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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Genomics DNA Analysis Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Genomics DNA Analysis Facility (RRID:SCR_014866) | Genomics Core at SBP | instrument supplier, material resource | Core facility that provides sequencing services, access to equipment and consultation on experimental design and data analysis. Available instruments include the Life Technologies Ion Torrent PGM and Ion Proton sequencers. Core also provides amplification-free analysis of RNA expression using the NanoString nCounter, and additionally provides sequencing and analysis services to investigators outside of SBP. Included in the cost of sequencing is basic bioinformatic analysis (SNP/InDel calling, transcript abundance). Lastly, the core also provides advice on experimental design, and guidance on the capabilities of next-generation sequencing. | facility, la jolla, genomics, core, SBP, analysis, sequencing, rna, snp, consultation | Available to external user | SCR_014866 | SBP, DNA Analysis Facility, Genomics Core, Medical Discovery Institute | 2026-02-07 02:15:54 | 0 | |||||||||
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Sanford Burnham Prebys Medical Discovery Institute High-content Screening Core Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute High-content Screening Core Facility (RRID:SCR_014869) | HCS | instrument supplier, material resource | Core facility that provides access to the HTS plate and liquid handling infrastructure of the screening center, as well as the screening center�s cell culture facility. Other services include assay development, screening, and data analysis/mining expertise and services for high content screens. Consultation from the team is available for high content image-based screens including sample preparation, image acquisition, image analysis, image data management, and algorithm development. | facility, la jolla, high content screening, assay, phenotype, data mining, analysis, image analysis, development | Commercially available | SCR_014869 | SBP Medical Discovery Institute High-content Screening Core Facility, SBP High-content Screening Core Facility | 2026-02-07 02:16:10 | 0 | |||||||||
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Sanford Burnham Prebys Medical Discovery Institute NMR Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute NMR Facility (RRID:SCR_014861) | instrument supplier, material resource | Facility that acts as a centralized shared resource for NMR studies on proteins, peptides, small molecules, and carbohydrates in solution or in solid state. It provides instrumentation and expertise for NMR data collection. It also provides consultation with investigators on the feasibility of NMR for structural studies of protein candidates, as well as the optimal method to obtain solution structures and binding information by multi-dimensional NMR techniques. It can also train users in basic spectrometer operations, trouble-shoot for instrumental and operational problems, and set up NMR experiments for users as requested. | facility, medical, nmr, protein, peptide, small molecules, carbohydrates, data collection, consultation, spectrometer, linux, software, analysis | Commercially available | SCR_014861 | SBP NMR Facility, SBP Medical Discovery Institute NMR Facility | 2026-02-07 02:16:10 | 0 | ||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core (RRID:SCR_014862) | instrument supplier, material resource | Facility that provides a variety of analytical services focused on biophysical characterization of structural and functional properties of proteins in solution, under native, non-denaturing conditions. Examples of services include quality control of protein samples (folding, stability, aggregation); measuring molecular weight of proteins, protein complexes, oligomers and assemblies; charcaterizing protein conformation and shape in solution; determining oligomeric state of protein (including stoichiometry and Kd for self-association) and measuring protein binding to proteins, peptides, small molecules, compounds, metals, nucleotides and other ligands (including determination of equilibrium (Kd) and kinetic rate (kon, koff) constants, stoichiometry, binding enthalpy and entropy). | facility, la jolla, protein, analysis, quality control, molecular weight, stoichiometry | Commercially available | SCR_014862 | SBP Medical Discovery Institute Protein Analysis Core, SBP Protein Analysis Core | 2026-02-07 02:15:54 | 0 | ||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators. | stem cell, facility, la jolla, pluripotent stem cells, ipsc, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014856 | SBP Medical Discovery Institute Stem Cell Core, SBP Stem Cell Core | 2026-02-07 02:14:45 | 0 | ||||||||||
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VisIt Resource Report Resource Website |
