis Network, McGill Cell Imaging and Analysis Network (CIAN), McGill University Cell Imaging and Analysis Network (CIAN) | 2026-02-17 10:02:14 | 1 | ||||||
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Sanford Burnham Prebys Medical Discovery Institute Medicinal Chemistry Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Medicinal Chemistry Facility (RRID:SCR_014872) | material resource, instrument supplier | Core facility that provides general synthetic and medicinal chemistry resources and expertise to the biomedical research community. Services include chemistry consulting for projects, grant applications, synthetic chemistry, medicinal chemistry, and analytical chemistry, as well as access to equipment for synthesis, purification, and analysis. | facility, la jolla, medicinal chemistry, synthesis, analysis, grant application, consultation | Commercially available | SCR_014872 | SBP Medicinal Chemistry Facility, SBP Medical Discovery Institute Medicinal Chemistry Facility | 2026-02-17 10:02:45 | 0 | ||||||||||
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Michigan Center for Diabetes Translational Research Methods and Measurements Core Resource Report Resource Website |
Michigan Center for Diabetes Translational Research Methods and Measurements Core (RRID:SCR_015188) | service resource, access service resource, core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Research core that works to assist investigators in designing studies, collecting data, and analyzing data to examine questions related to the causes, prevention, and control of diabetes, its complications, and comorbidities. | methodology, measurement technique, analysis, study design, diabetes research, translational research |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Michigan Medical School; Michigan; USA has parent organization: Michigan Center for Diabetes Translational Research is organization facet of: Michigan Center for Diabetes Translational Research |
Diabetes | NIDDK P30DK092926 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015188 | 2026-02-17 10:02:52 | 0 | ||||||||
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Harvard Bioinformatics Core at Joslin Diabetes Center Resource Report Resource Website |
Harvard Bioinformatics Core at Joslin Diabetes Center (RRID:SCR_009827) | service resource, access service resource, core facility | Core for data driven projects related to basic, clinical and translational research, with a particular emphasis on diabetes. Aims to ensure that researchers take advantage of the most modern and robust methods available in the field of Bioinformatics and Biostatistics. | computational, core, data, analysis, diabetes |
is listed by: Eagle I is related to: Joslin Diabetes Center has parent organization: Harvard University; Cambridge; United States |
Diabetes | nlx_156298 | http://www.joslin.org/bioinformatics.html | SCR_009827 | The Bioinformatics and Biostatistics Core at Joslin Diabetes Center, Bioinformatics and Biostatistics Core at Joslin Diabetes Center | 2026-02-17 10:01:37 | 0 | |||||||
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Harvard School of Public Health Environmental Statistics and Bioinformatics Core Facility Resource Report Resource Website 10+ mentions |
Harvard School of Public Health Environmental Statistics and Bioinformatics Core Facility (RRID:SCR_009822) | core facility, access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core provides intellectual guidance for quantitative aspects of the design and analysis of center studies and expertise in biostatistical methods, environmental risk assessment, Geographic Information System (GIS) , spatial statistics, molecular biology, bioinformatics and statistical genetics. Core runs a regular seminar series and often sponsors short courses on specialized topics of interest to the community. | core, design, analysis, guidance, biostatistical, methods, GIS, spatial, statistics, molecular, biology, genetics, seminar, course, sponsor |
is listed by: Eagle I is listed by: ScienceExchange has parent organization: Harvard T.H. Chan School of Public Health |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156290 | https://apps.sph.harvard.edu/publisher/upload/research/niehs/facility-cores/environmental-statistics-and-bioinformatics-core/index.html | SCR_009822 | Bioinformatics Core, HSPH, Environmental Statistics, Harvard School of Public Health | 2026-02-17 10:01:18 | 31 | |||||||
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Howard University Center for Computational Biology and Bioinformatics Core Facility Resource Report Resource Website |
