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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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msbwt Resource Report Resource Website |
msbwt (RRID:SCR_000458) | software resource | A software package for creating, merging, and querying multi-string BWTs. | standalone software, python |
is listed by: OMICtools has parent organization: Google Code |
PMID:25172922 | Free, Available for download, Freely available | OMICS_05976 | https://code.google.com/p/msbwt/ | SCR_000458 | multi-string BWT | 2026-09-12 12:55:09 | 0 | ||||||
|
MAXCHELATOR Resource Report Resource Website 50+ mentions |
MAXCHELATOR (RRID:SCR_000459) | MAXC | software resource | A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration. | metal, concentration, chelator |
is related to: WEBMAXC STANDARD is related to: WEBMAXC EXTENDED has parent organization: Stanford University; Stanford; California |
PMID:8201981 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156862 | SCR_000459 | 2026-09-12 12:55:09 | 74 | |||||||
|
Rdisop Resource Report Resource Website |
Rdisop (RRID:SCR_000453) | software resource | Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02416, biotools:rdisop | https://github.com/sneumann/Rdisop, https://bio.tools/rdisop | SCR_000453 | Rdisop - Decomposition of Isotopic Patterns, Rdisop: Decomposition of Isotopic Patterns, Decomposition of Isotopic Patterns | 2026-09-12 12:55:09 | 0 | |||||||
|
AdaptiveCrawler Resource Report Resource Website |
AdaptiveCrawler (RRID:SCR_000573) | AdaptiveCrawler | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers. | web crawler, acquire social media content on Internet, cancer research, |
is listed by: OMICtools has parent organization: Oak Ridge National Laboratory |
Cancer, Breast cancer, Lung cancer | PMID:24078710 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01170 | SCR_000573 | Adaptive Crawler, Smart Web Crawler | 2026-09-12 12:55:11 | 0 | |||||
|
National Spasmodic Dysphonia Association Resource Report Resource Website 1+ mentions |
National Spasmodic Dysphonia Association (RRID:SCR_000447) | data or information resource, portal, topical portal | The mission of the National Spasmodic Dysphonia Association is to advance medical research into the causes of and treatments for spasmodic dysphonia, promote physician and public awareness of the disorder, and provide support to those affected by spasmodic dysphonia. | patient support | nif-0000-00490 | SCR_000447 | NSDA | 2026-09-12 12:55:09 | 1 | ||||||||||
|
International Consortium for Brain Mapping Resource Report Resource Website 1+ mentions |
International Consortium for Brain Mapping (RRID:SCR_000445) | ICBM | atlas, data or information resource, database, reference atlas | Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis. | Brain atlases, fmri, genetics, anatomy, architecture, atlas, brainstem, cerebellum, cortex, gray matter, histology, imaging, map, morphology, mri, neuroinformatics, pet, receptor, segmentation, subcortical, volume, warping, white matter, brain, early adult human, structural anatomy, functional anatomy, in vivo, post mortem, neuroanatomy, image collection |
is related to: MINC/Atlases has parent organization: Laboratory of Neuro Imaging |
NIMH | PMID:9343592 PMID:11522763 |
Free, Freely available | nif-0000-00103, SCR_001948, nif-0000-00041 | https://resource.loni.usc.edu/ | http://www.loni.ucla.edu/ICBM/Databases/, http://www.loni.usc.edu/ICBM/ | SCR_000445 | , ICBM Subject Database, ICBM - International Consortium for Brain Mapping, International Consortium for Brain Mapping (ICBM), ICBM Atlas | 2026-09-12 12:55:09 | 6 | |||
|
Talairach Daemon Resource Report Resource Website 100+ mentions |
Talairach Daemon (RRID:SCR_000448) | talairach.org | atlas, data or information resource, database, software application, software resource | Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas. | anatomical structure, atlas, fmri, pet, activation foci, cognition, talairach, human, brain, brain mapping, atlas application, database application, atlas application, database application, java, magnetic resonance, os independent, label, probability map, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: WFU PickAtlas has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA |
EJLB Foundation ; Human Brain Project |
PMID:10912591 | Free, Available for download, Freely available | nif-0000-00042 | http://www.nitrc.org/projects/tal-daemon | SCR_000448 | Talairach Software | 2026-09-12 12:55:09 | 383 | ||||
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stsPlots Resource Report Resource Website |
stsPlots (RRID:SCR_000449) | software resource | Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems. | software package, r | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05141 | SCR_000449 | 2026-09-12 12:55:09 | 0 | |||||||||
|
HighWire Press Resource Report Resource Website 1+ mentions |
HighWire Press (RRID:SCR_000761) | data or information resource, database, publisher, service resource | A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content. | biomedical, communication, images, interactivity, literature, multimedia, science, scientific, scientific literature databases and services, technology |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21191 | SCR_000761 | HighWire Press | 2026-09-12 12:55:14 | 6 | ||||||||
