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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Genemed Resource Report Resource Website 1+ mentions |
Genemed (RRID:SCR_000070) | commercial organization | A supplier of cancer and infectious disease diagnostic reagents. The company also provides services such as tissue-based and molecular diagnostics to their partners to accelerate their in vitro diagnostic device (IVD) product development and commercialization. | antibody, diagnostic, research, development, commercialization, in vitro diagnostic device, IVD, cancer, infectious diseases | Commercial | nlx_152371 | SCR_000070 | 2026-08-08 11:57:12 | 1 | ||||||||||
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University of California at San Diego Cognitive Science Graduate Student Fellowship Opportunities Resource Report Resource Website |
University of California at San Diego Cognitive Science Graduate Student Fellowship Opportunities (RRID:SCR_000105) | funding resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. This resource is a frequently updated listing of graduate student in cognitive science fellowship opportunities. For current opportunities, please see the PDF document. | psychology | has parent organization: University of California at San Diego; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10500 | SCR_000105 | UCSD Cognitive Science Fellowships | 2026-08-08 11:57:13 | 0 | ||||||||
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National MS Society Resource Report Resource Website 10+ mentions |
National MS Society (RRID:SCR_000104) | National MS Society | data or information resource, topical portal, portal, funding resource, disease-related portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward. | multiple sclerosis, award, grant, postdoctoral fellowship | Multiple Sclerosis | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143693 | SCR_000104 | National Multiple Sclerosis Society | 2026-08-08 11:57:13 | 34 | |||||||
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Treephyler Resource Report Resource Website 1+ mentions |
Treephyler (RRID:SCR_000109) | Treephyler | software resource | A software tool for fast taxonomic profiling of metagenomes. | metagenome, perl, nucleotide, protein, next-generation sequencing | is listed by: OMICtools | PMID:20172941 | Free, Available for download, Freely available | OMICS_01469 | SCR_000109 | Treephyler: fast taxonomic profiling of metagenomes | 2026-08-08 11:57:13 | 1 | ||||||
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Ludwig Boltzmann Cluster Translationale Onkologie Resource Report Resource Website |
Ludwig Boltzmann Cluster Translationale Onkologie (RRID:SCR_000020) | Ludwig Boltzmann Cluster Translational Oncology | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project. | cancer, tumor, clinical, oncology, photodynamic therapy, gynecology, gynecologic oncology, stem cell transplantation, surgical oncology, tumor cell | is parent organization of: Ludwig Boltzman Tumour Bank | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143958 | SCR_000020 | 2026-08-08 11:57:11 | 0 | ||||||||
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GenomicRanges Resource Report Resource Website 50+ mentions |
GenomicRanges (RRID:SCR_000025) | GenomicRanges | software resource | Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. | genomic interval |
is used by: riboWaltz is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | SCR_018096, OMICS_01161 | SCR_000025 | GenomicRanges - Representation and manipulation of genomic intervals | 2026-08-08 11:57:11 | 56 | |||||||
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Neuroscience Link List Resource Report Resource Website |
Neuroscience Link List (RRID:SCR_000130) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A website that provides links to many neuroscience resources on the web as well as links to university neuroscience and neurobiology program home-pages. | link list, links, neuroscience resources, topical portal | has parent organization: Weill Cornell Medical College; New York; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00083 | SCR_000130 | World-Wide Web Virtual Library:Neuroscience, World-Wide Web Virtual Library:Neuroscience (Biosciences), The World-Wide Web Virtual Library:Neurosciences | 2026-08-08 11:57:14 | 0 | ||||||||
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Computational Neuroscience on the Web Resource Report Resource Website 1+ mentions |
Computational Neuroscience on the Web (RRID:SCR_000010) | data or information resource, portal, topical portal | Annotated index for computational neurobiology, focusing on compartmental modeling and realistic simulations of biological neural systems. Has resources to find modeling software and software for computational morphology, phase plane and spike train analysis, and web based neuroinformatics. Provides links to major laboratories, researchers, conferences, education and funding for theoretical neurobiology. | computational, neuroscience, compartmental, modeling, simulation, biological, neural, system, neuroinformatics, index | Free, Freely available | nif-0000-00107 | http://home.earthlink.net/~perlewitz/ | SCR_000010 | 2026-08-08 11:57:10 | 1 | |||||||||
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JChemPaint Resource Report Resource Website 1+ mentions |
JChemPaint (RRID:SCR_000095) | JCP | software resource | Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK). | applet, mac os x, unix/linux, windows, java | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_04959 | https://github.com/JChemPaint/jchempaint | SCR_000095 | 2026-08-08 11:57:13 | 1 | |||||||
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BSmooth-align Resource Report Resource Website 1+ mentions |
BSmooth-align (RRID:SCR_000013) | image analysis software, software resource, software application, data analysis software, alignment software, data processing software | Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements. | bisulfite sequence, read-level methylation, bisulfite sequence reads alignment, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01846 | SCR_000013 | 2026-08-08 11:57:10 | 1 | |||||||||
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Porifera Ontology Resource Report Resource Website 1+ mentions |
