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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data. | model, modelling, python, neuroelectrophysiology, object, neuroimaging, analysis, neurophysiology, electrophysiology, BRAIN Initiative | is recommended by: BRAIN Initiative | Human Frontiers Science Program RGY0088; NSF CBET-1351692; NSF IOS-1550994 |
Free, Available for download, Freely available | SCR_016209 | SciCrunch Registry | Nelpy (Neuroelectrophysiology) | 2026-11-07 11:58:33 | 3 | ||||||||
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UTHSCSA ImageTool Resource Report Resource Website 100+ mentions |
UTHSCSA ImageTool (RRID:SCR_016208) | IT | data processing software, image analysis software, image processing software, software application, software resource | Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images. | image, analysis, processing, data, acquisition, compression, modification | has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA | Free, Available for download, Runs on Windows | http://en.bio-soft.net/draw/ImageTool.html | SCR_016208 | SciCrunch Registry | UTHSCSA Image Tool, UTHSCSA ImageTool (IT) | 2026-11-07 11:58:23 | 120 | |||||||
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InterLex Resource Report Resource Website 1+ mentions |
InterLex (RRID:SCR_016178) | controlled vocabulary, data or information resource, narrative resource, ontology, wiki | The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. InterLex is being constructed to help improve the way that biomedical scientists communicate about their data, so that information systems like NIF and dkNET can find data more easily and provide more powerful means of integrating that data across distributed resources. One of the big roadblocks to data integration in the biomedical sciences is the inconsistent use of terminology in databases and other resources such as the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then it is hard to compare them. InterLex allows for the association of data values (i.e. the value of a field or text within a field) to terminologies enabling the crowdsourcing of data-terminology mappings. InterLex was built on the foundation of NeuroLex (see Larson and Martone 2013 Neurolex: An online framework for neuroscience knowledge. Frontiers in Neuroinformatics, 7:18) and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies. NIFSTD currently has about 60,000 concepts (includes both classes and synonyms) that span gross anatomy, cells, subcellular structures, diseases, functions and techniques. InterLex models terms using primitives of the Web Ontology Language (OWL) and can export directly to a variety of standard ontology formats. A primary goal of interlex is to provide a stable layer on top of the many other existing terminologies, lexicons, and ontologies (i.e. provide a way to federate ontologies for data applications) and to provide a set of inter-lexical and inter-data-lexical mappings. In the future, InterLex will support user specific namespaces so that users can customize the exact definitions or ontologies they source from, as well as the relationships on those terms. Importantly, however, InterLex enforces a simple rule which is that terms which represent the same concept under the same superclass will maintain the same identifier fragment (i.e. 'ilx_1234567'). However, each user will be able to 'fork' a term into their own namespace (e.g. http://uri.interlex.org/user/ilx_1234567). This enables the various perspectives on a term or concept to have equal space so that the full diversity of views on a term can be seen and expressed. Sign-up for updates to get notified about updates to InterLex and when new features are available. | terminology, lexicon, vocabulary |
is used by: SPARC Portal is related to: NeuroLex is related to: NIFSTD has parent organization: SciCrunch |
https://scicrunch.org/scicrunch/interlex/dashboard | SCR_016178 | SciCrunch Registry | 2026-11-07 11:58:12 | 6 | ||||||||||
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CATNAP Resource Report Resource Website 10+ mentions |
CATNAP (RRID:SCR_016170) | data analysis software, data processing software, software application, software resource | Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, analysis, | PMID:26044712 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016170 | SciCrunch Registry | CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels | 2026-11-07 11:58:33 | 49 | |||||||||
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L1000 Fireworks Display Resource Report Resource Website 10+ mentions |