|
University of Neurosurgery Webinar Series Resource Report Resource Website |
University of Neurosurgery Webinar Series (RRID:SCR_000639) | data or information resource, meeting resource, online course, training resource, video resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. A series of of webinars offered directly to users' computers. The webinars are offered in a variety of subjects, including neurotrauma, spine, tumor and vascular. Each webinars costs $35 US and offers CME credit. | medical, webinar, neurotrauma, spine, tumor, vascular, cme credit, video resource | has parent organization: Congress of Neurological Surgeons | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-06723 | SCR_000639 | Congress of Neurological Surgeons Webinar Series, CNS Webinar Series | 2026-09-12 12:55:12 | 0 | ||||||||
|
Neo Resource Report Resource Website 10+ mentions |
Neo (RRID:SCR_000634) | neo | software resource | A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion. | neurophysiology, electrophysiology, python, interoperability, intracellular, extracellular, eeg, electrode |
is used by: Elephant is used by: OpenElectrophy is used by: NetworkUnit has parent organization: NeuralEnsemble |
PMID:24600386 | Free, Available for download, Freely available | nlx_151874 | SCR_000634 | 2026-09-12 12:55:12 | 18 | |||||||
|
National Addiction and HIV Data Archive Program (NAHDAP) Resource Report Resource Website |
National Addiction and HIV Data Archive Program (NAHDAP) (RRID:SCR_000636) | NAHDAP | data or information resource, data repository, disease-related portal, portal, service resource, storage service resource, topical portal | Archive that acquires, preserves and disseminates data relevant to drug addiction and HIV research. Collection of data on drug addiction and HIV infection in United States. Most of datasets are raw data from surveys, interviews, and administrative records. They were originally gathered in research projects and for administrative purposes. Some datasets have been used in published studies. Bibliographies of these studies are available . Provides access to research data and technical assistance for data depositors. Provides e-workshops on data preparation and data systems. | drug addiction data, HIV infection data, |
uses: DataCite is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org has parent organization: Inter-university Consortium for Political and Social Research (ICPSR) |
Addiction, Human immunodeficiency virus, HIV | NIDA ; Office of Behavioral and Social Sciences Research |
Restricted | nif-0000-06713, r3d100010261, DOI:10.3886 | https://doi.org/10.3886/, https://dx.doi.org/10.3886/, https://doi.org/10.17616/R3PK64 | SCR_000636 | , National Addiction & HIV DATA Archive Program, National Addiction HIV Data Archive Program, National Addiction and HIV DATA Archive Program, NAHDAP, National Addiction and HIV DATA Archive Program (NAHDAP), National Addiction & HIV DATA Archive Program (NAHDAP), ICPSR/NAHDP | 2026-09-12 12:55:12 | 0 | ||||
|
CAST Resource Report Resource Website 10+ mentions |
CAST (RRID:SCR_000628) | CAST | data analysis software, data processing software, sequence analysis software, software application, software resource | A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity. | low-complexity region detection and selective masking, query sequence against twenty homopolymers, infinite gap penalties, masked query sequence, | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | European Molecular Biology Laboratory; Heidelberg; Germany ; European Union ; TMR Proramme ; IBM Research |
PMID:11120681 | nlx_151779 | http://www.ebi.ac.uk/research/cgg/services/cast/ | SCR_000628 | CAST - Compositional Bias Detection Algorithm | 2026-09-12 12:55:12 | 11 | |||||
|
VISAGES Research Resource Report Resource Website 1+ mentions |
VISAGES Research (RRID:SCR_000749) | VisAGeS | data or information resource, organization portal, portal, topical portal | Research team focused on research and development of new algorithms in medical imaging, information processing and computer assisted intervention in the context of the pathologies of the central nervous system. Research team jointly affiliated to INSERM (National Institute of Health and Scientific Research), Inria (National Institute of Research in Computer Sciences and Automation) and IRISA / UMR CNRS 6074, University of Rennes I. Multidisciplinary team merging researchers in image processing and medical doctors. | team, image, processing, researcher, medical, doctor, development, algorithm, information, pathology, central, nervous, system |
is related to: Empenn has parent organization: University of Rennes 1; Rennes; France is parent organization of: Anima is parent organization of: Anima scripts |
Multiple Sclerosis, Epilepsy, Parkinson, Dementia, Stroke, Depression, Schizophrenia | nif-0000-10223 | https://www.irisa.fr/RA/D5/VISAGES/2015/visages2015.pdf | SCR_000749 | Vision Action and information manaGEment System in health, VisAGeS, VISAGES | 2026-09-12 12:55:14 | 5 | ||||||
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BEBaC Resource Report Resource Website |
BEBaC (RRID:SCR_000621) | BEBaC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities. | linux, bayesian |
