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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Segmentation of Hippocampus Subfields Resource Report Resource Website 1+ mentions |
Segmentation of Hippocampus Subfields (RRID:SCR_005996) | ASHS | data processing software, image analysis software, segmentation software, software application, software resource | A software package for automatic segmentation of hippocampal subfields in magnetic resonance imges. Given a pair of T1-weighted and T2-weighted images (the latter acquired using a protocol tuned for hippocampus imaging), ASHS will automatically label main subfields of the hippocampus, and some extra-hippocampal structures, using multi-atlas segmentation. The main method is described in the Yushkevich et al. 2011 Neuroimage paper (http://tinyurl.com/cffrp3p). * execution requires: Advanced Normalization Tools, FSL | hippocampus, mri, t1-weighted image, t2-weighted image, ca1, ca2, ca3, statistical modeling, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ANTS - Advanced Normalization ToolS is related to: FSL has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:19405131 PMID:20600984 |
GNU General Public License | nlx_151370 | http://www.nitrc.org/projects/ashs | SCR_005996 | Automatic Segmentation of Hippocampal Subfields, HippocampalSubfieldSegmentation | 2026-09-12 12:56:34 | 8 | |||||
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Randomized Controlled Trials Ontology Resource Report Resource Website |
Randomized Controlled Trials Ontology (RRID:SCR_005992) | RCTONT | controlled vocabulary, data or information resource, ontology | Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis. | owl | is listed by: BioPortal | nlx_157568 | SCR_005992 | 2026-09-12 12:56:34 | 0 | |||||||||
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Artifact Detection Tools Resource Report Resource Website 100+ mentions |
Artifact Detection Tools (RRID:SCR_005994) | ART | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well. * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE | artifact removal, quality metrics, registration, motion analysis, neuroimaging, fmri, spike, motion, artifact, timeseries, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: RapidArt has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Free, Available for download | nlx_151369 | http://www.nitrc.org/projects/artifact_detect | SCR_005994 | 2026-09-12 12:56:34 | 244 | |||||||
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Allen Brain Atlas API Resource Report Resource Website 10+ mentions |
Allen Brain Atlas API (RRID:SCR_005984) | Allen Brain Atlas API | data or information resource, portal, software application, software resource, source code, topical portal | API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service | atlas application, expression data, 3d volume, 3d coordinate, gene, reference atlas, connectivity, histology, microarray, brain, rna sequencing, mri, dti, api, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics, ish, high resolution image, nissl, annotation, atlas, image, web service, neuroblast, gene expression, gene, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Mouse Brain Reference Atlas is related to: Allen Developing Mouse Brain Atlas is related to: International Neuroinformatics Coordinating Facility is related to: Brain Explorer Atlas and Teaching Tool is related to: CellTax vignette is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science |
Other/Commercial license License | nlx_151358 | http://www.nitrc.org/projects/incf_allen-brai | SCR_005984 | 2026-09-12 12:56:34 | 13 | |||||||
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NOVA Biologics Resource Report Resource Website |
NOVA Biologics (RRID:SCR_005985) | commercial organization | An Antibody supplier | nlx_152422 | SCR_005985 | NOVA Biologics Inc., NOVA Biologics Inc | 2026-09-12 12:56:34 | 0 | |||||||||||
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | collaboration tool, data management software, data processing software, software application, software resource | A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications. | annotation, 2d image, microscopy image, volume, serial section, 3d reconstruction, segmentation, microscopy, visualization, optical imaging, connectomics, synapse, retina, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC has parent organization: University of Utah; Utah; USA |
Research to Prevent Blindness ; University of Utah; Utah; USA ; Graduate Research Fellowship ; Utah Science Technology and Research Initiative ; NEI R01 EY02576; NEI R01 EY015128; NEI P01 EY014800; NSF 0941717; NIDCD T32DC008553; NIBIB EB005832 |
PMID:21118201 | Open source | nlx_151360 | http://www.nitrc.org/projects/viking_viewer | SCR_005986 | Viking, Viking Connectome Annotation System, Viking Annotation System | 2026-09-12 12:56:34 | 16 | |||||
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Hammer And WML Modules for 3D Slicer Resource Report Resource Website 1+ mentions |
