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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRAIG H. NEILSEN FOUNDATION Resource Report Resource Website 1+ mentions |
CRAIG H. NEILSEN FOUNDATION (RRID:SCR_014552) | CHN | institution | A non-profit organization that awards grants to a broad spectrum of charities, including those that benefit spinal cord injury efforts. The Foundation is primarily dedicated to funding extensive research, education and quality of life programs for improving the lives of people affected by spinal cord injury. | spinal cord, Paralysis, spinal cord injury | Crossref funder ID: 100005191, grid.428355.d | https://ror.org/00k0a6x92 | SCR_014552 | CRAIG NEILSEN FOUNDATION, NEILSEN FOUNDATION | 2026-08-01 12:05:04 | 9 | ||||||||
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ELIXIR Tools and Data Services Registry Resource Report Resource Website 10+ mentions |
ELIXIR Tools and Data Services Registry (RRID:SCR_014556) | topical portal, data or information resource, portal | Elixir Interoperability Platform to help people and machines to discover, access, integrate and analyse biological data. Encourages life science community to adopt standardized file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals. Bioinformatics resource registry that provides scientific and technical information about analytical tools and data services for bioinformatics. Gateway to databases and tools for life science data analysis.Provides comprehensive and up-to-date catalogue of resources that are interactive and downloadable, and that offer programmatic access. The registry also allows the community to upload their own resources to the registry following a simple log in procedure. | bioinformatics, data service registry, tool registry, resource registry, registry |
lists: gProfiler2 lists: Galactic Circos lists: bio.tools is affiliated with: bio.tools is related to: FAIRsharing is related to: Laniakea |
Free, Freely available | SCR_014556 | European Infrastructure for Biological Information Tools | 2026-08-01 12:05:13 | 20 | |||||||||
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UCSF Brain and Spinal Injury Center (UCSF-BASIC) Resource Report Resource Website |
UCSF Brain and Spinal Injury Center (UCSF-BASIC) (RRID:SCR_014553) | group | A center that conducts basic science and clinical research concerning spinal cord injury located at both the University of California San Francisco and the Zuckerberg San Francisco General Hospital. | spinal cord injury, traumatic brain injury, paralysis, neuroprotection, regeneration, clinical trials, translational research, syndromics | SCR_014553 | 2026-08-01 12:05:04 | 0 | ||||||||||||
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BioBlend Library Resource Report Resource Website 1+ mentions |
BioBlend Library (RRID:SCR_014557) | software resource, software library, software toolkit | A Python library which provides Python access to and interaction with Galaxy's API and CloudMan. The library allows users to create a CloudMan compute cluster via an API and directly from a local machine, reconnect to an existing CloudMan instance and manipulate it, and interact with Galaxy via a straightforward API and an object-oriented API. The library itself can be used with either service irrespective of the other. | python, library, cloudman, api, galaxy | is hosted by: GitHub | Available for download | SCR_014557 | BioBlend | 2026-08-01 12:05:04 | 8 | |||||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | software resource, software application, simulation software | Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. | simulation software, simulator, java, neuronal signaling pathway, neuron | HFSP ; NIMH K21-MH01141; NSF IBN 0077509; CRCNS program R01 AA16022; CRCNS program AA18066 |
Available for download | https://github.com/neurord/stochdiff/releases | SCR_014769 | 2026-08-01 12:05:08 | 13 | |||||||||
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COMSOL Multiphysics Resource Report Resource Website 10+ mentions |
COMSOL Multiphysics (RRID:SCR_014767) | software resource, software application, simulation software | General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating. | simulation software, software platform, physics, problem solver | is listed by: SoftCite | Commercially available | SCR_014767 | 2026-08-01 12:05:17 | 37 | ||||||||||
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Relibase Resource Report Resource Website 1+ mentions |
Relibase (RRID:SCR_014888) | software resource, data or information resource, web application, database | Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions. | structural biology, protein, ligand, protein data bank, pdb, visualization, analysis, molecular recognition | Available to the academic community | SCR_014888 | 2026-08-01 12:05:18 | 5 | |||||||||||
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ENIGMA-DTI Pipeline Resource Report Resource Website 10+ mentions |
ENIGMA-DTI Pipeline (RRID:SCR_014649) | protocol | Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols. | dti, enigma, protocol, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA has parent organization: ENIGMA |
