Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GeneWays Resource Report Resource Website |
GeneWays (RRID:SCR_000572) | Geneways | service resource | System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information. | pathway, molecule, literature, natural language processing, gene, protein, interaction, database |
is listed by: OMICtools has parent organization: Argonne National Laboratory has parent organization: Columbia University; New York; USA |
NSF ; DOE ; NIGMS GM61372 |
PMID:15016385 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30019, SCR_008368, OMICS_01182 | http://anya.igsb.anl.gov/genewaysApp | SCR_000572 | GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data, GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data | 2026-02-14 02:07:26 | 0 | ||||
|
NETMAGE Resource Report Resource Website 1+ mentions |
NETMAGE (RRID:SCR_021843) | data or information resource, 2d spatial image, image | Web tool for automated generation of interactive disease-disease network visualizations given input PheWAS summary data. Given genetic associations from Phenome-Wide Association Study, disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes. | PheWAS, genetic associations from Phenome Wide Association Study, disease-disease network construction, phenotypes, shared genetic associations between phenotypes | has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | NIGMS | DOI:10.1101/2020.10.27.357103 | Free, Available for download, Freely available | SCR_021851 | https://github.com/dokyoonkimlab/netmage | SCR_021843 | 2026-02-14 02:06:49 | 2 | ||||||
|
Knowledge Engineering from Experimental Design Resource Report Resource Website 1+ mentions |
Knowledge Engineering from Experimental Design (RRID:SCR_001238) | KEfED | software resource, software application | Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable. | experimental design, observation, interpretation, reasoning, experimental data, observational assertion, knowledge engineering, java |
is listed by: FORCE11 is related to: Bioscholar has parent organization: Biomedical Informatics Research Network |
NIGMS R01-GM083871; NIMH 1R01MH079068-01A2; NCRR 1 U24 RR025736-01 |
PMID:21859449 | Free, Available for download, Freely available | nif-0000-07745 | https://wiki.birncommunity.org/display/NEWBIRNCC/Knowledge+Engineering+from+Experimental+Design+%28%27KEfED%27%29 | SCR_001238 | 2026-02-14 02:06:31 | 1 | |||||
|
National Center for Macromolecular Imaging Resource Report Resource Website 1+ mentions |
National Center for Macromolecular Imaging (RRID:SCR_001445) | NCMI | biomedical technology research center, service resource, access service resource, training resource | Biomedical technology research center establishing the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy, computer reconstruction and modeling. Their emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography or NMR. The ultimate outcome of their research is a three-dimensional image of the complex that can be used for design of drugs and vaccines for a variety of diseases. The center is focused on extending the resolution, speed and flexibility of cryo-electron microscopy for the three-dimensional structure determination of biological macromolecular assemblies. Cryo-electron microscopy can visualize molecules under near-native conditions at resolutions ranging from 0.3 to 5 nm and can yield images of individual molecules in a range of different conformations as they exist in solution. Other cryo-electron mycroscopy techniques, such as cryo-electron tomography, are being developed to capture molecular structures in situ. The equipment, techniques and expertise developed are available to the research community through collaborative projects. The NCMI also provides training through workshops and other forms of dissemination via both traditional and modern Internet-based methods. | cryo-electron microscopy, structure determination, structure, macromolecule, assembly, model, reconstruction, subcellular complex, electron cryo-microscopy, 3d spatial image, structural biology technology center |
is related to: EMDataResource.org has parent organization: Baylor University; Texas; USA |
NIGMS 3R01GM079429-05S1 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152670 | SCR_001445 | 2026-02-14 02:07:49 | 1 | |||||||
|
National Biomedical Computation Resource Resource Report Resource Website 10+ mentions |
National Biomedical Computation Resource (RRID:SCR_002656) | NBCR | biomedical technology research center, training resource | Biomedical technology research center that conducts, catalyzes and enables multiscale biomedical research, focusing on four key activities: 1) integrating computational, data and visualization resources in a transparent, advanced grid environment to enable better access to distributed data, computational resources, instruments and people; 2) developing and deploying advanced computational tools for modeling and simulation, data analysis, query and integration, three-dimensional image processing and interactive visualization; 3) delivering and supporting advanced grid/cyberinfrastructure for biomedical researchers; and 4) training a cadre of new researchers to have an