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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-07-25 12:15:09 | 17 | |||||||||||
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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 | 2026-07-25 12:13:20 | 67 | |||||||||
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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 | 2026-07-25 12:13:02 | 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 | 2026-07-25 12:13:17 | 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 | 2026-07-25 12:13:17 | 0 | |||||||||
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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 | 2026-07-25 12:14:04 | 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 | 2026-07-25 12:14:04 | 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 | 2026-07-25 12:14:07 | 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 | 2026-07-25 12:14:07 | 0 | ||||||||||
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VisIt Resource Report Resource Website |
VisIt (RRID:SCR_024370) | software application, software resource | 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 | 2026-07-26 09:08:20 | 0 | ||||||||
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TARGETgene Resource Report Resource Website 1+ mentions |
TARGETgene (RRID:SCR_001392) | TARGETgene | software application, software resource | 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 | 2026-07-26 09:03:02 | 7 | ||||
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Nipype Resource Report Resource Website 500+ mentions |
Nipype (RRID:SCR_002502) | Nipype | software application, software resource | 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 | 2026-07-26 09:03:15 | 822 | |||||
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Blast2GO Resource Report Resource Website 5000+ mentions |
Blast2GO (RRID:SCR_005828) | B2G | software application, software resource | 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) | 2026-07-26 09:04:01 | 8422 | |||||
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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 application, software resource | 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 | 2026-07-26 09:03:20 | 81 | |||||
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Gephi Resource Report Resource Website 1000+ mentions |
Gephi (RRID:SCR_004293) | Gephi | software application, software resource, data processing software | Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions! | network, visualization, visual analytics, exploratory data analysis, graph, analysis, open source, plugin, filter, cluter, manipulate, export | is parent organization of: Diseasome | GNU General Public License | nlx_31183 | SCR_004293 | 2026-07-26 09:03:36 | 3059 | ||||||||
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FIVA - Functional Information Viewer and Analyzer Resource Report Resource Website 1+ mentions |
FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) | FIVA | software application, software resource, data processing software | Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: MolGen |
Netherlands Organization for Scientific Research ; industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes ; Center IOP Genomics ; European Union QLK3-CT-2001-01473 |
PMID:17237043 | Free for academic use | nlx_149245 | SCR_005776 | FIVA - Functional Information Viewer Analyzer, Functional Information Viewer and Analyzer (FIVA), Functional Information Viewer and Analyzer | 2026-07-26 09:04:04 | 1 | |||||
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GoBean - a Java application for Gene Ontology enrichment analysis Resource Report Resource Website 10+ mentions |
GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) | GoBean | software application, software resource, data processing software | GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible | java, gene ontology, ontology, gene association, analysis, enrichment, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Gachon University of Medicine and Science; Incheon; South Korea |
PMID:22360891 | Free for academic use | nlx_149296 | http://neon.gachon.ac.kr/GoBean/ | SCR_005808 | 2026-07-26 09:04:03 | 22 | ||||||
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SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | software application, software resource, data processing software | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2026-07-26 09:04:28 | 0 | |||||||
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Prophet Resource Report Resource Website 1+ mentions |
Prophet (RRID:SCR_017083) | software application, software resource, data processing software | Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton. | data, science, forecast, time, series, multiple, seasonality, linear, non linear, growth, analysis | is listed by: CRAN | DOI:10.7287/peerj.preprints.3190v2 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/prophet/, https://pypi.org/project/fbprophet/ | SCR_017083 | Prophet Automatic Forecasting Procedure | 2026-07-26 09:06:56 | 3 | |||||||
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gFACs Resource Report Resource Website 1+ mentions |
gFACs (RRID:SCR_022017) | software application, software resource, data processing software | Software package provides comprehensive framework for evaluating, filtering, and analyzing gene models from range of input applications and preparing these annotations for formal publication or downstream analysis. | filtering, analysis, conversion, unify genome annotations, alignment and gene prediction frameworks, | National Science Foundation Plant Genome Research Program of the United States 1444573 | DOI:10.1016/j.gpb.2019.04.002 | Free, Available for download, Freely available | SCR_022017 | 2026-07-26 09:07:41 | 5 |
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