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http://www.eurobiobank.org/

The EuroBioBank network is the first operating network of biobanks in Europe providing human DNA, cell and tissue samples as a service to the scientific community conducting research on rare diseases. It is the only network dedicated to rare disease research in Europe. By creating a critical mass of collections and facilitating the exchange of biological material, the EuroBioBank network helps accelerate research on these diseases. * Over 440,000 samples are available across the network and can be requested via the online catalogue. Approximately 13,000 samples are collected each year and 7,000 samples distributed in Europe and beyond. The biological samples are obtained from patients affected by rare diseases, including rare neuromuscular disorders. * The EuroBioBank Network is currently composed of 18 members, of which 16 biobanks from 8 European countries (France, Germany, Hungary, Italy, Malta, Slovenia, Spain and the United-Kingdom) as well as Israel and Canada. Goals * Identify and localize biological material of interest to researchers * Build a critical mass of rare disease sample collections * Distribute high quality material and associated data to users * Promote best-practice guidelines for biobanking activities * Disseminate knowledge and know-how to the scientific community through training courses * Enhance collaboration with the medical and scientific community in the field of rare diseases EuroBioBank acts as a clearing house or virtual bank, with all samples listed in the central online catalogue remaining in the possession of the member biobanks, where they are located and can be requested. The network was established by patients and researchers to facilitate research on rare diseases by guaranteeing quick and easy access to samples via an online catalogue. The catalogue lists the samples available throughout the EuroBioBank network by type of biomaterial. A search engine enables a search by disease or by bank contact. Once a sample has been located in the catalogue, it can be requested by email. Therefore, the biological material is exchanged faster. If a sample does not appear in the EuroBioBank catalogue, help can be provided to further search it at: eurobiobank (at) telethon.it Funding and Collaboration Originally funded by the EC between 2003-2006, the EuroBioBank received further EC support between 2007-2011 within the European Network of Excellence TREAT-NMD (FP6), which covered the cost sustained by Eurordis for the network coordination and website hosting. Each biobank of the network is financed by its own Institution or charitable organization. As of January 2012, the Fondazione Telethon provides the administrative support for coordinating the EuroBioBank network and hosting the website.

Proper citation: EuroBioBank (RRID:SCR_003599) Copy   

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http://www.tubafrost.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. In this web site you will find the central European database of OECI-TuBaFrost collecting the information of biobanks or in the project support environment on human material; i.e., frozen tumor tissue specimens, pathology blocks, blood samples in different forms, cell lines, Tissue Micro Arrays, etc. Our goal is by centralizing the tumor tissues information to facilitate the search of doctors / researchers for tumor materials, which they need for their cancer research there with facilitating cancer research. OECI members only can participate in the OECI-TuBaFrost exchange platform, or those introduced by an OECI member. We are a group of pathology and research departments as well as bio-bankers in clinical based biobanking based in comprehensive cancer centers or hospitals with a competence in comprehensive cancer care across Europe. Each participating institute is involved in cancer research resulting in innovative procedures, new drugs, improved diagnosis and new insights in disease development. The overall result is better care and treatment for cancer patients. To maximize the scientific value of the human tissue samples, information about the clinical status of the patient in combination with the quality and type of samples is very important. A TuBaFrost electronic database will securely store all this information. Within the closed project supporting environments, the data collected will include: * Diagnosis - identification of the type of cancer * Type of tissue collected - the origin, i.e. breast, skin, colorectal * Quality of tissue collected - collection and storage details The tissue is stored in the hospital where the donor was diagnosed/treated. It stays there until it is used or sent to another hospital or research center within the TuBaFrost group. The electronic database will track samples throughout the network. The tissue is not sold. The exchange of tissue to other hospitals is regulated by a contract, which uses the national regulations of the country supplying the tissue. Tissue samples within the TuBaFrost collection will only be used for research, which has been approved by ethics committees. This ensures that the tissue is only used for the best quality research and only for the specific reasons given to the ethics committee.

Proper citation: OECI - Tubafrost: The European Human Frozen Tissue Bank (RRID:SCR_004280) Copy   

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https://github.com/DiltheyLab/HLA-LA

Software implements new graph alignment model for human leukocyte antigen, based on projection of linear alignments onto variation graph. Enables accurate HLA type inference from whole genome and whole exome Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data and from genome assemblies.

Proper citation: HLA-LA (RRID:SCR_022283) Copy   

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https://biofam.github.io/MOFA2/

Software framework for unsupervised integration of multi-omics data sets. Used for discovering principal sources of variation in multi omics data sets.

Proper citation: MOFA (RRID:SCR_022992) Copy   

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https://lsbr.niams.nih.gov/bsoft/

Software package and a platform for the processing of electron micrographs in structural biology. Supports different image file formats used in electron microscopy (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bsoft (RRID:SCR_016503) Copy   

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http://scipion.i2pc.es/

Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe

Proper citation: SCIPION (RRID:SCR_016738) Copy   

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http://biodev.extra.cea.fr/interoporc/

Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.