NIBIB U54 EB020403 | Available for download from NITRC | http://www.nitrc.org/projects/enigma_dti | SCR_014649 | ENIGMA-DTI protocol, ENIGMA DTI pipeline, ENIGMA DTI protocol | 2026-08-01 12:05:06 | 47 | |||||||
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BatchTINT Resource Report Resource Website 1+ mentions |
BatchTINT (RRID:SCR_014804) | BatchTINTV2, BatchTINTV3 | software repository, data analysis software, software application, software resource, data processing software | GUI created by the Taub Institute in order to create an end-user friendly batch processing solution to complement Axona's new command line modification of TINT. This GUI allows the user to define a directory. Within this directory it will be continuously (unless closed) searching for new files to analyze via TINT. | python, gui, batch processing, tint, axona, directory | NIA R01 AG050425; Alzheimer’s Association 2015NIRG341570 |
DOI:10.5281/zenodo.200977 | Open access, Available for download, Operates on Windows | https://doi.org/10.5281/zenodo.200977 | https://github.com/GeoffBarrett/BatchTINTV2/tree/2.0.0 | SCR_014804 | BatchTINTV2, BatchTINTV3 | 2026-08-01 12:05:09 | 3 | |||||
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HIPPIE Resource Report Resource Website 100+ mentions |
HIPPIE (RRID:SCR_014651) | software resource, web application | Web tool used to generate confidence scored and functionally annotated human protein-protein interaction networks. Users can run a protein query using a UniProt identifier (ID or accession), gene symbol or Entrez gene id, or a network query using set fields. | web tool, web application, protein protein interaction, reference tool, protein query, network query, human protein protein interaction network | Helmholtz Alliance in Systems Biology ; BMBF 01GS08170 |
DOI:10.1371/journal.pone.0031826 | Available on the web, Available for download, Acknowledgement requested | SCR_014651 | Human Integrated Protein Protein Interaction Reference, Human Integrated Protein-Protein Interaction rEference, Human Integrated Protein-Protein Interaction rEference (HIPPIE) | 2026-08-01 12:05:15 | 135 | ||||||||
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iResearch Library Resource Report Resource Website 1+ mentions |
iResearch Library (RRID:SCR_014890) | software resource, data or information resource, web application, database | Database of commercially accessible screening compounds from international chemistry suppliers. iResearchLibrary is updated on a weeky basis and offers support for creating internal screening libraries containing commercially accessible compounds, developing exploratory and targeted libraries, selecting commercially accessible compounds for SAR, lead expansion, and hit follow-up projects, and using structures for pharmacophore searching, virtual screening and other computational work. | research, database, library, chemistry, suppliers, pharmacology, screening, computation | Commercial, Freely available to National Institutes of Health (NIH) researchers | SCR_014890 | 2026-08-01 12:05:09 | 2 | |||||||||||
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PCSIM Resource Report Resource Website 1+ mentions |
PCSIM (RRID:SCR_014770) | software resource, software application, simulation software | Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI. | simulation software, simulator, heterogenous network, model, neuron, synapse | is related to: CSIM | DOI:10.3389/neuro.11.011.2009 | Available for download | SCR_014770 | Parallel neural Circuit SIMulator, Parallel Neural Circuit Simulator (PCSIM), Parallel Neural Circuit Simulator | 2026-08-01 12:05:08 | 4 | ||||||||
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EcoCyte Bioscience Resource Report Resource Website 1+ mentions |
EcoCyte Bioscience (RRID:SCR_014773) | commercial organization | Supplier and servicer of products for expression studies in Xenopus laevis oocytes. Products include overnight delivery of freshly prepared Xenopus laevis oocytes, Cell & Tissue Media necessary during preparation, maintenance, and recording of Xenopus oocytes and lab chemicals. Services for pharmacological studies include heterologous expression and in vitro electrophysiology. | supplier, commercial, xenopus, xenopus laevis, laboratory equipment, oocyte, pharmacology, heterologous expression, electrophysiology | is parent organization of: Ecocyte Bioscience Xenopus laevis oocytes delivery service | SCR_014773 | 2026-08-01 12:05:17 | 6 | |||||||||||
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RepeatScout Resource Report Resource Website 500+ mentions |
RepeatScout (RRID:SCR_014653) | data analysis software, software application, data processing software, sequence analysis software, software resource, algorithm resource | Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | algorithm, sequence analysis, repeat, genome sequence, de novo, repeat family, repeat library, bio.tools |