VisIt (RRID:SCR_024370) | software resource, software application | Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations. | generate visualizations, animation, analysis, save resulting images and animations for presentations, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/visit/ | SCR_024370 | visit | 2026-02-07 02:14:59 | 0 | ||||||||
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Hunter NMR Spectroscopy Facility Resource Report Resource Website |
Hunter NMR Spectroscopy Facility (RRID:SCR_000883) | instrument supplier, material resource | A service facility with four main spectrometers. The facility consists of four NMR instruments: a JEOL GX-400, a Varian Inova 500, a Bruker Avance 500 equipped with a 13C-1H cryoprobe, and a Bruker Avance III 600 MHz spectrometer equipped with a cryoprobe. These spectrometers are utilized by scientists from Hunter College, as well as from the entire CUNY community. The large variety of available probes allows detection of virtually any MR-active nuclide. Data analysis is performed either at the spectrometer workstation with vendor software or off-line with third party software packages. | spectrometer, spectroscopy, analysis, cuny, nuclide, data analysis |
is listed by: Eagle I has parent organization: Hunter College; New York; USA |
nlx_156342 | http://hunter-cuny.eagle-i.net/i/00000136-79a2-306f-949b-425080000000 | SCR_000883 | 2026-02-07 02:15:02 | 0 | |||||||||
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Wyss Institute Imaging Core Resource Report Resource Website |
Wyss Institute Imaging Core (RRID:SCR_000898) | instrument supplier, material resource | A core facility with access to imaging equipment and analysis software such as wide-field light microscopy, Total Internal Reflection Fluorescence microscopy (TIRF), confocal microscopy, Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), small animal imaging, spectroscopy, and flow cytometry. | wide field light microscopy, total internal reflection fluorescence microscopy, tirf, confocal microscopy, atomic force microscopy, afm, transmission electron microscopy, tem, small animal imaging, spectroscopy, flow cytometry, imaging, analysis |
is listed by: Eagle I has parent organization: Harvard University; Cambridge; United States |
nlx_156690 | http://harvard.eagle-i.net/i/00000133-a87a-55d3-809a-235280000000 | SCR_000898 | 2026-02-07 02:15:02 | 0 | |||||||||
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ADInstruments - Data Acquisition Systems for Life Science Resource Report Resource Website 50+ mentions |
ADInstruments - Data Acquisition Systems for Life Science (RRID:SCR_001620) | instrument supplier, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 19, 2018; A provider of computer-based data acquisition and analysis systems for life science. Products enable users to record and analyze life science data quickly and efficiently. ADInstruments product range is based on the PowerLab data acquisition system with LabChart software. The PowerLab system (also MacLab) is used in universities, hospitals, research institutes, pharmaceutical companies, contract research organizations and other private industry research sectors. | acquisition, analysis, biomedical, computer, life science, research, education, pharmaceutical research, transducer, part, signal conditioner, system | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10146 | SCR_001620 | AD Instruments | 2026-02-07 02:15:05 | 66 | |||||||||
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Incucyte Cell-By-Cell Analysis Software Module Resource Report Resource Website 1+ mentions |
Incucyte Cell-By-Cell Analysis Software Module (RRID:SCR_025367) | software resource, software application | Software for analysis to determine live versus dead cells – no fluorescent dyes needed. | determine live versus dead cells, no fluorescent dyes needed, analysis | Restricted | SCR_025367 | 2026-02-07 02:16:50 | 1 | |||||||||||
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TraceDrawer Resource Report Resource Website 10+ mentions |
TraceDrawer (RRID:SCR_025782) | software resource | Software for evaluating, comparing and presenting real-time interaction data. Used for quantification of kinetics and affinity through curve fitting, with large number of binding models to choose from. Can extract experimental information from measurement, requiring minimal user input. | kinetics, affinity, analysis, evaluating, comparing, presenting, real-time interaction data, | Restricted | SCR_025782 | 2026-02-07 02:16:59 | 17 | |||||||||||
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TARGETgene Resource Report Resource Website 1+ mentions |