Howard University Center for Computational Biology and Bioinformatics Core Facility (RRID:SCR_009864) | Howard CCBB, CCBB | core facility, access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core for bioinformatics consultation and software access. Laboratory of Molecular Computations and Bioinformatics (LMCB) is a resource facility dedicated to the support of computational biomedical research at Howard University. Provides molecular modeling, molecular dynamics, bioinformatics, and computational quantum chemistry capabilities and support to a variety of research projects at Howard University. | data, analysis, bioinformatics, software, access, consultation, molecular, computation, biomedical, quantum, chemistry |
is listed by: Eagle I has parent organization: Howard University; Washington D.C. |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156335 | https://rcmi.howard.edu/ccbb-3/ | http://www.howard.edu/medicine/rcmi/LMCB/default.htm | SCR_009864 | , LMCB, Laboratory of Molecular Computations and Bioinformatics, Howard, CCBB | 2026-02-17 10:01:19 | 0 | |||||
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Tuskegee University Computational Biology and Bioinformatics - Biomedical Information Management Services Resource Report Resource Website |
Tuskegee University Computational Biology and Bioinformatics - Biomedical Information Management Services (RRID:SCR_010065) | TU BIMS | core facility, access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core provides services and training in computational biology, bioinformatics, experimental design and statistical analysis to the RCMI researchers and the biomedical research community at Tuskegee University. | service, training, computational, biology, bioinformatics, experimental, design, statistical, analysis |
is listed by: Eagle I has parent organization: Tuskegee University; Alabama; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156535 | SCR_010065 | TU, Computational Biology, BIMS, Tuskegee University, Information Management Services, Bioinformatics, Biomedical | 2026-02-17 10:01:36 | 0 | |||||||
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ArcGIS for Desktop Basic Resource Report Resource Website 5000+ mentions |
ArcGIS for Desktop Basic (RRID:SCR_011081) | ArcGIS for Desktop | commercial organization, software resource | Geographical information system software produced by Esri. | spatial analysis, analysis, geoprocessing, data management, mapping, visualization, geocoding, imagery, data sharing | SciRes_000116 | http://www.esri.com/software/arcgis/arcview | SCR_011081 | ArcView | 2026-02-17 10:02:03 | 6328 | ||||||||
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University at Albany Center for Functional Genomics DNA Microarray Core Facility Resource Report Resource Website |
University at Albany Center for Functional Genomics DNA Microarray Core Facility (RRID:SCR_012502) | UAlbany CFG DNA Microarray Core Facility | service resource, access service resource, core facility | Core provides microarray services for Affymetrix GeneChip arrays, Agilent microarrays, NimbleGen microarrays and custom-produced spotted cDNA microarrays. Projects developed through DNA Microarray Center have made use of arrays from variety of genomes, eukaryotic, prokaryotic, and plant. Core services includes RNA/DNA isolation, gene expression, miRNA, Chip-chip, Rip-chip and DNA methylation services. Provides bioinformatics tools for further analysis of results of expression experiments. | DNA, microarray, functional, genomics, RNA, isolation, gene, expression, Chip-chip, Rip-chip, methylation, experiment, analysis |
is listed by: ScienceExchange has parent organization: University at Albany Center for Functional Genomics |
Restricted | SciEx_30 | SCR_012502 | CFG, University at Albany DNA Microarray Core Facility, University at Albany, UAlbany, Functional Genomics, Center for Functional Genomics, DNA Microarray | 2026-02-17 10:02:18 | 0 | |||||||
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TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | data analysis service, production service resource, analysis service resource, service resource | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | 2026-02-17 10:00:35 | 5 | ||||||
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GraphWeb Resource Report Resource Website 10+ mentions |
GraphWeb (RRID:SCR_005746) | GraphWeb | data analysis service, production service resource, analysis service resource, service resource | GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online tool | analysis, biological network, ontology or annotation visualization, protein interaction, gene id conversion, orthology mapping, network visualization, graph clustering, gene ontology, cis-regulatory motif, module, network, pathway, biological pathway, motif, visualization, protein interaction, orthology mapping, network visualization, graph clustering, analysis, statistical analysis, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group |
European Union FP6 ENFIN LSHG-CT-2005-518254; European Union FP6 COBRED LSHB-CT-2007-037730; Estonian Science Foundation ETF7437 |
