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on page 1 showing 20 out of 119 results from 1 sources

    ABACAS

Cite this (ABACAS, RRID:SCR_015852)

URL: http://abacas.sourceforge.net

Resource Type: Resource, software resource, software application

Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.

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Cite this (AddNeuroMed, RRID:SCR_003819)

URL: http://www.innomed-addneuromed.com/

Resource Type: Resource, organization portal, database, portal, consortium, data or information resource

Project portal for a cross European study designed to find biomarkers, or tests, for Alzheimer's disease. Its objectives are to produce and improve experimental models of Alzheimer's for biomarker discovery and to identify a biomarker for Alzheimer's disease suitable for diagnosis, prediction, and monitoring disease progression for use in clinical trials and in clinical practice. The baseline dataset database was scheduled to be completed and locked in 2008 and become available to researchers by 2009. Requests to access the data will be reviewed by the scientific projects committee.

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Cite this (Alzheimer Europe, RRID:SCR_003802)

URL: http://www.alzheimer-europe.org/

Resource Type: Resource, disease-related portal, topical portal, portal, data or information resource

A non-governmental organization aimed at raising awareness of all forms of dementia by creating a common European platform through co-ordination and co-operation between Alzheimer organizations throughout Europe. Alzheimer Europe is also a source of information on all aspects of dementia.

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    aneurIST

Cite this (aneurIST, RRID:SCR_007427)

URL: http://www.aneurist.org/

Resource Type: Resource, topical portal, production service resource, analysis service resource, data analysis service, standard specification, narrative resource, service resource, portal, knowledge environment, data or information resource

An IT infrastructure for the management, integration and processing of data associated with the diagnosis and treatment of cerebral aneurysm and subarachnoid hemorrhage. This new paradigm to understand and manage cerebral aneurysms, provides an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. aneurIST benefits patients with better diagnostics, prevention and treatment because it combines efforts of clinicians and industry. Through research clinicians gain a greater insight in aneurysm understanding, while industry will be dragged by these achievements to develop more suitable medical devices to treat the disease. This infrastructure : * Facilitate clinicians the diagnosis and study of the disease, as a result of providing a seamless access to patient data using data fusion and processing of complex information spanning from the molecular to the personal level. * Provide a better planning and personalization of minimally invasive interventional procedures for patients, after linking modern diagnostic imaging to computational tools. * Collaborate in the development, extension and exploitation of standards and protocols at all project stages. * Share biomedical knowledge providing access to a set of software tools and platforms such as aneuLink, aneuFuse, aneuRisk, aneuEndo, aneuCompute and aneuInfo. * Create awareness through scientific dissemination and collaboration. * Explore the business opportunities directly arising from aneurIST. It intends to provide an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. Software: * aneuLink will create an IT environment with the goal of establishing a link between genomics and disease. * aneuFuse will fuse diagnostic, modelling and simulation data into a coherent representation of the patient''s condition. * aneuRisk will provide clinicians with a tool to facilitate the personalized risk assessment and guidelines establishment to treat patients. * aneuEndo will develop computational tools to optimize and customize the design of endovascular devices. * aneuInfo will enable access to clinical and epidemiological data distributed in public and project-specific protected databases. * aneuCompute will provide aneurIST with distributed computing capabilities ensuring secure data transport.

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Cite this (Arabidopsis Reactome, RRID:SCR_002063)

URL: http://www.arabidopsisreactome.org

Resource Type: Resource, data or information resource, database

Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.

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Cite this (ArrayExpress, RRID:SCR_002964)

URL: http://www.ebi.ac.uk/arrayexpress/

Resource Type: Resource, database, catalog, service resource, storage service resource, data repository, data or information resource

Database of functional genomics experiments including gene expression where you can query and download data collected to MIAME and MINSEQE standards. It includes gene expression data from microarray and high throughput sequencing studies. Gene Expression Atlas contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. The ArrayExpress Archive is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy. The Repository contains data from over 47787 experiments comprising approximately 1361377 assays (March 2014). The majority of the data are array based, but other data types are included, including ultra high-throughput sequencing transcriptomics and epigenetic data. All the data and array designs in ArrayExpress are available for direct download in a number of different formats. Submissions are welcome.

