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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

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://search.driver.research-infrastructures.eu/

Data infrastructure project that merged with OpenAIRE. Cohesive, robust and flexible, pan-European infrastructure for digital repositories, offering sophisticated services and functionalities for researchers, administrators and the general public. Access the network of freely accessible digital repositories with content across academic disciplines with over 3,500,000 scientific publications, found in journal articles, dissertations, books, lectures, reports, etc., harvested regularly from more than 295 repositories, from 38 countries. DRIVER has established a network of relevant experts and Open Access repositories. DRIVER-II will consolidate these efforts and transform the initial testbed into a fully functional, state-of-the art service, extending the network to a larger confederation of repositories. It aims to optimize the way the e-Infrastructure is used to store knowledge, add value to primary research data and information making secondary research more effective, provide a valuable asset for industry, and help bridging research and education. The objectives of DRIVER-II, the second phase of the project, include efforts to expand, enrich, and strengthen the results of DRIVER, in the following areas: * strategic geographic and community expansion by means of the DRIVER confederation * establish a robust, scalable repository infrastructure accompanied by an open source software package D-Net * broader coverage of content through the use of enhanced publications * advanced end-user functionality to support scientific exploration of complex digital objects * larger outreach and advocacy programs * continued repository support * guidelines for interoperability in the larger European digital library community

Proper citation: Digital Repository Infrastructure Vision for European Research (RRID:SCR_002752) Copy   

•   Source: SciCrunch Registry

http://www.ihop-net.org/UniPub/iHOP/

Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.

Proper citation: Information Hyperlinked Over Proteins (RRID:SCR_004829) Copy   

•   Source: SciCrunch Registry

http://www.erasmusmc.nl/pathologie/clinicalpathology/tissuebank/161255/?lang=en

The Erasmus MC Virtual Tissue Bank is embedded in the department of Pathology. The collection is meant for medical research purposes only. This concerns a typical clinical based pathology biobank. Tissue samples left over from surgical resection specimen are stored under liquid nitrogen and can be requested by Erasmus MC scientists for medical scientific experiments. An application has been developed to enable scientists to search the collection on-line and request tissue samples over the Erasmus MC Intranet. Every request shall be judged according to procedures determined by the Erasmus MC Tissue Bank. A growing need is anticipated for large collections of well-diagnosed fresh frozen tumor tissue and, if available, corresponding pre-malignant and normal tissue samples. Scientific research on patient residual material has to comply with strict rules and regulations. Equipment The Erasmus MC Tissue bank manages the PALM microdissection laser for the center for Biomics, which is available through the center for Biomics ONLY after having followed an introduction course. Additionally, a complete TMA (Tissue Micro Array) platform, fully funded by the Josephine Nefkens Stichting, consisting of a Beecher Automated Tissue Arrayer ATA 27 and a Virtual Microscope or Nanozoomer from Hamamatsu and Medical Solutions with TMA analyses software strongly supports translational research on tissue samples. Complete histologic Images from the Virtual Microscope are available within the Erasmus MC Intranet or available on the Internet either by overview or a direct example.

Proper citation: Erasmus MC Tissue Bank (RRID:SCR_004945) Copy   

•   Source: SciCrunch Registry

http://tomcat.esat.kuleuven.be/txtgate/

TXTGate is a literature index database and is part of an experimental platform to evaluate (combinations of) information extraction and indexing from a variety of biological annotation databases. It is designed towards the summarization and analysis of groups of genes based on text. By means of tailored vocabularies, selected textual fields and MedLine abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles. You need to be registered in order to use the TXTGate application. Platform: Online tool

Proper citation: TXTGate (RRID:SCR_005812) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/home/recombinase

Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies.

Proper citation: Recombinase (cre) Activity (RRID:SCR_006585) Copy   

•   Source: SciCrunch Registry

http://athina.biol.uoa.gr/PRED-CLASS/

A system of cascading neural networks that classifies any protein, given its amino acid sequence alone, into one of four possible classes: membrane, globular, fibrous, mixed.

Proper citation: PRED-CLASS (RRID:SCR_006216) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/compneur-srv/LGICdb/

Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.

Proper citation: Ligand-Gated Ion Channel Database (RRID:SCR_002418) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/db/Search

Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.

Proper citation: Genes to Cognition Database (RRID:SCR_002735) Copy   

•   Source: SciCrunch Registry

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

A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines.

Proper citation: IPD - Immuno Polymorphism Database (RRID:SCR_003004) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. 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.

Proper citation: Brede Database (RRID:SCR_003327) Copy   

•   Source: SciCrunch Registry

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

IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.

Proper citation: IntEnz- Integrated relational Enzyme database (RRID:SCR_002992) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.bibsonomy.org

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.

Proper citation: BibSonomy (RRID:SCR_013756) Copy   

•   Source: SciCrunch Registry