PMID:18460544 | Open unspecified license - Free for academic use | nlx_149205 | SCR_005746 | 2026-02-17 10:00:38 | 12 | ||||||
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CateGOrizer Resource Report Resource Website 50+ mentions |
CateGOrizer (RRID:SCR_005737) | CateGOrizer | data analysis service, production service resource, analysis service resource, service resource | CateGOrizer takes batch input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, or a self-defined classification list, find its parental branch and performs an accumulative classification count, and returns the results in a sorted table of counts, percentages, and a pie chart (if it takes longer than standard time out period, it will email the user with a URL link to the results). This tool is comprised with a set of perl CGI programs coupled with a MySQL DBMS that stores the GO terms DAG data. Platform: Online tool | gene ontology, statistical analysis, slimmer-type tool, go term classification, classification, analysis, go slim |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: NAGRP Bioinformatics Coordination Program |
Free for academic use | nlx_149197 | SCR_005737 | GO Terms Classifications Counter | 2026-02-17 10:00:58 | 81 | |||||||
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AltaiR Resource Report Resource Website 1+ mentions |
AltaiR (RRID:SCR_024752) | software application, data compression software, data processing software, data analysis software, software resource, data visualization software | Software C toolkit for alignment free and spatial temporal analysis of multi-FASTA data. Used for entangling presence of multiple sequences from epidemic and pandemic events. | alignment free, spatial temporal analysis, multi-FASTA data, sequence, analysis, multiple sequences entangling presence, , FASTA format, epidemic and pandemic events, | European Commision 101081813; Genomic Data Infrastructure Fundação para a Ciência e a Tecnologia; CEECINST/00026/2018 Fundação para a Ciência e a Tecnologia |
Free, Available for download, Freely available | SCR_024752 | 2026-02-17 10:04:13 | 2 | ||||||||||
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PEPATAC Resource Report Resource Website 1+ mentions |
PEPATAC (RRID:SCR_024758) | software resource, software toolkit | Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats. | ATAC-seq analysis pipeline, ATAC-seq data, analysis, serial alignments, | NHGRI RM1 HG007735; NIGMS R35 GM128636; Howard Hughes Medical Institute ; American Society of Hematology |
PMID:34859208 | Free, Available for download, Freely available | https://github.com/databio/PEPATAC/releases | SCR_024758 | 2026-02-17 10:04:52 | 2 | ||||||||
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The Cancer Genome Atlas Resource Report Resource Website 5000+ mentions |
The Cancer Genome Atlas (RRID:SCR_003193) | TCGA | biomaterial supply resource, material resource | Project exploring the spectrum of genomic changes involved in more than 20 types of human cancer that provides a platform for researchers to search, download, and analyze data sets generated. As a pilot project it confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Its success committed resources to collect and characterize more than 20 additional tumor types. Components of the TCGA Research Network: * Biospecimen Core Resource (BCR); Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient. * Genome Characterization Centers (GCCs); Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers. * Genome Sequencing Centers (GSCs); High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer. * Proteome Characterization Centers (PCCs); The centers, a component of NCI's Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples. * Data Coordinating Center (DCC); The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal. * Cancer Genomics Hub (CGHub); Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments. * Genome Data Analysis Centers (GDACs) - Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data. TCGA is actively developing a network of collaborators who are able to provide samples that are collected retrospectively (tissues that had already been collected and stored) or prospectively (tissues that will be collected in the future). | genome, genome sequencing, breast, central nervous system, endocrine, gastrointestinal, gynecologic, head, neck, hematologic, skin, soft tissue, thoracic, urologic, clinical, genomic characterization, analysis, tumor genome, demographic, gene expression, copy number alteration, epigenetic, dna sequence, exome, snp, methylation, mrna, mirna, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is used by: BioXpress is used by: cancerRxTissue is listed by: One Mind Biospecimen Bank Listing is related to: Cancer3D is related to: Cancer Research Data Commons is related to: CancerMIRNome is related to: Broad Institute Genomics Platform has parent organization: National Cancer Institute works with: FireBrowse |