interdisciplinary, working knowledge of computational technology relevant to biomedical scientists. NBCR enables biomedical scientists to address the challenge of integrating detailed structural measurements from diverse scales of biological organization that range from molecules to organ systems in order to gain quantitative understanding of biological function and phenotypes. Predictive multi-scale models and their driving biological research problems together address issues in modeling of sub-cellular biophysics, building molecular modeling tools to accelerate discovery, and defining tools for patient-specific multi-scale modeling. NBCR furthers these driving problems by developing tools and models based on rapid advances in mathematics and information technology, incorporating them into NBCR pipelines or problem solving environments, and addressing the inevitable changes in the underlying cyber-infrastructure technologies and continually adapting codes over time. Their technology focus integrates both the biological applications and the underlying support software into reproducible science workflows that can function across a number of physical infrastructures. | computation, molecule, visualization, software, cyberinfrastructure, biomedical, computing, informatics, computational tool, modeling, simulation, data analysis, query, integration, image processing, grid computing, cluster, computing and informatics technology center |
has parent organization: University of California at San Diego; California; USA is parent organization of: MEME Suite - Motif-based sequence analysis tools is parent organization of: Grid Enabled Molecular Science Through Online Networked Environments |
NIGMS GM103426; NCRR P41 RR08605 |
Free, Available for download, Freely available | nif-0000-22270 | SCR_002656 | NBCR - National Biomedical Computation Resource | 2026-02-14 02:07:19 | 15 | ||||||
|
National Center for Microscopy and Imaging Research Resource Report Resource Website 100+ mentions |
National Center for Microscopy and Imaging Research (RRID:SCR_002655) | NCMIR | biomedical technology research center, training resource | Biomedical technology research center that develops computer-aided, advanced microscopy for the acquisition of structural and functional data in the dimensional range of 1 nm to 100 um, a range encompassing macromolecules, subcellular structures and cells. Novel specimen-staining methods, imaging instrumentsincluding intermediate high-voltage transmission electron microscopes (IVEMs) and high-speed, large-format laser-scanning light microscopesand computational capabilities are available for addressing mesoscale biological microscopy of proteins and macromolecular complexes in their cellular and tissue environments. These technologies are developed to bridge understanding of biological systems between the gross anatomical and molecular scales and to make these technologies broadly available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes may be accurately and easily obtained and analyzed. NCMIR fulfills its mission through technology development, collaboration, service, training, and dissemination. It aims to develop preparative methods and analytical approaches to 3D microscopy applicable to neurobiology and cell biology, incorporating equipment and implementing software that expand the analysis of 3D structure. The core research activities in the areas of specimen development, instrument development, and software infrastructures maximize the advantages of higher voltage electron microscopy and correlated light microscopies to make ambitious imaging studies across scales routine, and to facilitate the use of resources by biomedical researchers. NCMIR actively recruits outside users who will not only make use of these resources, but who also will drive technology development and receive training. | microscopy, electron microscopy, electron tomography, 3d imaging, instrumentation, intermediate voltage electron microscopy, light microscopy, specimen preparation, telemicroscopy, image, software, tissue, cell, macromolecular complex, macromolecule, subcellular structure, 3d microscopy, neurobiology, cell biology, 3d structure, imaging technology center |
has parent organization: University of California at San Diego; California; USA is parent organization of: XFido is parent organization of: Xvoxtrace is parent organization of: National Center for Microscopy and Imaging Research: SAGE is parent organization of: Combine RTS2000 is parent organization of: Montage RTS2000 is parent organization of: Manual Align RTS2000 |
NIGMS ; NCRR P41 GM103412 |
Free, Available for download, Freely available | nif-0000-22234, SCR_016627 | SCR_002655 | National Center for Microscopy and Imaging Research | 2026-02-14 02:07:51 | 252 | ||||||
|
MacCHESS Resource Report Resource Website 1+ mentions |