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Cite this (BibSonomy, RRID:SCR_013756)

URL: http://www.bibsonomy.org

Resource Type: Resource, software resource, collaboration tool

A software application which assists in managing and sharing scientific literature. Users can collect and share publications, collaborate with other researchers, and find new resources and publications for research.

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Cite this (Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), RRID:SCR_004226)

URL: http://bbmri-eric.eu

Resource Type: Resource, topical portal, database, biomaterial supply resource, portal, material resource, data or information resource

BBMRI is a pan-European and internationally broadly accessible research infrastructure and a network of existing and de novo biobanks and biomolecular resources. The infrastructure will include samples from patients and healthy persons, representing different European populations (with links to epidemiological and health care information), molecular genomic resources and biocomputational tools to optimally exploit this resource for global biomedical research. During the past 3 years BBMRI has grown into a 53-member consortium with over 280 associated organizations (largely biobanks) from over 30 countries, making it the largest research infrastructure project in Europe. During the preparatory phase the concept of a functional pan-European biobank was formulated and has now been presented to Member States of the European Union and for associated states for approval and funding. BBMRI will form an interface between specimens and data (from patients and European populations) and top-level biological and medical research. This can only be achieved through a distributed research infrastructure with operational units in all participating Member States. BBMRI will be implemented under the ERIC (European Research Infrastructure Consortium) legal entity. BBMRI-ERIC foresees headquarters (central coordination) in Graz, Austria, responsible for coordination of the activities of National Nodes established in participating countries. BBMRI is in the process of submitting its application to the European Commission for a legal status under the ERIC regulation, with an expected start date at the end of 2011. Major synergism, gain of statistical power and economy of scale will be achieved by interlinking, standardizing and harmonizing - sometimes even just cross-referencing - a large variety of well-qualified, up-to date, existing and de novo national resources. The network should cover (1) major European biobanks with blood, serum, tissue or other biological samples, (2) molecular methods resource centers for human and model organisms of biomedical relevance, (3) and biocomputing centers to ensure that databases of samples in the repositories are dynamically linked to existing databases and to scientific literature as well as to statistical expertise. Catalog of European Biobanks www.bbmriportal.eu Username: guest / Password: catalogue The catalogue is intended to be used as a reference for scientists seeking information about biological samples and data suitable for their research. The BBMRI catalogue of European Biobanks provides a high-level description of Europe''s biobanks characteristics using a portal solution managing metadata and aggregate data of biobanks. The catalogue can be queried by country, by biobank, by ICD-groups, by specimen types, by specific strengths, by funding and more. A search function is available for all data.

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Cite this (Biocatalogue - The Life Science Web Services Registry, RRID:SCR_001679)

URL: http://www.biocatalogue.org/

Resource Type: Resource, web service, software resource, data or information resource, data access protocol, database

Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services.

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Cite this (BovMap Database, RRID:SCR_008145)

URL: http://locus.jouy.inra.fr/cgi-bin/bovmap/intro.pl

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.

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Cite this (Brede Database, RRID:SCR_003327)

URL: http://hendrix.imm.dtu.dk/services/jerne/brede/

Resource Type: Resource, data or information resource, database

A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments.

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    BRENDA

Cite this (BRENDA, RRID:SCR_002997)

URL: http://www.brenda-enzymes.org/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resource

Main database of functional biochemical and molecular enzyme data that provides access to seven interconnected databases. It contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. The majority of the data are manually extracted from the primary literature. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910 000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalyzed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. BRENDA provides viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models. The enzymes are classified according to the Enzyme Commission list of enzymes. Some 5000 different enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. Although they intend to give a representative overview on the characteristics and variability of each enzyme the Handbook is not a compendium. The reader will have to go to the primary literature for more detailed information. Naturally it is not possible to cover all the numerous literature references for each enzyme (for some enzymes up to 40000) if the data representation is to be concise as is intended. The data collection is being developed into a metabolic network information system with links to Enzyme expression and regulation information. BRENDA SOAP Webservice is available.