Hammer And WML Modules for 3D Slicer (RRID:SCR_005980) | HAMMER, hammerwml | data processing software, image analysis software, registration software, segmentation software, software application, software resource | A software plugin for 3D Slicer that matches morphological signatures of medical images automatically. HAMMER is an acronym for Hierarchical Attribute Matching Mechanism for Elastic Registration (Dinggang Shen, Christos Davatzikos, HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002) - an elastic registration algorithm for medical images, matching morphological signatures of images in a hierarchical multi-scale regime. White matter lesion (WML) segmentation is a novel multi-spectral WML segmentation protocol via incorporating information from T1-w, T2-w, PD-w and FLAIR MR brain images. (Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition, Academic Radiology, 15(3):300-313, March 2008). | mri, registration, white matter lesion, segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:12575879 PMID:18280928 |
3D Slicer License | nlx_151352 | http://www.nitrc.org/projects/hammerwml | SCR_005980 | HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, Hierarchical Attribute Matching Mechanism for Elastic Registration and White matter lesion Modules for 3D Slicer | 2026-09-12 12:56:34 | 1 | |||||
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ABC (Atlas Based Classification) Resource Report Resource Website 1+ mentions |
ABC (Atlas Based Classification) (RRID:SCR_005981) | ABC | data processing software, image analysis software, software application, software resource, workflow software | A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput. | brain, image, image registration, filter, segmentation, inhomogeneity correction, beta, c++, linux, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is related to: INCF Software Center has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: University of Utah; Utah; USA |
3D Slicer License | nlx_151362 | SCR_005981 | 2026-09-12 12:56:34 | 3 | ||||||||
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ChiCTR - Chinese Clinical Trial Registry Resource Report Resource Website 10+ mentions |
ChiCTR - Chinese Clinical Trial Registry (RRID:SCR_006037) | ChiCTR | clinical trial, data or information resource, data repository, database, registry, service resource, storage service resource | National clinical trial registry by Ministry of Health of China to join World Health Organization International Clinical Trial Registration Platform (WHO ICTRP Primary Registry), and the approved Primary Registry of WHO ICTRP. It registers both Chinese and global clinical trials, receives data from Partner Registers certified by the WHO ICTRP, and submits data to the WHO ICTRP Central Repository for global search. Moreover, based upon the talent and technical platform, consisting of Chinese Evidence-based Medicine Centre of Ministry of Health of China, Virtual Research Centre of Evidence-Based Medicine of Ministry of Education of China, Chinese Cochrane Centre, UK Cochrane Centre and International Clinical Epidemiology Network Resource and Training Centre in West China Hospital, Sichuan University (INCLEN CERTC), ChiCTR is responsible for providing consultations on trial design, central randomization service, guidance on the writing of clinical trial reports and relevant training. WHO takes the lead in establishing the global clinical trial registration system, which is agreed upon by governments from all over the world. There are both ethical and scientific reasons for clinical trial registration. Trial participants expect that their contributions to biomedical knowledge will be used to improve health care for everyone. Open access to information about ongoing and completed trials meets the ethical duty to trial participants, and promotes greater trust and public confidence in clinical research. Furthermore, trial registration ensures that the results of all trials can be tracked down and should help to reduce unnecessary duplication of research through greater awareness of existing trials and results. The mission of ChiCTR is to Unite clinicians, clinical epidemiologists, biostatisticians, epidemiologists and health care managers both at home and abroad, to manage clinical trials in a strict and scientific manner, and to promote their quality in China, so as to provide reliable evidences from clinical trials for health care workers, consumers and medical policy decision makers, and also to use medical resources more effectively to provide better service for Chinese people and all human beings. Any trial performed in human beings is considered as a clinical trial, and should be registered before its implementation. All the registered clinical trials will be granted a unique registration number by WHO ICTRP. | clinical trial, registry, registration, clinical, trial, china |
is related to: WHO International Clinical Trials Registry Platform has parent organization: Sichuan University; Sichuan; China |
nlx_151504 | SCR_006037 | Chinese Clinical Trial Registry | 2026-09-12 12:56:34 | 42 | ||||||||
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Simulator for Neural Networks and Action Potentials Resource Report Resource Website 1+ mentions |