TARGETgene (RRID:SCR_001392) | TARGETgene | software resource, software application | MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7 | disease target, drug discovery, drug, matlab, gene network, genetic interaction, gene, drug screening, mutation driver, therapeutic target, drug candidate, compound, mapping, analysis | has parent organization: Biomedical Simulations Resource | Cancer | NIBIB P41-EB001978 | PMID:22952662 | Free, Under the terms of a Release Agreement., Please cite | nlx_152573 | http://bmsr.usc.edu/Software/TARGET/TARGET.html | SCR_001392 | 2026-02-07 02:14:13 | 7 | ||||
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Primate Embryo Gene Expression Resource Resource Report Resource Website 1+ mentions |
Primate Embryo Gene Expression Resource (RRID:SCR_002765) | PREGER | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods. | primate, embryo, gene, expression, embryologist, microarray, rhesus, monkey, oocyte, embryo, cdna, library, molecular, analysis, stem cell, oocyte quality, preimplantation development, transcription |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Temple University School of Medicine; Pennsylvania; USA |
NIH Office of the Director R24 OD012221; NCRR RR15253 |
PMID:14724133 PMID:17147927 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24366 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | SCR_002765 | PREGER Online, Preger.org | 2026-02-07 02:14:30 | 6 | ||||
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AltAnalyze - Alternative Splicing Analysis Tool Resource Report Resource Website 50+ mentions |
AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) | AltAnalyze | software resource, software application | Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph. | analysis, alternative splicing, microarray, calculate, pathway, ontology, domain, microrna, targeting, splicing, microarry, rna-seq, metabolomics, mac osx, windows, ubuntu, cross platform, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Cytoscape has parent organization: University of California at San Francisco; California; USA |
PMID:20513647 | Free, Available for download, Freely available | nif-0000-30083, OMICS_02250, biotools:altanalyze | https://bio.tools/altanalyze | SCR_002951 | Alternative Splicing Analysis Tool | 2026-02-07 02:14:15 | 78 | |||||
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Nipype Resource Report Resource Website 500+ mentions |
Nipype (RRID:SCR_002502) | Nipype | software resource, software application | A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. | magnetic resonance, python, workflow, analysis, pipeline, interface, data processing, neuroimaging |
is used by: Forward: Accurate finite element electromagnetic head models is used by: fMRIPrep is used by: NHP BIDS is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
PMID:21897815 | Free, Available for download, Freely available | nlx_155901 | http://www.nitrc.org/projects/nipype | SCR_002502 | Nipype: Neuroimaging in Python Pipeline and Interfaces, NIPY Pipeline and Interfaces | 2026-02-07 02:13:53 | 764 | |||||
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Blast2GO Resource Report Resource Website 5000+ mentions |
Blast2GO (RRID:SCR_005828) | B2G | software resource, software application | An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, visualization, analysis, functional genomics, editor, statistical analysis, slimmer-type tool, ontology or annotation editor, functional analysis, direct acyclic graph, analysis, high throughput, functional genomics |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Principe Felipe Research Centre; Valencia; Spain |
MCyT GEN 2001 - 4885-C05-03; eTumour Project FP6-2002-LIFESCIHEALTH 503094 |
PMID:16081474 | Free for academic use | OMICS_01475, nlx_149335 | SCR_005828 | Blast2GO (B2G) | 2026-02-07 02:14:09 | 8345 | |||||
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Gene Map Annotator and Pathway Profiler Resource Report Resource Website 100+ mentions |
Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) | data visualization software, software resource, software application, data processing software | GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options. | expression, gene, analysis, biological, mapping, microarray, network, pathway, protein, visualization, ontology, proteomics, FASEB list |
has parent organization: University of California at San Francisco; California; USA is parent organization of: MAPPFinder |
Agilent Foundation ; BayGenomics ; NIGMS |
PMID:17588266 | nif-0000-00244 | SCR_005094 | GenMAPP | 2026-02-10 09:55:12 | 211 | |||||||
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nSolver Analysis Software Resource Report Resource Website 100+ mentions |
nSolver Analysis Software (RRID:SCR_003420) | nSolver Analysis Software | software resource, software application, data processing software | Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages. | normalization, analysis, ncounter, os x, windows, quality control | is listed by: OMICtools | Restricted | OMICS_02309 | https://nanostring.app.box.com/v/nSolver-AdvancedAnalysis https://nanostring.com/products/ncounter-analysis-system/ncounter-analysis-solutions/nsolver-data-analysis-support/ |