MacCHESS (RRID:SCR_001443) | MacCHESS | access service resource, service resource | MacCHESS Synchrotron Source for Structural Biology advances structural characterization of proteins and biomolecules critical for understanding key biological processes and properties through leveraging both established and emerging X-ray synchrotron technologies. Used to collect data that comprises all or part of research programs. | structure, macromolecule, crystallography, beamlne, x-ray, bending magnet, unit-cell diffraction, ultra-high-resolution diffraction, dispersion phasing, drug design, structural genomics, microdiffraction, cryo-cooling, high pressure cooling, diffraction, software, synchrotron, cryo-crystallography, small-angle x-ray solution scattering, microcrystallography, structural biology, structural biology technology center | has parent organization: Cornell University; New York; USA | NIGMS GM103485 | Free, Freely Available | nlx_152668 | SCR_001443 | MacCHESS Synchrotron Source for Structural Biology | 2026-02-14 02:07:45 | 9 | ||||||
|
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-02-14 02:07:19 | 35 | ||||||
|
National Center for X-ray Tomography Resource Report Resource Website 1+ mentions |
National Center for X-ray Tomography (RRID:SCR_001433) | NCXT | biomedical technology research center, training resource | Biomedical technology research center that develops novel cellular imaging technologies, specifically soft X-ray tomography, for visualizing and quantifying the internal structure of whole, hydrated cells, and high-numerical aperture fluorescence microscopy for locating the position of specific cellular molecules. Data from these two imaging modalities can be combined to form a single, correlated imaging view of a cell. | x-ray tomography, cell, imaging, microscopy, x-ray, tomography, imaging technology center |
has parent organization: Lawrence Berkeley National Laboratory has parent organization: University of California at San Francisco; California; USA |
NIGMS ; DOE |
Free, Freely Available | nlx_152657 | http://ncxt.lbl.gov/ | SCR_001433 | National Center for X-ray Tomography: Cellular imaging at the mesoscale | 2026-02-14 02:07:18 | 6 | |||||
|
Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | 2026-02-14 02:07:20 | 3 | |||||||
|
Ultrafast Optical Processes Laboratory Resource Report Resource Website 1+ mentions |
Ultrafast Optical Processes Laboratory (RRID:SCR_006582) | Ultrafast Optical Processes Laboratory | biomedical technology research center, service resource, access service resource, training resource | Biomedical technology research center and training resource that develops time-resolved laser technologies and instrumentation, with a focus on 2-D IR spectroscopy. The technologies enable atomic-level measurements of the fastest steps in biological processes to elucidate structure and dynamics in biological macromolecules, assemblies and cells. The Center makes most of its instrumentation available for service research projects to outside users nation-wide. | spectroscopy, structure, dynamics, macromolecule, assembly, cell, optical and laser technology center, laser spectroscopy, biochemical, biophysical, biomedical, laser, biological process | has parent organization: University of Pittsburgh; Pennsylvania; USA | NIGMS 9P41GM104605; NCRR P41RR001348 |
nlx_152664 | SCR_006582 | Laser and Biomedical Technology Laboratories | 2026-02-14 02:07:52 | 1 | |||||||
|
VU National Research Resource for Imaging Mass Spectrometry Resource Report Resource Website |
VU National Research Resource for Imaging Mass Spectrometry (RRID:SCR_006904) | National Research Resource for Imaging Mass Spectrometry | biomedical technology research center, training resource | Biomedical technology research center that advances the technology of Imaging Mass Spectrometry, facilitates the application of this novel imaging modality to problems of biological and clinical significance, and promotes the adoption of these technologies by a larger community of scientists and clinicians. Technical innovations include next-generation hardware, software and methods. Technology development is conducted by an interdisciplinary team of scientists and engineers, both within the Resource and through collaborative relationships with other universities, research institutes, and private industry. Development milestones are guided by Driving Biological Projects that require specific advancements in Imaging Mass Spectrometry in order to address biological problems. By working together, they anticipate new insights into these biological systems and a better understanding of health and disease at the molecular level that translates to improved patient care. The training mission of the Resource is accomplished through a variety of educational programs where Resource scientists and collaborators share their knowledge and experience with those interested in learning more about the technology. | imaging, mass spectrometry, imaging technology center | has parent organization: Vanderbilt University; Tennessee; USA | NIGMS | nlx_152658 | SCR_006904 | Vanderbilt University National Research Resource for Imaging Mass Spectrometry | 2026-02-14 02:07:23 | 0 | |||||||
|
NRCAM Resource Report Resource Website 50+ mentions |