Simulator for Neural Networks and Action Potentials (RRID:SCR_006031) | data or information resource, narrative resource, simulation software, software application, software resource, training material | SNNAP (Simulator for Neural Networks and Action Potentials) is a tool for rapid development and simulation of realistic models of single neurons and neural networks. It includes mathematical descriptions of ion currents and intracellular second messengers and ions. In addition, you can simulate current flow in multicompartment models of neurons by using the equations describing electric coupling. SNNAP also includes mathematical descriptions of intracellular second messengers and ions, and simulate the modulation of membrane currents and synaptic transmission, , either enhancement or inhibition. Other advantages of SNNAP include: * Written in JAVA and can run on virtually any type of computer system. * Graphical user interface * Ability to simulate common experimental manipulations. * Modular organizations of input files. Agencies: NCRR, FOSR grant F49620-93-1-0272, as well as NIH grants R01-RR11626 and P01-NS38310 | has parent organization: University of Texas System; Texas; USA | nif-0000-00086 | SCR_006031 | SNNAP | 2026-09-12 12:56:34 | 5 | ||||||||||
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RIO-DB - Research Information Database Resource Report Resource Website |
RIO-DB - Research Information Database (RRID:SCR_006105) | RIO-DB | data or information resource, data set, portal | RIO-DB (Research Information Database) is a multimedia one concerning various research information which is developed and accumulated through many AIST R&D projects. RIO-DB project aims to contribute to the creation and promotion of new businesses from academic society to industrial community by spreading the research information via internet. This is a portal to many database resources in the following categories: * Standard * Chemistry * Earth sciences * Energy * Biology * Material * Information Technology * Safety | database, standard, chemistry, earth science, energy, biology, material, information technology, safety, listing |
has parent organization: National Institute of Advanced Industrial Science and Technology is parent organization of: Brain Atlas Database of Japanese Monkey for WWW |
All materials presented on this database are the exclusive property of the AIST. Unauthorized reproduction or use of all or part of these materials is prohibited. http://riodb.ibase.aist.go.jp/copyrighte.html | nlx_151576 | SCR_006105 | Research Information Database | 2026-09-12 12:56:35 | 0 | |||||||
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DAM-Bio Resource Report Resource Website |
DAM-Bio (RRID:SCR_006226) | DAM-Bio | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource | An integrated environment designed to support protein sequence and structure analysis on the web. | protein sequence, structure analysis, sequence, platform, environment, module |
is related to: FT is related to: SecStr is related to: DnaProt is related to: PRED-TMR is related to: PRED-TMR2 is related to: orienTM is related to: PRED-CLASS is related to: SCAR has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
Greek General Secretariat of Research and Technology | nlx_151780 | SCR_006226 | DAM Bio, DAMBio | 2026-09-12 12:56:36 | 0 | |||||||
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LepChorionDB Resource Report Resource Website |
LepChorionDB (RRID:SCR_006222) | LepChorionDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A relational database of Lepidoptera chorion proteins. The proteinaceous Lepidopteran chorions are used in our lab, as a model system towards unraveling the routes and rules of formation of natural protective amyloids. Therefore, we constructed LepChorionDB a relational database, containing all Lepidoptera chorion proteins identified to date. Lepidoptera chorion proteins can be classified in two major protein families, A and B. This classification was based on multiple sequence alignments of conserved key residues, in the central domain of, well characterized, silkmoth chorion proteins. These alignments were used to build Hidden Markov Models in order to search various DataBases. This work was a collaboration of the Department of Cell Biology and Biophysics, University of Athens and the Centre of Immunology & Transplantation Biomedical Research Foundation, Academy of Athens. | lepidoptera, chorion, protein, proteome, silkmoth, insect | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | nlx_151769 | SCR_006222 | Lepidoptera chorion protein database, LepChorionDB - Lepidoptera chorion protein database | 2026-09-12 12:56:36 | 0 | ||||||||
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OMPdb Resource Report Resource Website |
OMPdb (RRID:SCR_006221) | OMPdb | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database''s protein entries or run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | beta-barrel, outer membrane protein, gram-negative bacteria, protein, protein sequence, transmembrane, annotation, genome-wide analyses, comparative genomics, sequence, structure, blast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:20952406 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01611, biotools:ompdb, nlx_151768 | https://bio.tools/ompdb | SCR_006221 | OMPdb - A database of Beta-barrel outer membrane proteins from Gram-negative bacteria | 2026-09-12 12:56:36 | 0 | |||||
