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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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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 | SciCrunch Registry | Research Information Database | 2026-10-24 12:45:37 | 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 | SciCrunch Registry | DAM Bio, DAMBio | 2026-10-24 12:45:40 | 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 | SciCrunch Registry | Lepidoptera chorion protein database, LepChorionDB - Lepidoptera chorion protein database | 2026-10-24 12:45:40 | 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 | SciCrunch Registry | OMPdb - A database of Beta-barrel outer membrane proteins from Gram-negative bacteria | 2026-10-24 12:45:39 | 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 | SciCrunch Registry | Michael J. Fox Foundation for Parkinson's Research, Michael J. Fox Foundation | 2026-10-24 12:45:38 | 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 | SciCrunch Registry | 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 | 2026-10-24 12:45:39 | 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 | SciCrunch Registry | 2026-10-24 12:45:38 | 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 | SciCrunch Registry | GeneVito: Genome Visualization Tool, GeneViTo (Genome Visualization Tool), Genome Visualization Tool | 2026-10-24 12:45:38 | 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 | SciCrunch Registry | 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 | 2026-10-24 12:45:39 | 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 | SciCrunch Registry | deepSNV - Detection of subclonal SNVs in deep sequencing experiments | 2026-10-24 12:45:40 | 34 | |||||
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Mammalian Adult Neurogenesis Gene Ontology Resource Report Resource Website 50+ mentions |
Mammalian Adult Neurogenesis Gene Ontology (RRID:SCR_006176) | MANGO | controlled vocabulary, data or information resource, database, ontology | Database of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus. | adult neurogenesis, adult, neurogenesis, hippocampus, gene, annotation, cell type, process, FASEB list | has parent organization: Dresden University of Technology; Saxony; Germany | nlx_151684 | SCR_006176 | SciCrunch Registry | 2026-10-24 12:45:39 | 64 | |||||||||
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IRIS DMC FDSNWS station Web Service Resource Report Resource Website |
IRIS DMC FDSNWS station Web Service (RRID:SCR_006177) | FDSNWS Station, fdsnws-station, FDSNWS: station | data access protocol, software resource, web service | Web service that returns International Federation of Digital Seismograph Networks (FDSN) station metadata in FDSN StationXML format or as delimited text. Results are available at multiple levels of granularity: network, station, channel and response. Metadata may be selected based on channel descriptors, time ranges, geographic regions, and more. This service is an implementation of the FDSN web service specification version 1. | seismology, fdnws, station, metadata, time series, seed, wadl |
is listed by: CINERGI has parent organization: IRIS DMC Web Services |
SciRes_000179 | SCR_006177 | SciCrunch Registry | International Federation of Digital Seismograph Networks Web Service Station, IRIS FDSNWS Station, FDSNWS Station Web service, International Federation of Digital Seismograph Networks (FDSN) Web Service Station | 2026-10-24 12:45:38 | 0 | ||||||||
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Deciphering Developmental Disorders Resource Report Resource Website 10+ mentions |
Deciphering Developmental Disorders (RRID:SCR_006171) | DDD | biospecimen repository, data or information resource, disease-related portal, material storage repository, portal, research forum portal, service resource, storage service resource, topical portal | The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible. | microarray, sequencing, child, genome, chromosome, dna sequencing, ethics, interview, dna, saliva, clinical, genetics, gene, diagnosis, phenotype, clinical data, FASEB list |
is related to: DECIPHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Genetic disorder, Parent, Neurodevelopmental disorder, Congenital anomaly, Abnormal growth, Dysmorphic feature, Unusual behavioral phenotype | Wellcome Trust ; Health Innovation Challenge Fund |
PMID:21679367 | nlx_151673 | SCR_006171 | SciCrunch Registry | Deciphering Developmental Disorders (DDD) | 2026-10-24 12:45:39 | 42 | |||||
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crowdLabs Resource Report Resource Website 1+ mentions |
crowdLabs (RRID:SCR_006294) | crowdLabs | analysis service resource, community building portal, data analysis service, data or information resource, portal, production service resource, service resource, storage service resource | A social visualization repository for the scientific workflow management system VisTrails providing a platform for sharing and executing computational tasks. It adopts the model used by social Web sites and that integrates a set of usable tools and a scalable infrastructure to provide an environment for scientists to collaboratively analyze and visualize data. crowdLabs aims to foster collaboration but was specifically designed to support the needs of computational scientists, including the ability to access high-performance computers and manipulate large volumes of data. By providing mechanisms that simplify the publishing and use of analysis pipelines, it allows IT personnel and end users to collaboratively construct and refine portals. This lowers the barriers for the use of scientific analyses and enables broader audiences to contribute insights to the scientific exploration process, without the high costs incurred by traditional portals. In addition, it supports a more dynamic environment where new exploratory analyses can be added on-the-fly. | platform, computation, data sharing |
is listed by: FORCE11 is related to: VisTrails |