NRCAM (RRID:SCR_006134) | NRCAM | biomedical technology research center, service resource, access service resource, training resource | Biomedical technology research center that develops new technologies for modeling cell biological processes. The technologies are integrated through Virtual Cell, a problem-solving environment built on a central database and disseminated as a Web application for the analysis, modeling and simulation of cell biological processes. NRCAM resides at the Center for Cell Analysis and Modeling, CCAM, and provides a vast array of laboratory equipment that can be used for obtaining experimental data needed to create and enhance Virtual Cell models. Microscopy instrumentation includes three confocal laser scanning microscopes including UV excitation, nonlinear optical microscopy utilizing a titanium sapphire pulsed laser, confocal-based fluorescence correlation spectroscopy, wide-field imaging workstation with cooled CCD and rapid excitation filter wheel, and dual-wavelength spectrofluorometer. Access to the facilities and technical staff is open to all researchers., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | modeling, simulation, cell, microscopy, software, biological process, model, cell model, informatics, computing and informatics technology center, FASEB list |
is listed by: 3DVC has parent organization: University of Connecticut; Connecticut; USA is parent organization of: Virtual Cell at the National Resource for Cell Analysis and Modeling |
NIGMS ; NCRR ; NIH Blueprint for Neuroscience Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03953 | SCR_006134 | The National Resource for Cell Analysis and Modeling, National Resource of Cell Analysis and Modeling, National Resource of Cell Analysis and Modeling (NRCAM), National Resource for Cell Analysis and Modeling, National Resource of Cell Analysis & Modeling (NRCAM) | 2026-02-14 02:07:52 | 76 | ||||||
|
Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING Resource Report Resource Website 1+ mentions |
Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING (RRID:SCR_007412) | data or information resource, data set | Data sets, tools and computational techniques for modeling of protein interactions, including docking benchmarks, docking decoys and docking templates. Adequate computational techniques for modeling of protein interactions are important because of the growing number of known protein 3D structures, particularly in the context of structural genomics. The first release of the DOCKGROUND resource (Douguet et al., Bioinformatics 2006; 22:2612-2618) implemented a comprehensive database of cocrystallized (bound) protein-protein complexes in a relational database of annotated structures. Additional releases added features to the set of bound structures, such as regularly updated downloadable datasets: automatically generated nonredundant set, built according to most common criteria, and a manually curated set that includes only biological nonobligate complexes along with a number of additional useful characteristics. Also included are unbound (experimental and simulated) protein-protein complexes. Complexes from the bound dataset are used to identify crystallized unbound analogs. If such analogs do not exist, the unbound structures are simulated by rotamer library optimization. Thus, the database contains comprehensive sets of complexes suitable for large scale benchmarking of docking algorithms. Advanced methodologies for simulating unbound conformations are being explored for the next release. The Dockground project is developed by the Vakser lab at the Center for Bioinformatics at the University of Kansas. Parts of Dockground were co-developed by Dominique Douguet from the Center of Structural Biochemistry (INSERM U554 - CNRS UMR5048), Montpellier, France. | protein 3d structure, protein interaction, protein interface, protein model, structural genomics, co-crystallized, protein complex, protein recognition, protein modeling, structure prediction, protein-protein complex, benchmark |
is listed by: 3DVC is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Kansas; Kansas; USA |
NIH ; NIGMS R01 GM074255; NIGMS R01 GM61889 |
PMID:17803215 PMID:16928732 |
nif-0000-02757 | SCR_007412 | Dockground, Dockground: Benchmarks Docoys Templates other knowledge resources for DOCKING, Dockground: Benchmarks Docoys Templates and other knowledge resources for DOCKING | 2026-02-14 02:07:31 | 8 | |||||||
|
Northeastern Collaborative Access Team Resource Report Resource Website 10+ mentions |
Northeastern Collaborative Access Team (RRID:SCR_008999) | NE-CAT, NECAT | biomedical technology research center, service resource, access service resource, training resource | Biomedical technology research center for macromolecular crystallography at Sector 24 of the Advanced Photon Source at Argonne National Laboratory. The macromolecules studied by resource users often involve large unit cells, small crystals, weakly diffracting crystals and crystals with weak anomalous scattering. Technological research includes use of silicon monochromators, focusing optics, methods of phase determination, radiation damage, X-ray detectors, automated sample mounting, microdiffraction and crystallographic software. | synchrotron, x-ray, beamline, structural biology, macromolecular crystallography, macromolecule, crystallography, structural biology technology center | has parent organization: Cornell University; New York; USA | NIGMS | nlx_152674 | SCR_008999 | Northeastern CAT, Northeastern Collaborative Access Team Undulator Resource for Structural Biology | 2026-02-14 02:07:56 | 16 | |||||||