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Michael J. Fox Foundation for Parkinsons Research Resource Report Resource Website 50+ mentions |
Michael J. Fox Foundation for Parkinsons Research (RRID:SCR_006183) | MJFF | data or information resource, disease-related portal, funding resource, portal, topical portal | A Parkinson's research foundation dedicated to finding a cure for Parkinson's disease and to ensuring the development of improved therapies. Pipeline Programs fund investigator-initiated proposals focused on the following critical points along the translational pathway to new therapies for Parkinson's disease. | parkinson's disease, clinical, translational, foundational, research, funding resource |
is related to: Biomarkers Across Neurodegenerative Diseases is parent organization of: Michael J. Fox Foundation Funded Grants is parent organization of: Biomarkers Across Neurodegenerative Diseases is parent organization of: Parkinson's Progression Markers Initiative is parent organization of: Parkinson's Disease Online Research |
Public, Funding available to researchers | nif-0000-00518 | SCR_006183 | Michael J. Fox Foundation for Parkinson's Research, Michael J. Fox Foundation | 2026-09-12 12:56:36 | 76 | |||||||
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University of Athens Biophysics and Bioinformatics Laboratory Resource Report Resource Website 1+ mentions |
University of Athens Biophysics and Bioinformatics Laboratory (RRID:SCR_006180) | University of Athens Biophysics & Bioinformatics Laboratory | data or information resource, degree granting program, graduate program resource, laboratory portal, organization portal, portal, training resource, undergraduate program resource | Laboratory focuses on research related to the elucidation of the principles governing protein structure and function, under the supervision of Professor Stavros J. Hamodrakas. In particular, original research is carried out along two main axes: # Algorithm development for the prediction of protein structure, function and interactions from amino acid sequence as well as construction of relevant databases. # Application of a variety of Biophysical methods and techniques for protein structure determination and for structural studies of complex, physiologically important, Biological tissues such as insect chorion and cuticle. More than 15 individuals (including post-doctoral researchers, PhD students, MSc and undergraduate students) are currently involved in several ongoing research projects. Apart from research, our lab offers undergraduate courses in Bioinformatics and Molecular Biophysics, which are elective for the degrees (BSc) in Biology (Faculty of Biology) and Physics (Faculty of Physics) of the University of Athens. At the same time, our lab is actively involved in the organization and co-ordination of the MSc Programme in Bioinformatics of the Faculty of Biology. | biophysics, bioinformatics, protein structure, protein function, protein, protein interaction, amino acid sequence, algorithm, prediction, structure, function, interaction |
has parent organization: University of Athens; Athens; Greece is parent organization of: PredSL is parent organization of: CAST is parent organization of: PRED-SIGNAL is parent organization of: AMYL-PRED is parent organization of: HMM-TM is parent organization of: PRED-LIPO is parent organization of: CW-PRED is parent organization of: PRED-TMBB is parent organization of: PRED-COUPLE 2 is parent organization of: ConBBPRED is parent organization of: PRED-GPCR is parent organization of: MCMBB is parent organization of: waveTM is parent organization of: PRED-TMR is parent organization of: GeneVito is parent organization of: PRED-CLASS is parent organization of: CoPreTHi is parent organization of: orienTM is parent organization of: SecStr is parent organization of: OMPdb is parent organization of: LepChorionDB is parent organization of: Human-gpDB is parent organization of: hPATM is parent organization of: NON-RED is parent organization of: DAM-Bio is parent organization of: SCAR is parent organization of: FT is parent organization of: DnaProt is parent organization of: CuticleDB is parent organization of: gpDB - a database of GPCRs G-proteins Effectors and their interactions is parent organization of: TMRPres2D is parent organization of: ExTopoDB |
nlx_151727 | SCR_006180 | Biophysics and Bioinformatics Laboratory at University of Athens, Biophysics and Bioinformatics Laboratory of the Department of Cell Biology and Biophysics of the University of Athens | 2026-09-12 12:56:36 | 2 | ||||||||
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DataCite Ontology Resource Report Resource Website |
