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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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