Proper citation: InteroPorc (RRID:SCR_002067) Copy   

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http://www.controlled-trials.com

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.

Proper citation: Current Controlled Trials (RRID:SCR_002325) Copy   

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http://www.nitrc.org/projects/pyxnat/

Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data.

Proper citation: pyxnat (RRID:SCR_002574) Copy   

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

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.

Proper citation: Colon Therapy Research Consortium (COLTHERES) (RRID:SCR_013690) Copy   

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https://github.com/ledancs/hFigures

A Javascript library that aims to deliver a starting point for interactive health data visualization. Examples and demos are available on the site. hFigures was built with d3.js and a copy of the library is included in this repository. All rights and license terms apply to the d3.js library accordingly.

Proper citation: hFigures (RRID:SCR_014201) Copy   

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http://www.itera-ls.org/

A forum for scientists specialized in stem cells, tissue engineering and regenerative medicine. The international board of the ITERA Life-Sciences Forum is composed of researchers and physicians from universities, university hospitals, stem cell and research institutes and biotechnological companies. The annual international ITERA Life-Sciences Forum workshop is dedicated to the latest developments in stem cell research. Cryo-Save, Europe''''s leading provider of stem cell banks, is a founding member of ITERA and sponsors the yearly workshops with an unrestricted educational grant. Members of ITERA Life-Sciences are participating members in three EU-Framework projects: e.a. CRYSTAL and HEPADIP and were recently awarded the HYPERLAB project. The IWT (Agency for Innovation by Science and Technology) recently confirmed that ITERA members will be involved in the HEPSTEM project with participating groups from the Flemish Universities and one research group (KUL, UGENT, VUB and IMEC). ITERA Life Sciences Forum has created this networking to share the knowledge of the academic world with the knowledge of small and middle sized enterprises (SME''''s), with the aim to participate in the Framework programs of the European Union. At the third Workshop in Maastricht (25-26 October 2007) we asked some opinion leaders who participated to explain their actual vision about stem cells of the cord, cord blood and placenta. The videos on what they had to say are available.

Proper citation: ITERA Life - Sciences (RRID:SCR_008758) Copy   

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

The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.

Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy   

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http://www.rhea-db.org/

Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.

Proper citation: RHEA (RRID:SCR_004713) Copy   

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https://datashare.ed.ac.uk/handle/10283/3844

Genome transcriptome atlas by RNA in situ hybridization on sagittal sections of developing mouse at embryonic day 14.5. Consists of searchable database of annotated images that can be interactively viewed. Anatomy based expression profiles for coding genes and microRNAs, tissue specific genes. Expression data generated by using human and murine tissue arrays.

Proper citation: Eurexpress (RRID:SCR_005093) Copy   

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http://www.dcc.ac.uk/resources/standards/diffuse

DCC DIFFUSE Standards Frameworks is a browsable database with information on both standards and the organizations which sponsor them. Entries can currently be browsed either by category, alphabetically by title or by sponsoring body. Although no further work on DIFFUSE is planned, frameworks that were created remain an accessible and relevant resource. These include frameworks developed from existing publications or specifications as well as those developed specifically for the DIFFUSE project. The DCC DIFFUSE Standards Frameworks were developed in partnership with a number of organizations with the aim of presenting searchable frameworks of standards relevant to digital curation and preservation. DCC DIFFUSE Standards Frameworks provides information about sets of standards, used by specific domains, which enable curation and preservation of, and access to, data across all stages of the DCC Curation Lifecycle Model. The project maintains information about current and emerging standards and specifications which are used. Entries for individual standards and specifications include: * Links to database entries concerning sponsoring bodies * Links to the official documentation * Links to additional documentation such as user guides, tutorials, implementation profiles and registers, XML DTD or Schema * A description of the scope of the standard or specification * A description of the development of the standard or specification * Practical examples of the standard or specification in use Entries for sponsoring bodies include: * Contact details * Organizational objectives * Areas of activity * Membership details DCC DIFFUSE includes published standards which are included in frameworks used for curation and preservation of access to digital material, for example: * Standards ratified by national or international standards organizations or bodies * Standards developed by, or ratified by, professional organizations * Publicly available specifications developed by, or ratified by, a consortia or fora

Proper citation: DCC DIFFUSE Standards Frameworks (RRID:SCR_005086) Copy   

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http://smart.embl.de/

Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.

Proper citation: SMART (RRID:SCR_005026) Copy   

•   Source: SciCrunch Registry

http://prosite.expasy.org/

Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.

Proper citation: PROSITE (RRID:SCR_003457) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9,2023. 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.

Proper citation: AddNeuroMed (RRID:SCR_003819) Copy   

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http://www.evocontology.org/site/Main/EvocOntologyDotOrg

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.

Proper citation: eVOC (RRID:SCR_010704) Copy   

•   Source: SciCrunch Registry