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Cite this (Brian Simulator, RRID:SCR_002998)

URL: http://briansimulator.org/

Resource Type: Resource, software resource, software application, simulation software

Software package for simulating spiking neural networks. Specifically, it is a package for the Python programming language providing functions and classes designed to make writing simulations of neural networks as easy and flexible as possible. Brian uses vector-based computation to allow for efficient simulations. It is particularly useful for neuroscientific modelling at the systems level, and for teaching computational neuroscience.

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    CAST

Cite this (CAST, RRID:SCR_000628)

URL: http://athina.biol.uoa.gr/CAST/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service 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.

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Cite this (Causal Cognition Group, RRID:SCR_004780)

URL: http://causal.uma.es

Resource Type: Resource, topical portal, training resource, graduate program resource, undergraduate program resource, portal, degree granting program, data or information resource

At the Website of the Causal Cognition Group (CCG) of the University of M??laga, you may read information about our group, its members, our research, main activities, and more. Our main interests are cognitive psychology and learning, and more recently cognitive neuroscience, physiological correlates of learning and cognitive control. This site is in constant evolution... though there are things that hardly change: Cognitio rei per causas.

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Cite this (Chernobyl Tissue Bank, RRID:SCR_010662)

URL: http://www.chernobyltissuebank.com/

Resource Type: Resource, biomaterial supply resource, material resource

The CTB (Chernobyl Tissue Bank) is an international cooperation that collects, stores and disseminates biological samples from tumors and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The main objective of this project is to provide a research resource for both ongoing and future studies of the health consequences of the Chernobyl accident. It seeks to maximize the amount of information obtained from small pieces of tumor by providing multiple aliquots of RNA and DNA extracted from well documented pathological specimens to a number of researchers world-wide and to conserve this valuable material for future generations of scientists. It exists to promote collaborative, rather than competitive, research on a limited biological resource. Tissue is collected to an approved standard operating procedure (SOP) and is snap frozen; the presence or absence of tumor is verified by frozen section. A representative paraffin block is also obtained for each case. Where appropriate, we also collect fresh and paraffin-embedded tissue from loco-regional metastases. Currently we do not issue tissue but provide extracted nucleic acid, paraffin sections and sections from tissue microarrays from this material. The project is coordinated from Imperial College, London and works with Institutes in the Russian Federation (the Medical Radiological Research Centre in Obninsk) and Ukraine (the Institute of Endocrinology and Metabolism in Kiev) to support local scientists and clinicians to manage and run a tissue bank for those patients who have developed thyroid tumors following exposure to radiation from the Chernobyl accident. Belarus was also initially included in the project, but is currently suspended for political reasons.

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Cite this (Colon Therapy Research Consortium (COLTHERES), RRID:SCR_013690)

URL: http://cordis.europa.eu/project/rcn/98370_en.html

Resource Type: Resource, organization portal, portal, consortium, data or information resource

The Colon Therapy Research (COLTHERES) consortium brings together clinical centers and translational researchers funded in the European Union to define and perform biomarker driven clinical trials to improve cancer therapy outcomes. This 4-year consortium will use comprehensively molecularly-annotated colon cancers as a "test-bed" to define specific biomarkers of response or resistance to signaling pathway agents.

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Cite this (ConsensusPathDB, RRID:SCR_002231)

URL: http://cpdb.molgen.mpg.de

Resource Type: Resource, data or information resource, database

An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.

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Cite this (Current Controlled Trials, RRID:SCR_002325)

URL: http://www.controlled-trials.com

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Free-to-view clinical trials register of clinical trials worldwide, it allows users to search, register and share information about randomized controlled trials. Publication services are also available via the range of open access peer-reviewed journals published by BioMed Central. Current Controlled Trials is run by an editorial and technical in-house team. It receives advice from an international Advisory Group, including academics, doctors and health care specialists of international renown. The Advisory Group provides valuable guidance on the current activities and possible new directions of Current Controlled Trials' two databases, the metaRegister of Controlled Trials (mRCT) and the International Standard Randomised Controlled Trial Number (ISRCTN) scheme.

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Cite this (CYGD - Comprehensive Yeast Genome Database, RRID:SCR_002289)

URL: http://mips.gsf.de/genre/proj/yeast/index.jsp

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis.

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