Cancer, Tumor, Normal, Breast cancer, Central Nervous System cancer, Endocrine cancer, Gastrointestinal cancer, Gynecologic cancer, Head cancer, Neck cancer, Hematologic cancer, Skin cancer, Soft tissue cancer, Thoracic cancer, Urologic cancer | NCI 261200800001E-12-0-1 | nlx_156913 | SCR_003193 | Cancer Genome Atlas | 2026-02-17 10:00:13 | 6292 | ||||||
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Cerebellar Platform Resource Report Resource Website 1+ mentions |
Cerebellar Platform (RRID:SCR_001700) | Cerebellar Platform | software resource, software repository | THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation. | electrophysiology, function, analysis, cerebellar, data, imaging, mathematical, model, molecular biology, paper, plasticity, program, review, script, structure, theory, book, cerebellum |
is used by: NIF Data Federation is related to: Integrated Software has parent organization: RIKEN Brain Science Institute |
Japan Society for the Promotion of Science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10193 | SCR_001700 | 2026-02-17 09:59:44 | 1 | |||||||
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Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis (RRID:SCR_014851) | biomaterial supply resource, material resource | Animal imaging and analysis lab that provides imaging and analytical services for SBP investigators. The facility can perform in vivo non-invasive luminescence and fluorescence imaging for xenograft tumor growth and metastasis studies. Analytical equipment supports complete blood cell counts (CBC) and analysis of serum components revealing metabolic or organ stress from small samples of mouse blood. | animal, facility, imaging, analysis, in vivo, non invasive, luminescence imaging, fluorescence imaging, tumor, metastasis, complete blood cell count, cbc, serum, organic, mouse, blood | Commercially available | SCR_014851 | SBP Animal Imaging and Analysis, SBP Medical Discovery Institute Animal Imaging and Analysis | 2026-02-17 10:02:43 | 0 | ||||||||||
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Donald Danforth Plant Science Center Bioanalytical Chemistry Facility Resource Report Resource Website |
Donald Danforth Plant Science Center Bioanalytical Chemistry Facility (RRID:SCR_001047) | service resource, access service resource, core facility | Facility provides tools for high quality plant and biological sample analysis in proteomics, mass spectrometry, metabolomics, ionomics, and related analytical fields. It works with academic and commercial institutions and has established collaborations with many principle investigators. | Plant, sample, analysis, proteomics, mass spectrometry, metabolomics, ionomics, elemental profiling |
is listed by: ABRF CoreMarketplace has parent organization: Donald Danforth Plant Science Center |
Restricted | ABRF_194 | https://coremarketplace.org/?FacilityID=194 | http://www.scienceexchange.com/facilities/proteomics-and-mass-spectrometry-facility, https://www.danforthcenter.org/scientists-research/core-technologies/proteomics-mass-spectrometry | SCR_001047 | Danforth Center Proteomics and Mass Spectrometry Facility, Donald Danforth Plant Science Center Proteomics and Mass Spectrometry Facility, Proteomics and Mass Spectrometry Facility, Danforth Center Ionomics, Danforth Center Mass Spectrometry Facility, Danforth Center Proteomics Facility | 2026-02-17 09:59:33 | 0 | ||||||
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UAlbany Proteomics Core Facility Resource Report Resource Website |
UAlbany Proteomics Core Facility (RRID:SCR_001048) | service resource, access service resource, core facility | A core facility that provides services in the identification of individual proteins, characterization of entire protein complexes or biosimilars, and global analysis to discover changes in the proteomes of different samples. The core also specializes in the development of custom assays for quantitation of specific molecules in complex clinical samples. | proteins, biosimilars, analysis, proteomics, core facility, custom assays, quantitation |
is listed by: ScienceExchange has parent organization: University at Albany Center for Functional Genomics |
Available to the research community, Fee-for-service basis, Available to investigators at the University at Albany, Available to academic institutions, Available to commercial entities | SciEx_537 | http://www.scienceexchange.com/facilities/proteomics-core-facility-ualbany | SCR_001048 | UAlbany CFG Proteomics Core Facility, University at Albany CFG Proteomics Core Facility, University at Albany Center for Functional Genomics Proteomics Core Facility | 2026-02-17 09:59:33 | 0 |
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