|
National Resource for the Mass Spectrometric Analysis of Biological Macromolecules Resource Report Resource Website |
National Resource for the Mass Spectrometric Analysis of Biological Macromolecules (RRID:SCR_009007) | National Resource for the Mass Spectrometric Analysis of Biological Macromolecules | biomedical technology research center, training resource | Biomedical technology research center that develops cutting-edge mass spectrometric tools for analyzing peptides and proteins. It makes its software tools developed for data analysis freely available. | systems biology technology center, mass spectrometric, analysis, peptide, protein, software, proteomic, cellular function | has parent organization: Rockefeller University; New York; USA | NIGMS | nlx_152683 | SCR_009007 | 2026-02-14 02:08:00 | 0 | ||||||||
|
National Center for Multiscale Modeling of Biological Systems Resource Report Resource Website 1+ mentions |
National Center for Multiscale Modeling of Biological Systems (RRID:SCR_009005) | MMBioS | biomedical technology research center, training resource | Biomedical technology research center that develops and makes available to the scientific community high performance computing algorithms, tools and software to leverage modeling efforts at disparate scales of structural biology, cellular microphysiology and large-scale bioimage processing and analysis, with the goal of advancing understanding of the molecular and cellular organization and functional mechanisms that underlie synaptic signaling and regulation. | systems biology technology center, computing algorithm, software, structural biology, cellular microphysiology, image processing, image analysis, molecule, cell, synaptic signaling, regulation, signaling | has parent organization: University of Pittsburgh School of Medicine; Pennsylvania; USA | NIGMS | nlx_152681 | SCR_009005 | MMBioS - National Center for Multiscale Modeling of Biological Systems, National Center for Multiscale Modeling of Biological Systems (MMBioS) | 2026-02-14 02:07:56 | 1 | |||||||
|
National Bio-Organic Biomedical Mass Spectrometry Resource Center Resource Report Resource Website 1+ mentions |
National Bio-Organic Biomedical Mass Spectrometry Resource Center (RRID:SCR_009004) | Mass Spectrometry Facility | biomedical technology research center, training resource | Provides high-performance tandem mass spectrometry and proteomics, including multiplexed quantitative comparative analysis of protein and post-translational modifications, and a suite of tools for the analysis of mass spectrometry proteomics data. It provides both scientific and technical expertise and state-of-the-art high-performance, tandem mass spectrometric instrumentation. The facility also provides a service for small molecule analysis. Significant instrumentation in the facility includes three QSTAR quadrupole orthogonal time of flight instruments, and both an LTQ-Orbitrap platform with electron transfer dissociation (ETD) and an LTQ-FT linear ion trap FT-ICR instrument equipped with the ability to perform electron capture dissociation (ECD). The Center also has a 4700 Proteomic Analyzer MALDI tandem time of flight instrument; as well as a QTRAP 5500 hybrid triple quadrupole linear ion trap instrument; and a Thermo Fisher LTQ Orbitrap Velos. Major research focuses within the Center are the analysis of post-translational modifications, including phosphorylation and O-GlcNAcylation and development of methods for quantitative comparative analysis of protein and post-translational modification levels. The program also continues to develop one of the leading suites of tools for analysis of mass spectrometry proteomics data, Protein Prospector. The current web-based release allows unrestricted searching of MS and MSMS data, as well as the ability to perform comparative quantitative analysis of samples using isotopic-labeling reagents. It is the only freely-available web-based resource that allows this type of analysis. | systems biology technology center, mass spectrometry, proteomics | has parent organization: University of California at San Francisco; California; USA | NCRR ; NIGMS P41GM103481 |
nlx_152680 | SCR_009004 | UCSF Mass Spectrometry Facility | 2026-02-14 02:07:25 | 2 | |||||||
|
BioMesh3D Resource Report Resource Website 1+ mentions |
BioMesh3D (RRID:SCR_009534) | BioMesh3D | software resource, software application | A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. | mesh, simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
PMID:23367171 | MIT License | nlx_155708 | http://www.nitrc.org/projects/biomesh3d | SCR_009534 | 2026-02-14 02:07:15 | 3 | |||||
|
eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software resource, software application | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM071558; NIDDK R01 DK088541; NLM RC2 LM010994; NIDDK P01 DK056492; NIDDK RC4DK090860; NCRR KL2 RR029885 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k http://www.maayanlab.net/X2K/ |
SCR_016307 | eXpression2Kinases, X2K | 2026-02-14 02:07:23 | 4 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