is listed by: OMICtools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:22406836 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01440 | SCR_000621 | Bayesian estimation of bacterial communities | 2026-09-12 12:55:12 | 0 | ||||||
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Genboree Discovery System Resource Report Resource Website 10+ mentions |
Genboree Discovery System (RRID:SCR_000747) | Genboree | data or information resource, data processing software, database, software application, software resource | A software application and database viewing system for genomic research, more specifically formulti-genome comparison and pattern discovery via genome self-comparison. Data are available for a range of species including Human Chr3, Human Chr12, Sea Urchin, Tribolium, and cow. The Genboree Discovery System is the largest software system developed at the bioinformatics laboratory at Baylor in close collaboration with the Human Genome Sequencing Center. Genboree is a turnkey software system for genomic research. Genboree is hosted on the Internet and, as of early 2007, the number of registered users exceeds 600. While it can be configured to support almost any genome-centric discovery process, a number of configurations already exist for specific applications. Current focus is on enabling studies of genome variation, including array CGH studies, PCR-based resequencing, genome resequencing using comparative sequence assembly, genome remapping using paired-end tags and sequences, genome analysis and annotation, multi-genome comparison and pattern discovery via genome self-comparison. Genboree database and visualization settings, tools, and user roles are configurable to fit the needs of specific discovery processes. Private permanent project-specific databases can be accessed in a controlled way by collaborators via the Internet. Project-specific data is integrated with relevant data from public sources such as genome browsers and genomic databases. Data processing tools are integrated using a plug-in model. Genboree is extensible via flexible data-exchange formats to accommodate project specific tools and processing steps. Our Positional Hashing method, implemented in the Pash program, enables extremely fast and accurate sequence comparison and pattern discovery by employing low-level parallelism. Pash enables fast and sensitive detection of orthologous regions across mammalian genomes, and fast anchoring of hundreds of millions of short sequences produced by next-generation sequencing technologies. We are further developing the Pash program and employing it in the context of various discovery pipelines. Our laboratory participates in the pilot stage of the TCGA (The Cancer Genome Atlas) project. We aim to develop comprehensive, rapid, and economical methods for detecting recurrent chromosomal aberrations in cancer using next-generation sequencing technologies. The methods will allow detection of recurrent chromosomal aberrations in hundreds of small ( | genome, genomic, next generation sequencing |
is related to: Spark has parent organization: Baylor University; Texas; USA |
nif-0000-08906 | SCR_000747 | Genboree Discovery System | 2026-09-12 12:55:14 | 11 | ||||||||
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FlipFlop Resource Report Resource Website |
FlipFlop (RRID:SCR_000625) | software resource | Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. | standalone software, unix/linux, mac os x, windows, r, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24813214 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04028, biotools:flipflop | https://bio.tools/flipflop | SCR_000625 | flipflop - Fast lasso-based isoform prediction as a flow problem | 2026-09-12 12:55:12 | 0 | ||||||
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CryptoBase Resource Report Resource Website 1+ mentions |
CryptoBase (RRID:SCR_000780) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San Francisco | has parent organization: University of California at San Francisco; California; USA | Herb and Marion Sandler Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30395 | http://archive.is/YgVX4 | SCR_000780 | 2026-09-12 12:55:14 | 2 | ||||||||
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Wnt homepage Resource Report Resource Website 10+ mentions |
Wnt homepage (RRID:SCR_000662) | Wnt homepage | data or information resource, portal, topical portal | A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year. | wnt signaling, wnt, wnt protein, wnt pathway, signaling, pathway, method, protein, reagent, bibliography | has parent organization: Stanford University; Stanford; California | Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156863 | SCR_000662 | the Wnt homepage | 2026-09-12 12:55:13 | 13 | ||||||
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FileMaker Resource Report Resource Website 50+ mentions |
FileMaker (RRID:SCR_000783) | software resource | A database software for managing, analyzing and sharing information across multiple devices and people, both online and offline. | file, maker, information, sharing, analyze, sync, devices, windows, apple, ios, FASEB list | Restricted | nif-0000-30436 | SCR_000783 | FileMaker | 2026-09-12 12:55:14 | 65 |
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