L1000 Fireworks Display (RRID:SCR_016175) | L1000FWD | data processing software, data visualization software, software application, software resource, web application | Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase. | drug, small molecule, gene, expression, signature, moa, clinical, phase | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | PMID:29420694 | Freely available, Free, Available for download | SCR_016175 | SciCrunch Registry | L1000FWD: Large-scale Visualization of Drug-Induced Transcriptomic Signatures | 2026-11-07 11:58:22 | 16 | |||||||
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ObservableHQ Resource Report Resource Website 1+ mentions |
ObservableHQ (RRID:SCR_016173) | application programming interface, data access protocol, software resource, web application | Web application for a code and text writing environment. It uses javascript and can be used to produce executable papers. | code, text, environment, writing, paper, research, journal, execute, programming, javascript | Open source, Freely available, Account required, Account required for full access | SCR_016173 | SciCrunch Registry | 2026-11-07 11:58:12 | 7 | |||||||||||
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Necklace Resource Report Resource Website 1+ mentions |
Necklace (RRID:SCR_016103) | alignment software, data processing software, image analysis software, software application, software resource | Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations. | RNA, Transcriptome, Non-model species, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:28836999 | Free, Available for download | biotools:necklace | https://bio.tools/necklace | SCR_016103 | SciCrunch Registry | Lace software | 2026-11-07 11:58:11 | 3 | ||||||
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Wave_clus Resource Report Resource Website 50+ mentions |
Wave_clus (RRID:SCR_016101) | algorithm resource, data analysis software, data processing software, software application, software resource | Algorithm for spike detection and sorting that uses wavelets and super-paramagnetic clustering. It generates an unsupervised solution, but this can be modified according to the experimenters’ preference for semi-automatic sorting. | spike, detection, wave, wavelet, magnetic, para-magnetic, solution, sorting, Automatic | requires: MATLAB | Free for non-commercial use, Available for download, Tutorial available | SCR_016101 | SciCrunch Registry | WaveClus, WaveClus spike-sorting algorithm | 2026-11-07 11:58:32 | 67 | |||||||||
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GoldWave Resource Report Resource Website 50+ mentions |
GoldWave (RRID:SCR_016189) | data analysis software, data processing software, software application, software resource | Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes. | audio, sound, analysis, acquisition, visualization, record, edit, analysis, auditory | Commercially available, Available for purchase | SCR_016189 | SciCrunch Registry | 2026-11-07 11:58:39 | 88 | |||||||||||
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Scientific Filesystem Resource Report Resource Website 1+ mentions |
Scientific Filesystem (RRID:SCR_016105) | SCIF | data management software, data or information resource, knowledge environment resource, portal, software application, software resource | Organizational software that supports exposure of executables and metadata for discoverability. The software includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within. | organization, executable, metadata, file, library, interaction, container, file, data environment | Public, Freely available, Tutorial available | https://github.com/sci-f/sci-f.github.io | SCR_016105 | SciCrunch Registry | The Scientific Filesystem, Scientific Filesystem (SCIF) | 2026-11-07 11:58:32 | 1 | ||||||||
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Prucka CardioLab System Resource Report Resource Website |
Prucka CardioLab System (RRID:SCR_016180) | resource | Prucka CardioLab system delivers the EP data and visualization we need for electrophysiological study and catheter ablation. | hardware, instrument, equipment, cardiology, heart, electrophysiology, catheter, ablation | SCR_016180 | SciCrunch Registry | 2026-11-07 11:58:33 | 0 | ||||||||||||
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LINCS Joint Project - Breast Cancer Network Browser Resource Report Resource Website 1+ mentions |
LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) | LJP-BCNB, LJP, BCNB | data access protocol, service resource, software resource, web service | Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations. | breast, cancer, tissue, cluster, drug, perturbation, cell, line, gene, expression |
is related to: L1000 Characteristic Direction Signature Search Engine is related to: LINCS Project |
Breast cancer | NCI U54 CA189201; NHGRI U54 HG006093; NHLBI U54 HL127365; NHLBI U54 HL127624 |