SCR_003420 | 2026-02-10 09:54:54 | 393 | |||||||
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Kidney Tissue Atlas Resource Report Resource Website 10+ mentions |
Kidney Tissue Atlas (RRID:SCR_021626) | atlas, data or information resource | Atlas is set of interactive tools built to promote retrieval, exploration, discovery, and analysis of Kidney Precision Medicine Project data by greater research community. Datasets available in repository are combination of raw and processed data from KPMP participant biopsies and reference tissue samples. | Interactive tools, retrieval, exploration, discovery, analysis, Kidney Precision Medicine Project data | is related to: Kidney Precision Medicine Project | Free, Freely available | SCR_021626 | 2026-02-10 09:58:05 | 21 | ||||||||||
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Genetic Analysis Workshop Resource Report Resource Website 10+ mentions |
Genetic Analysis Workshop (RRID:SCR_008350) | workshop, training resource | The Genetic Analysis Workshops (GAWs) are a collaborative effort among genetic epidemiologists to evaluate and compare statistical genetic methods. For each GAW, topics are chosen that are relevant to current analytical problems in genetic epidemiology, and sets of real or computer-simulated data are distributed to investigators worldwide. Results of analyses are discussed and compared at meetings held in even-numbered years. The GAWs began in 1982 were initially motivated by the development and publication of several new algorithms for statistical genetic analysis, as well as by reports in the literature in which different investigators, using different methods of analysis, had reached contradictory conclusions. The impetus was initially to determine the numerical accuracy of the algorithms, to examine the robustness of the methodologies to violations of assumptions, and finally, to compare the range of conclusions that could be drawn from a single set of data. The Workshops have evolved to include consideration of problems related to analyses of specific complex traits, but the focus has always been on analytical methods. The Workshops provide an opportunity for participants to interact in addressing methodological issues, to test novel methods on the same well-characterized data sets, to compare results and interpretations, and to discuss current problems in genetic analysis. The Workshop discussions are a forum for investigators who are evolving new methods of analysis as well as for those who wish to gain further experience with existing methods. The success of the Workshops is due at least in part to the focus on specific problems and data sets, the informality of sessions, and the requirement that everyone who attends must have made a contribution. Topics are chosen and a small group of organizers is selected by the GAW Advisory Committee. Data sets are assembled, and six or seven months before each GAW, a memo is sent to individuals on the GAW mailing list announcing the availability of the GAW data. Included with the memo is a short description of the data sets and a form for requesting data. The form contains a statement to be signed by any investigator requesting the data, acknowledging that the data are confidential and agreeing not to use them for any purpose other than the Genetic Analysis Workshop without written permission from the data provider(s). Data are distributed by the ftp or CD-ROM or, most recently, on the web, together with a more complete written description of the data sets. Investigators who wish to participate in GAW submit written contributions approximately 6-8 weeks before the Workshop. The GAW Advisory Committee reviews contributions for relevance to the GAW topics. Contributions are assembled and distributed to all participants approximately two weeks before the Workshop. Participation in the GAWs is limited to investigators who (1) submit results of their analyses for presentation at the Workshop, or (2) are data providers, invited speakers or discussants, or Workshop organizers. GAWs are held just before the meetings of the American Society of Human Genetics or the International Genetic Epidemiology Society, at a meeting site nearby. We choose a location that will encourage interaction among participants and permit an intense period of concentrated work. The proceedings of each GAW are published. Proceedings from GAW16 were published in part by Genetic Epidemiology 33(Suppl 1), S1-S110 (2009) and in part by Biomed Central (BMC Proceedings, Volume 3, Supplement 7, 2009). Sponsors: GAW is funded by the Southwest Foundation for Biomedical Research. | epidemiologist, epidemiology, genetic, algorithm, analysis, method, statistical | nif-0000-25214 | SCR_008350 | GAW | 2026-02-10 09:55:47 | 19 |
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