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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Localite TMS Navigator Resource Report Resource Website 1+ mentions |
Localite TMS Navigator (RRID:SCR_016126) | resource | An instrument. Navigation system for transcranial magnetic stimulation (TMS). | hardware, instrument, equipment, tms, neuroimaging, neuroscience, neurology, transcranial, magnetic, stimulation | SCR_016126 | 2026-08-08 12:00:28 | 4 | ||||||||||||
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Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. | editing, database, management, plasmid maps, restriction, ligation, alignments, sequence, data, import, calculator, gel, image, display, PCR, cloning, genetic |
is listed by: Debian is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Free Software Foundation | Free, Available for download | OMICS_18307 | https://sources.debian.org/src/gentle/ | SCR_016127 | GENtle | 2026-08-08 12:00:48 | 6 | ||||||
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Singularity Hub Resource Report Resource Website 1+ mentions |
Singularity Hub (RRID:SCR_016248) | SHUB | data or information resource, web service, software resource, data access protocol, software application, software development tool, application programming interface, database | Database for singularity containers. It hosts container collections as well as articles about scientific advancements. | container, linux-container, singularity, singularity-container, builder, cloud-builder, google, storage | Stanford Research Computing and the School of Medicine | PMID:29186161 | Open source, Free, Available for download | SCR_016247 | SCR_016248 | singularity-registry, SingularityHub, shub, Singularity Registry | 2026-08-08 12:00:51 | 2 | ||||||
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Exonerate Resource Report Resource Website 100+ mentions |
Exonerate (RRID:SCR_016088) | software toolkit, image analysis software, software resource, software application, alignment software, data processing software | Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, pairwise, comparison, dynamic, programming, heuristic, bio.tools |
is used by: ExonerateTransferAnnotation is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:15713233 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:exonerate | https://bio.tools/exonerate | SCR_016088 | 2026-08-08 12:00:48 | 376 | |||||||
|
MICtools Resource Report Resource Website 10+ mentions |
MICtools (RRID:SCR_016121) | software resource, software application, data analysis software, data processing software | Software which combines the TICe and MICe measures into a two-step procedure that allows to identify relationships of various degrees of complexity in large datasets. TICe is used to perform an efficient high throughput screening of all the possible pairwise relationships and a permutation based approach is used to assess their significance. | tice, mice, dataset, permutation, statistic | Open source | SCR_016121 | Maximal Information Coefficient (MIC) Tools, MIC Tools, Maximal Information Coefficient Tools | 2026-08-08 12:00:48 | 12 | ||||||||||
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nelpy Resource Report Resource Website 1+ mentions |
nelpy (RRID:SCR_016209) | software toolkit, software resource, software application, data analysis software, data visualization software, data processing software | 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 | NSF CBET-1351692; NSF IOS-1550994; Human Frontiers Science Program RGY0088 |
Free, Available for download, Freely available | SCR_016209 | Nelpy (Neuroelectrophysiology) | 2026-08-08 12:00:29 | 3 | ||||||||
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UTHSCSA ImageTool Resource Report Resource Website 100+ mentions |
UTHSCSA ImageTool (RRID:SCR_016208) | IT | image processing software, image analysis software, software resource, software application, data processing software | 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 | UTHSCSA Image Tool, UTHSCSA ImageTool (IT) | 2026-08-08 12:00:51 | 120 | |||||||
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InterLex Resource Report Resource Website 1+ mentions |
InterLex (RRID:SCR_016178) | wiki, ontology, data or information resource, narrative resource, controlled vocabulary | 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 | 2026-08-08 12:00:50 | 6 | ||||||||||
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CATNAP Resource Report Resource Website 10+ mentions |
CATNAP (RRID:SCR_016170) | software resource, software application, data analysis software, data processing software | 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 | CATNAP - Compile Analyze and Tally Neutralizing Antibody Panels | 2026-08-08 12:00:50 | 49 | |||||||||
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L1000 Fireworks Display Resource Report Resource Website 10+ mentions |
L1000 Fireworks Display (RRID:SCR_016175) | L1000FWD | web application, software resource, software application, data visualization software, data processing software | 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 | L1000FWD: Large-scale Visualization of Drug-Induced Transcriptomic Signatures | 2026-08-08 12:00:50 | 16 | |||||||
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ObservableHQ Resource Report Resource Website 1+ mentions |
ObservableHQ (RRID:SCR_016173) | web application, application programming interface, software resource, data access protocol | 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 | 2026-08-08 12:00:49 | 7 | |||||||||||
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Necklace Resource Report Resource Website 1+ mentions |
Necklace (RRID:SCR_016103) | image analysis software, software resource, software application, alignment software, data processing software | 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 | Lace software | 2026-08-08 12:00:49 | 3 | ||||||
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Wave_clus Resource Report Resource Website 50+ mentions |
Wave_clus (RRID:SCR_016101) | software resource, software application, algorithm resource, data analysis software, data processing software | 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 | WaveClus, WaveClus spike-sorting algorithm | 2026-08-08 12:00:28 | 67 | |||||||||
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GoldWave Resource Report Resource Website 50+ mentions |
GoldWave (RRID:SCR_016189) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:29 | 88 | |||||||||||
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Scientific Filesystem Resource Report Resource Website 1+ mentions |
Scientific Filesystem (RRID:SCR_016105) | SCIF | data or information resource, knowledge environment resource, software resource, software application, data management software, portal | 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 | The Scientific Filesystem, Scientific Filesystem (SCIF) | 2026-08-08 12:00:48 | 1 | ||||||||
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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 | software resource, data access protocol, web service, service resource | 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 | NHLBI U54 HL127624; NHLBI U54 HL127365; NHGRI U54 HG006093; NCI U54 CA189201 |
PMID:29084964 | Free, Freely available | https://github.com/MaayanLab/LJP | SCR_016181 | LINCS Joint Project, Breast Cancer Network Browser | 2026-08-08 12:00:50 | 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 | 2026-08-08 12:00:50 | 4 | |||||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | storage service resource, data repository, 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 | 2026-08-08 12:00:50 | 36 | |||||||||
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GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | data or information resource, web service, software resource, data access protocol, database | 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 |
NIH MH111099; NSERC Discovery Grant ; Canadian Foundation for Innovation infrastructure ; CIHR |
DOI:10.1101/320861 | Free, Available for download, Freely available | https://github.com/PavlidisLab/gotrack, https://omictools.com/gotrack-tool | SCR_016399 | 2026-08-08 12:00:31 | 1 | |||||||
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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 | Avanti, Avanti Lipids, , Avanti Polar Lipids Inc | 2026-08-08 12:00:31 | 566 |
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