Porifera Ontology (RRID:SCR_000134) | PORO | ontology, data or information resource, controlled vocabulary | An ontology covering the anatomy of Porifera (sponges). | owl, anatomy |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is listed by: Ontobee is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157558 | https://code.google.com/p/porifera-ontology/, http://purl.bioontology.org/ontology/PORO, http://purl.obolibrary.org/obo/poro.owl | http://purl.obolibrary.org/obo/poro | SCR_000134 | 2026-08-08 11:57:12 | 1 | ||||||
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Leica: DMRE Fluorescence Microscope Resource Report Resource Website 1+ mentions |
Leica: DMRE Fluorescence Microscope (RRID:SCR_000011) | Leica DMRE microscope | instrument resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Microscope that enables bright field and fluorescence imaging options. | microscope, fluorescence, imaging, hardware, instrument, equipment, USEDit | has parent organization: Leica Microsystems | THIS RESOURCE IS NO LONGER IN SERVICE | https://drive.google.com/file/d/1wdHpvLSM220N2HdsOjW8rK2mWlPoJEcP/view?usp=drivesdk | SciRes_000155 | SCR_000011 | Fluorescence Leica DMRE microscope | 2026-08-08 11:57:10 | 9 | ||||||
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Sequence Read Format Resource Report Resource Website 1+ mentions |
Sequence Read Format (RRID:SCR_000132) | SRF | data or information resource, interchange format, narrative resource, standard specification | A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology. | dna sequence, dna sequencing, interchange format |
is listed by: OMICtools has parent organization: SourceForge |
Public, A C++ implementation of Sequence Read Format is available | OMICS_05130 | SCR_000132 | Sequence Read Format (SRF) | 2026-08-08 11:57:14 | 1 | |||||||
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EPIGEN Resource Report Resource Website 10+ mentions |
EPIGEN (RRID:SCR_000093) | EPIGEN | portal, data or information resource, consortium, organization portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | epilepsy, genetics, gene, mri, genetic variation, clinical |
has parent organization: Duke University; North Carolina; USA has parent organization: University College London; London; United Kingdom has parent organization: Beaumont Hospital; Dublin; Ireland has parent organization: Royal College of Surgeons in Ireland; Dublin; Ireland has parent organization: Free University of Brussels; Brussels; Belgium |
Epilepsy | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143740 | SCR_000093 | EPIGEN: An international consortium dedicated to tackling epilepsy through genetics, EPIGEN Consortium | 2026-08-08 11:57:13 | 24 | ||||||
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University of Algarve; Faro; Portugal Resource Report Resource Website |
University of Algarve; Faro; Portugal (RRID:SCR_000006) | UAlg | university | A young state university located in the southern part of Portugal. | university, portugal, topical portal | is parent organization of: Unified Human Interactome | nlx_157657 | SCR_000006 | University of the Algarve, Universidade do Algarve, Universidade Algarve, University of Algarve | 2026-08-08 11:57:10 | 0 | ||||||||
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G Biosciences Resource Report Resource Website |
G Biosciences (RRID:SCR_000007) | commercial organization | Commercial antibody supplier that provides research materials for projects such as: protein purification, protein analysis, protein estimation assays, DNA purification, plasmid DNA isolation and transformation, protein quantification assays, and coupled assays for methylation. This supplier also provides buffers, reagents, education programs, and training programs. | antibody vendor, buffer vendor, education programs, training programs, reagent | nlx_152367 | SCR_000007 | 2026-08-08 11:57:10 | 0 | |||||||||||
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DOCK Resource Report Resource Website 10+ mentions |
DOCK (RRID:SCR_000128) | DOCK | software resource | An algorithm used to predict and analyse binding modes of docking molecules. Users can search ligand databases for compounds that inhibit enzymatic activity and bind to particular molecules and nucleic acid targets. Molecular docking is used to predict a predominant binding mode(s) of a ligand in three-dimensional structure. This method can be used for molecular biology and computer-assisted drug design. | molecule docking, ligand model, drug design, molecular biology |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
Available to the research community, Free for the academic community, License fee for industrial organizations, Available for download | OMICS_01598 | SCR_000128 | UCSF DOCK | 2026-08-08 11:57:14 | 16 | |||||||
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GE Healthcare Resource Report Resource Website 10000+ mentions |
GE Healthcare (RRID:SCR_000004) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 10,2024. A commercial antibody supplier and provider of various services., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | antibody supplier, service provider, commercial |
lists: Amersham Biosciences is related to: Cytiva is parent organization of: ImageQuant |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152368 | SCR_000004 | GE Healthcare Life Sciences, Amersham Biosciences | 2026-08-08 11:57:10 | 18879 | ||||||||
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Neuroshare - Open data specifications and software for neurophysiology Resource Report Resource Website |
