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http://www.eurordis.org/

EURORDIS is a non-governmental patient-driven alliance of patient organizations and individuals active in the field of rare diseases, dedicated to improving the quality of life of all people living with rare diseases in Europe. It is a not-for-profit organization and represents more than 479 rare disease organizations in 45 different countries (of which 25 are EU Member States), covering more than 4,000 rare diseases. It is therefore the voice of the 30 million patients affected by rare diseases throughout Europe. EURORDIS aims at improving the quality of life of people living with rare diseases in Europe through advocacy at the European level, support for research and drug development, networking patient groups, raising awareness and other actions designed to fight against the impact of rare diseases on the lives of patients and family. EURORDIS' training programs and resources are designed to strengthen the capacity of rare disease patients' representatives. Training empowers patients' representatives to advocate effectively for rare diseases at both the local and EU level. Key issues affecting patients of Rare Diseases on which we actively work: * Sustaining rare diseases as an EU public health priority * Making Rare Diseases A Public Health Priority In All Member States * Rare Diseases: An International Public Health Priority * Improving Access To Orphan Drugs * Improving Access To Quality Care * Promoting cross-border healthcare and patient mobility * Bridging Patients And Research * Genetic testing and newborn screening

Proper citation: EURORDIS (RRID:SCR_003814) Copy   

•   Source: SciCrunch Registry

http://www.mighealth.net/uk/index.php/Main_Page

The MIGHEALTHNET wiki has been set up to gather information about the health of migrants and ethnic minorities in the United Kingdom. It forms part of the project MIGHEALTHNET, currently being carried out in 16 countries and co-funded by DG SANCO, the Health and Consumer Protection Directorate-General of the European Commission. We invite you to add your contributions to it and to pass on the address of this site to others who may be interested. This website is part of an EU Project that aims to give professionals, policy makers including health authorities, researchers, educators and representatives of migrant and minority groups easy access to a dynamically evolving body of knowledge and a virtual network of expertise. It will stimulate the formation of networks of individuals and organizations concerned with migrant and minority health.

Proper citation: MIGHEALTHNET (Migrant Health) (RRID:SCR_004701) Copy   

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

Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy   

•   Source: SciCrunch Registry

http://eurofung.net/index.php?option=com_content&task=section&id=3&Itemid=4

The Eurofung project is a Coordination Action with the aim of developing a strategy to build up and maintain an integrated, sustainable European genomic database required for innovative genomics research of filamentous fungal model organisms of interest. This database will become a crystallization point for related systems and then could be integrated and conserved in a central European genomic database. The consortium counts 32 member laboratories, three of which have partner status. A Fungal Industrial Platform (FIP) of 13 members is also associated with the project. The project focuses on several filamentous fungi for different reasons. Aspergillus nidulans has a long record of use as a fungal model organism. Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum are important cell factories used for the production of enzymes and metabolites including compounds such as Beta-lactams with benefits to human health. The human pathogen Aspergillus fumigatus serves not only as a model pathogen, but becomes more and more a serious threat to human health. The project contributes to create the conditions and facilities within Europe to widely apply all genomics technologies in filamentous fungal research. This will greatly expand our knowledge about filamentous fungi. This new genomics information will thus be beneficial to European biotechnology industries and help to improve the prevention and treatment of fungal disease. Expected results: The main results expected from this project are: - The contribution of the community to the manual annotation of important fungal genomes through annotation jamborees. - The realization of an integrated sustainable fungal genomic database through collaboration with bioinformatics centers and incorporation of the community data. - The realization of a fungal genomics knowledge base for the Eurofungbase community and the European fungal biotech industry through meetings, workshops and web-based information. - Intensified collaboration between the members of the network including the participating industries, thus strengthening the infrastructure for high quality fungal genomics research in Europe and furthermore determining joint research targets for the future. -Individualized training of a next generation of young scientists in fungal genomics and biotechnological research.