PMID:29084964 | Free, Freely available | https://github.com/MaayanLab/LJP | SCR_016181 | SciCrunch Registry | LINCS Joint Project, Breast Cancer Network Browser | 2026-11-07 11:58:39 | 1 | ||||
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IHM-dictionary Resource Report Resource Website 1+ mentions |
IHM-dictionary (RRID:SCR_016186) | software resource | Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures. | macromolecule, mmcif, pdb, protein, database, databank, spectroscopy, microscopy, crystallography, proteomic | is related to: PDB-Dev | NSF DBI-1519158 | Free, Available for download | SCR_016186 | SciCrunch Registry | 2026-11-07 11:58:33 | 4 | |||||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | data repository, service resource, storage service resource | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | SciCrunch Registry | 2026-11-07 11:58:22 | 36 | |||||||||
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GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | data access protocol, data or information resource, database, software resource, web service | Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis. | database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformatics |
is listed by: OMICtools is related to: University of British Columbia; British Columbia; Canada |
Canadian Foundation for Innovation infrastructure ; CIHR ; NIH MH111099; NSERC Discovery Grant |
DOI:10.1101/320861 | Free, Available for download, Freely available | https://github.com/PavlidisLab/gotrack, https://omictools.com/gotrack-tool | SCR_016399 | SciCrunch Registry | 2026-11-07 11:58:41 | 1 | |||||||
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Archive of Data on Disability to Enable Policy (ADDEP) Resource Report Resource Website |
Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) | ADDEP | data or information resource, data repository, service resource, storage service resource | Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies. | Data, access, disability | is recommended by: National Library of Medicine | NIBIB ; NICHD ; NINDS |
SCR_016315 | SciCrunch Registry | Archive of Data on Disability to Enable Policy | 2026-11-07 11:58:40 | 0 | ||||||||
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Avanti Polar Lipids Resource Report Resource Website 500+ mentions |
Avanti Polar Lipids (RRID:SCR_016391) | APL | commercial organization | Supplier of polar lipids. | lipid, fat, molecule, supply, distributer, lipidomic, reagent, adjuvant, immunotherapy | ISNI: 0000 0004 0595 5711, Wikidata: Q30284101, grid.423085.8 | https://ror.org/03n3jmy18 | SCR_016391 | SciCrunch Registry | Avanti, Avanti Lipids, , Avanti Polar Lipids Inc | 2026-11-07 11:58:26 | 566 | ||||||||
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RELION Resource Report Resource Website 100+ mentions |
RELION (RRID:SCR_016274) | data analysis software, data processing software, software application, software resource, standalone software | Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy. | cryo, cryogenic, cryo em, determination, analysis, bayesian, statistic, map, maximum a posteriori, electron, cryomicroscopy |
is listed by: Debian is listed by: OMICtools |
UK Medical Research Council | PMID:23000701 | Free, Available for download, Tutorial available | OMICS_15597 | https://sources.debian.org/src/relion-bin+mpi+gui/ | SCR_016274 | SciCrunch Registry | RELION, REgularised LIkelihood OptimisatioN, RELION-3 | 2026-11-07 11:58:24 | 440 | |||||
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HIRN Coordinating Center Resource Report Resource Website |
HIRN Coordinating Center (RRID:SCR_016395) | HIRN CC, HIRNCC | consortium, data or information resource, organization portal, portal | Consortium that provides infrastructure to promote communication and collaboration among current and future HIRN participants, facilitating scientific advances and the sharing of data, tools, and reagents among HIRN members and the research community at large. | coordination, hirn, human, islet, research, center, administration | is organization facet of: Human Islet Research Network (HIRN) | NIDDK U01 DK104162 | SCR_016395 | SciCrunch Registry | Human Islet Research Center Coordinating Center | 2026-11-07 11:58:26 | 0 | ||||||||
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Vensim Resource Report Resource Website 10+ mentions |
Vensim (RRID:SCR_016394) | simulation software, software application, software resource | Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models. | performance, system, Ventana Systems Inc, model, modelling, analysis | Commercially available, Available for purchase | SCR_016394 | SciCrunch Registry | 2026-11-07 11:58:16 | 14 |
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