Neuroshare - Open data specifications and software for neurophysiology (RRID:SCR_000005) | software library, software resource, software toolkit | Neuroshare aims to develop a standard for accessing neurophysiological data from any vendor's acquisition device or software. An API is defined, and vendors and communities are encouraged to provide implementations of a library of functions that can read data files collected with that vendor's instrument or software. The neuroshare.org website is a collaborative, vendor-neutral area dedicated to public domain standards and software for neurophysiology.This website is part of an SBIR program funded by the National Institute for Neural Disorders and Stroke and it is currently being administered by Bionic Technologies, LLC. The goals of the SBIR program are to (Phase I) create open library and format standards for neurophysiological experiment data and (Phase II) create a set of free, open-source software tools for low-level handling and processing of neurophysiological data. Upon completion of Phase I and II, neuroshare.org will be maintained by a yet to be determined consortium of government, academic and industry partners. The SBIR was awarded in the fall of 2001 and Phase I officially began in Dec, 2001. The detailed goals of the program are summarized below:Phase I goals :(1) Establish a working group to develop and define the API library of functions.(2) A vendor-neutral web site to facilitate the development of the standards and software and publish the completed products. This site has been dubbed Neuroshare. The home page can be found at neuroshare.sourceforge.net.(3) An open, standardized API library definition for accessing neurophysiology data files. This will allow developers to produce analysis programs that can access a variety of proprietary data formats through libraries supplied by the data format owners. The manner of support will be completely determined by the research groups and vendors that supply the libraries. The Phase I standard was created by a working group consisting of international members from industry and academia. Draft standards were published for public review and comment on the neuroshare web site and revised by the working group.The grant has been awarded as a fast-track program so that Phase II begins immediately upon completion of the Phase I milestones in June 2002. Phase II will produce :(1) A set of neuroshare-compliant API libraries for existing data formats developed in collaboration with individual equipment vendors and research groups.(2) A utility for analyzing compliant API libraries for integrity and specification conformance, as well as for error checking imported data files.(3) A set of template programs in C that are meant to be used as an example on how to create a Neuroshare API compliant library and how to call it from an application,(4) An open, standardized file format for neurophysiological experiment data. This format will provide research groups and vendors with a file format for exchanging and/or publishing neural data. The format will also be powerful enough for use as a native format for researchers or vendors that wish to support it in data acquisition hardware/software.(5) Import filters that interface neuroshare-compliant API libraries to Visual Basic, MATLAB, and LabVIEW, NeuroExplorer, and Stranger analysis environments.(6) A utility program for quick header information viewing and searching to aid the organization and management of data files in the standard and proprietary formats.(7) A data file editing program for reviewing, editing, annotating, and splicing neural data files through the neuroshare API libraries and/or standard file formats. The suite will be developed in C, optimized for speed, and will run within 32-bit Windows operating systems. The availability of source code will enable eventual ports to Unix/Linux if desired(8) An add-on for the editing program that will allow review and real-time playback of multi-modal data accessible through the API and/or standard file format. These modes will include neurophysiological signals such as spikes, local field potentials and EEG, as well as experimental signals such as kinematics, stimulation, audio, video, and imaging data.(9) C and MATLAB framework programs for detection and classification of extracellular spikes in the standard data files based on classical and user-supplied algorithms.(10) A complete MATLAB application for reading data from the standard format and performing reverse correlation analysis. This program will serve as a tutorial and modifiable template for users performing analysis in MATLAB.(11) A set of export filters for creating neurophysiological data files with the neural simulation environments NEURON, NEOSIM, GENESIS, and NSL.(12) A comprehensive documentation, and help file set for all of the developed applications.Phase II will require two years of development work and software products will be made available as they are completed. As stated above, the Phase II software products will be made available as free, open-source tools. We have not decided on a license model yet, but are currently leaning towards the GNU General Public License. Revisions and bug-fixes will be maintained through the neuroshare.org website. The mission of neuroshare.org is very focused, but the specific goal list of Phase II may evolve somewhat as software is released and user feedback is received. We very interested in public suggestions about how to improve this development effort and web site. Please direct your feedback to commentsneuroshare.org or refer to our contacts page for other addresses.BackgroundThis endeavor grew out of a meeting held at the Society for Neuroscience 2000 Annual Conference in New Orleans (agenda posted here) to discuss the development of standard data formats for neuroscience. From this meeting, it was clear that although everyone supported the idea of better data portability, many vendors present wanted a standardized API (Application Program Interface) library rather than a universal data format. Based on this meeting, we submitted an SBIR application (with letters of support from key attendants of the SFN meeting) to fund the development of a standardized API definition, data format, and a suite of open source data handling and review tools. | data management, development, interoperability software, software | is related to: BrainLiner | nif-0000-00023 | SCR_000005 | Neuroshare.org | 2026-08-08 11:57:10 | 0 | |||||||||
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exomeSuite Resource Report Resource Website |
exomeSuite (RRID:SCR_000129) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease. | standalone software, c, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24603341 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04839 | SCR_000129 | 2026-08-08 11:57:12 | 0 |
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