Proper citation: Eurofungbase (RRID:SCR_007094) Copy   

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http://www.wf4ever-project.org/

Project to addresses challenges associated with the preservation of scientific experiments in data-intensive science, including: * The definition of models to describe, in a standard way, scientific experiments by means of workflow-centric Research Objects, which comprise scientific workflows, the provenance of their executions, interconnections between workflows and related resources (e.g., datasets, publications, etc.), and social aspects related to such scientific experiments. * The collection of best practices for the creation and management of Research Objects. * The analysis and management of decay in scientific workflows. To address these challenges they are creating an architecture and tooling for the access, manipulation, sharing, reuse and evolution of Research Objects in a range of disciplines. This will result into the next generation RO-enabled myExperiment.

Proper citation: Workflow4Ever (RRID:SCR_005939) Copy   

•   Source: SciCrunch Registry

http://www.semantic-mediawiki.org/wiki/Semantic_MediaWiki

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.

Proper citation: Semantic MediaWiki (RRID:SCR_006246) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/mouseportal/

Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.

Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy   

•   Source: SciCrunch Registry

http://www.genomeutwin.org/index.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study of genetic and life-style risk factors associated with common diseases based on analysis of European twins. The population cohorts used in the Genomeutwin study consist of Danish, Finnish, Italian, Dutch, English, Australian and Swedish twins and the MORGAM population cohort. This project will apply and develop new molecular and statistical strategies to analyze unique European twin and other population cohorts to define and characterize the genetic, environmental and life-style components in the background of health problems like obesity, migraine, coronary heart disease and stroke, representing major health care problems worldwide. The participating 8 twin cohorts form a collection of over 0.6 million pairs of twins. Tens of thousands of DNA samples with informed consents for genetic studies of common diseases have already been stored from these population-based twin cohorts. Studies targeted to cardiovascular traits are now being undertaken in MORGAM, a prospective case-cohort study. MORGAM cohorts include approximately 6000 individuals, drawn from population-based cohorts consisting of more than 80 000 participants who have donated DNA samples.

Proper citation: GenomEUtwin (RRID:SCR_002843) Copy   

•   Source: SciCrunch Registry

http://bbmri-eric.eu

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.

Proper citation: Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) (RRID:SCR_004226) Copy   

•   Source: SciCrunch Registry

http://causal.uma.es

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.

Proper citation: Causal Cognition Group (RRID:SCR_004780) Copy   

•   Source: SciCrunch Registry

http://www.orpha.net/

European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Reference portal for rare diseases and orphan drugs to help improve diagnosis, care and treatment of patients with rare diseases.

Proper citation: Orphanet (RRID:SCR_006628) Copy   

•   Source: SciCrunch Registry

http://briansimulator.org/

Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator.

Proper citation: Brian Simulator (RRID:SCR_002998) Copy   

•   Source: SciCrunch Registry

https://juaml.github.io/julearn

Software library of easy testing ML models directly from pandas DataFrames, while keeping the flexibility of using scikit-learn’s models.

Proper citation: Julearn (RRID:SCR_024881) Copy   

•   Source: SciCrunch Registry

http://www.gotaxexplorer.de/

GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GOTaxExplorer (RRID:SCR_005720) Copy   

•   Source: SciCrunch Registry

https://www.infrafrontier.eu/emma/

Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide.

Proper citation: European Mouse Mutant Archive (RRID:SCR_006136) Copy   

•   Source: SciCrunch Registry

http://dictybase.org/

Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.

Proper citation: Dictyostelium discoideum genome database (RRID:SCR_006643) Copy   

•   Source: SciCrunch Registry

http://www.ensemblgenomes.org/

Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

Proper citation: Ensembl Genomes (RRID:SCR_006773) Copy   

•   Source: SciCrunch Registry

http://www.innatedb.com

Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.

Proper citation: InnateDB (RRID:SCR_006714) Copy   

•   Source: SciCrunch Registry

http://www.proteomexchange.org

A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.

Proper citation: ProteomeXchange (RRID:SCR_004055) Copy   

•   Source: SciCrunch Registry

http://www.pathbase.net/

Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)

Proper citation: Pathbase (RRID:SCR_006141) Copy   

•   Source: SciCrunch Registry