NSF | nif-0000-06716 | http://www.force11.org/node/4666 | SCR_006294 | SciCrunch Registry | crowd Labs | 2026-10-24 12:45:41 | 1 | ||||||
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VizHub Resource Report Resource Website 1+ mentions |
VizHub (RRID:SCR_006209) | VizHub | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource | A visualization hub displaying sequencing data from the Roadmap Epigenomics project. It hosts high volume of tracks from ENCODE and Roadmap Epigenomics projects, supports multiple organisms, visualizes chromatin-interaction data (e.g. Hi-C), performs gene set view, gene plot, and many others. All delivered on the web at high performance. | epigenomics, neandertal, genome, visualization, browser, sequencing |
uses: UCSC Genome Browser uses: Roadmap Epigenomics Project uses: ENCODE is related to: WashU Epigenome Browser has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Roadmap Epigenomics Project |
nlx_151756 | SCR_006209 | SciCrunch Registry | Roadmap Epigenomics Visualization Hub, Visualization Hub | 2026-10-24 12:45:39 | 6 | ||||||||
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PHYLIP Resource Report Resource Website 1000+ mentions |
PHYLIP (RRID:SCR_006244) | PHYLIP | data processing software, software application, software resource, source code | A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. | phylogeny prediction, evolutionary tree, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Washington; Seattle; USA works with: PAML |
NSF ; NIGMS ; DOE |
Free | nif-0000-06708, OMICS_04240, biotools:phylip | https://bio.tools/phylip, https://sources.debian.org/src/phylip/ | SCR_006244 | SciCrunch Registry | PHYLogeny Inference Package | 2026-10-24 12:45:40 | 3544 | |||||
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Semantic MediaWiki Resource Report Resource Website 1+ mentions |
Semantic MediaWiki (RRID:SCR_006246) | SMW | software resource | A free, open-source extension to MediaWiki - the wiki software that powers Wikipedia - that helps to search, organize, tag, browse, evaluate, and share the wiki''s content. While traditional wikis contain only text which computers can neither understand nor evaluate, SMW adds semantic annotations that allow a wiki to function as a collaborative database. Semantic MediaWiki introduces some additional markup into the wiki-text which allows users to add semantic annotations to the wiki. While this first appears to make things more complex, it can also greatly simplify the structure of the wiki, help users to find more information in less time, and improve the overall quality and consistency of the wiki. A large number of related extensions have been created that extend the ability to edit, display and browse through the data stored by SMW: the term Semantic MediaWiki is sometimes used to refer to this entire family of extensions. | extension, wiki, semantic annotation, authoring tool |
is listed by: FORCE11 has parent organization: MediaWiki |
European Union | Open unspecified license | nif-0000-06677 | SCR_006246 | SciCrunch Registry | Semantic Media Wiki | 2026-10-24 12:45:40 | 3 | ||||||
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Human Imaging Database Resource Report Resource Website 1+ mentions |
Human Imaging Database (RRID:SCR_006126) | HID | data management software, data or information resource, data repository, database, image repository, service resource, software application, software resource, source code, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented October 5, 2017. Database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. The HID can be extended to contain relevant information concerning experimental subjects, assessments of subjects, the experimental data collected, the experimental protocols, and other metadata normally included with experiments. |
imaging, fmri, clinical, behavior, biomedical imaging data, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cognitive Paradigm Ontology is related to: XCEDE Schema has parent organization: Biomedical Informatics Research Network |
Schizophrenia | PMID:19826494 PMID:18348946 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00269 | http://www.nitrc.org/projects/hid | http://fbirnbdr.nbirn.net:8080/BDR/ | SCR_006126 | SciCrunch Registry | fBIRN Data Repository, Human Imaging Database (HID) System, Function BIRN Data Repository | 2026-10-24 12:45:37 | 3 | |||
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pepStat Resource Report Resource Website 1+ mentions |
pepStat (RRID:SCR_006240) | software resource | Software for statistical analysis of peptide microarrays. It uses an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization. | standalone software | is listed by: OMICtools | PMID:23770318 | OMICS_04027 | SCR_006240 | SciCrunch Registry | 2026-10-24 12:45:40 | 8 | |||||||||
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ScerTF Resource Report Resource Website 10+ mentions |
ScerTF (RRID:SCR_006121) | ScerTF | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Catalog of over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors (TFs). They've curated 11 literature sources, benchmarked the published position-specific scoring matrices against in-vivo TF occupancy data and TF deletion experiments, and combined the most accurate models to produce a single collection of the best performing weight matrices for Saccharomyces cerevisiae. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors. Enter a TF name to find the recommended matrix for a particular TF, or enter a nucleotide sequence to identify all TFs that could bind a particular region. | binding site, transcription factor, regulatory site, gene, regulation, regulatory interaction, matrix, nucleotide sequence, dna sequence, yeast, position weight matrix, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIGMS R01 GM078222; NHGRI HG00249 |
PMID:22140105 | biotools:scertf, nlx_151599, OMICS_00542 | http://ural.wustl.edu/ScerTF, https://bio.tools/scertf | http://ural.wustl.edu/TFDB/ | SCR_006121 | SciCrunch Registry | 2026-10-24 12:45:38 | 19 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