DataCite Ontology (RRID:SCR_006215) | DataCite Ontology | controlled vocabulary, data or information resource, ontology | An ontology written in OWL 2 DL to enable the metadata properties of the DataCite Metadata Kernel Specification version 2.2 (http://test.datacite.org/schema/meta/kernel-2.2/index.html) to be described in RDF. This version of the DataCite Ontology has been completely revised and significantly expanded to permit accurate mapping of this new version of the DataCite Metadata Kernel Specification to RDF. | annotation, alternate resource identifier, description type, funder identifier, funder identifier scheme, identifier, identifier scheme, personal identifier, personal identifier scheme, primary resource identifier, resource identifier, resource identifier scheme, owl, rdf, metadata |
is listed by: FORCE11 has parent organization: DataCite |
Creative Commons Attribution License | nlx_151759 | https://www.force11.org/node/4673 | SCR_006215 | 2026-09-12 12:56:36 | 0 | |||||||
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GeneVito Resource Report Resource Website |
GeneVito (RRID:SCR_006211) | GeneVito | data processing software, data visualization software, software application, software resource | A JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of poor annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. GeneViTo has already been applied to visualize the genomes of two microbial organisms: the bacterion Chlamydia trachomatis and the archaeon Methanococcus jannaschii. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment (Java 1.4.1) is already installed in the system. | java, genome-wide analysis, genome, visualization, gene, function, structure, dna, protein sequence, genomic, proteomic | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | PMID:14594459 | Free for academic use, Acknowledgement requested | nlx_151776 | SCR_006211 | GeneVito: Genome Visualization Tool, GeneViTo (Genome Visualization Tool), Genome Visualization Tool | 2026-09-12 12:56:36 | 0 | ||||||
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BioMedBridges Resource Report Resource Website 1+ mentions |
BioMedBridges (RRID:SCR_006179) | BioMedBridges | consortium, data or information resource, organization portal, portal | Consortium of 12 Biomedical sciences research infrastructure (BMS RI) partners to develop a shared e-infrastructure to allow interoperability between data and services in the biological, medical, translational and clinical domains (providing a complex knowledge environment comprising standards, ontologies, data and services) and thus strengthen biomedical resources in Europe. The BMS RIs are on the roadmap of the European Strategy Forum on Research Infrastructures (ESFRI). Connecting several European research infrastructures brings a diversity of ethical, legal and security concerns including data security requirements for participating e-Infrastructures that are storing or processing patient-related data (or biosamples): EATRIS, ECRIN, BBMRI, EuroBioImaging and EMBL-EBI. In addition, INSTRUCT is interested in secure sample transport and in intellectual property rights; Infrafrontier stores high-throughput data from mice. BBMRI with its focus on the availability of biomaterials is currently emphasizing aspects like k-anonymity and metadata management for its data. Sharing of imaging data by Euro-BioImaging poses challenges with respect to anonymisation and intellectual property. Therefore, an ethical, regulatory and security framework for international data sharing that covers these diverse areas and different types of data (e.g. clinical trials data, mouse data, and human genotype and DNA sequence data) is of crucial importance. The outcomes will lead to real and sustained improvement in the services the biomedical sciences research infrastructures offer to the research community. Data curation and sample description will be improved by the adoption of best practices and agreed standards. Many improvements will emerge from new interactions between RIs created by data linkage and networking. Ensuring access to relevant information for all life science researchers across all BMS RIs will enable scientists to conduct and share cutting-edge research. | clinical, biomedical, infrastructure, technology, biology, medicine, translational, data sharing, biobank, genetic, stem cell, clinical trial, imaging, genotype, dna sequence, standard specification, interoperability |
is listed by: Consortia-pedia is related to: Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) has parent organization: European Bioinformatics Institute |
European Union FP7 Capacities Specific Programme 284209 | nlx_151726 | SCR_006179 | Building data bridges between biological and medical infrastructure in Europe (BioMedBridges), Building data bridges between biological and medical infrastructures in Europe, Building data bridges from biology to medicine in Europe | 2026-09-12 12:56:36 | 7 | |||||||
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deepSNV Resource Report Resource Website 10+ mentions |
deepSNV (RRID:SCR_006214) | deepSNV | software resource | Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants). | data import, genetic variability, genetics, snp, sequencing, single nucleotide variant, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24443148 | GNU General Public License, v3 | OMICS_02239, biotools:deepsnv | https://bio.tools/deepsnv | SCR_006214 | deepSNV - Detection of subclonal SNVs in deep sequencing experiments | 2026-09-12 12:56:36 | 34 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