is used by: RepeatModeler is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:15961478 | THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:RepeatScout, biotools:RepeatScout | https://bio.tools/RepeatScout, https://bio.tools/RepeatScout, https://bio.tools/RepeatScout | SCR_014653 | 2026-08-01 12:05:06 | 815 | |||||||
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Genezilla Resource Report Resource Website 10+ mentions |
Genezilla (RRID:SCR_014657) | data analysis software, software application, software resource, sequence analysis software, data processing software | Reconfigurable eukaryotic gene finder based on the Generalized Hidden Markov Model framework. The run time and memory requirements are linear in the sequence length. Genezilla utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, and CAP sites. | eukaryotic gene finder, markov, framework, c++, signal peptide, branch point, tata, cap site | Available for download | SCR_014657 | 2026-08-01 12:05:06 | 19 | |||||||||||
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Eelbrain Resource Report Resource Website 10+ mentions |
Eelbrain (RRID:SCR_014661) | data processing software, data analysis software, software application, software resource | Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases. | statistical analysis, analysis toolbox, electrical brain activity, meg, eeg | is hosted by: GitHub | NYU Abu Dhabi Institute G1001 | Open source, Acknowledgement requested | https://github.com/christianbrodbeck/Eelbrain | SCR_014661 | 2026-08-01 12:05:07 | 11 | ||||||||
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Zero Mode Waveguide Imaging and Analysis package tools Resource Report Resource Website 1+ mentions |
Zero Mode Waveguide Imaging and Analysis package tools (RRID:SCR_014660) | image analysis software, data acquisition software, software application, software resource, data processing software | MATLAB software tool collection for data acquisition and image analysis from zero mode waveguides. | software tool collection, matlab, data acquisition, image analysis, zero mode waveguide, package tools | is hosted by: GitHub | Available for download, Documentation is currently lacking | https://github.com/marcel-goldschen-ohm | SCR_014660 | 2026-08-01 12:05:15 | 5 | |||||||||
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MetaboLights Resource Report Resource Website 500+ mentions |
MetaboLights (RRID:SCR_014663) | data or information resource, data repository, storage service resource, database, service resource | A cross-species, cross-technique database for metabolomics experiments, data, and derived information. It includes metabolite structures and their reference spectra, their biological roles, locations and concentrations, and experimental data from metabolic experiments. | metabolomics, database, structure, spectra, experimental data |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Metabolomics Workbench |
BBSRC BB/L024152/1 | Publicly available, The community can contribute to this resource | r3d100011556 | SCR_014663 | MetaboLights | 2026-08-01 12:05:16 | 741 | |||||||
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Schrodinger Resource Report Resource Website 500+ mentions |
Schrodinger (RRID:SCR_014879) | commercial organization | Commercial ogranization which provides molecular and drug discovery software and services to researchers. American software company that develops chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Provides products ranging from general molecular modeling programs to a full suite of chemical simulation and drug design software, including ligand- and structure-based methods. | software solution, drug discovery, small molecule, computational chemistry |
is parent organization of: Epik is parent organization of: Ligprep is parent organization of: Glide is parent organization of: Phase is parent organization of: MacroModel is parent organization of: Maestro is parent organization of: Protein preparation Wizard is parent organization of: Shape screening |
Wikidata: Q7432923, ISNI: 0000 0001 0903 5603, grid.421925.9, SCR_014879 | https://ror.org/05a3z6914 | SCR_014879 | Schrodinger Inc. | 2026-08-01 12:05:09 | 782 | ||||||||
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NeuroExperimenter Resource Report Resource Website 1+ mentions |
NeuroExperimenter (RRID:SCR_014759) | NEx | data visualization software, data analysis software, software application, software resource, data processing software | Software which provides an interface for MindWave Mobile hardware, allowing users to view and listen to brainwave output of different "mind states". Users can: view any or all brainwaves, specify a combination of brainwaves via a formula, compare a base line session to a performance session, and create a log and run it through the application to view different graphical outputs. NeuroExperimenter only runs on Windows | data visualization, data analysis, software, interface, brainwave, brain wave, mind state | Freely available, Available for download, Under active development | https://sites.google.com/site/fredm/neuroexperimenter | SCR_014759 | NeuroExperimenter (NEx) | 2026-08-01 12:05:07 | 1 |
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