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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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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   

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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   

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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   

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http://www.chernobyltissuebank.com/

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.

Proper citation: Chernobyl Tissue Bank (RRID:SCR_010662) Copy   

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http://ki.se/en/meb/twingene-and-genomeeutwin

In collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo��protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed)

Proper citation: KI Biobank - TwinGene (RRID:SCR_006006) 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   

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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   

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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   

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http://degradome.uniovi.es

A database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647.

Proper citation: Mammalian Degradome Database (RRID:SCR_007624) Copy   

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https://github.com/farkkilab/tribus

Software tool for cell type based analysis of multiplexed imaging data. Interactive knowledge-based classifier for multiplexed images and proteomic datasets that avoids hard-set thresholds and manual labeling. Recovers fine-grained cell types, matching the gold standard annotations by human experts, can target ambiguous populations and discover phenotypically distinct cell subtypes.

Proper citation: TRIBUS (RRID:SCR_027367) Copy   

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http://simbioms.org/

SIMBioMS (System for Information Management in BioMedical Studies) is a multi-module solution for data management in biomedical studies. Any research concerning human samples and/or utilizing high-throughput technologies yields such amount of information that conventional data storage solution might not be sufficient. We offer here three software modules: * Sample Information Management System (SIMS), * Assay Information Management System (AIMS) * Sample avAILability system (SAIL) * Emanta Administration tool (Emanta) All three software modules were developed as a part of the integrated EU project MolPAGE (Molecular Phenotyping to Accelerate Genomic Epidemiology) and the collaborative research project ENGAGE (European Network of Genomic and Genetic Epidemiology). SIMS and AIMS can work either as united system or as two completely independent components. In turn, SAIL is an independent web-based system for indexing of phenotypes availability in different cohorts and collections. All systems are packaged in such a way that they can easily be installed either as local (e.g. on a laptop) or as centralized databases (to be used by a group of people). SIMS and AIMS benefit from customizable interface, editable vocabularies and a choice of options for tackling data confidentiality issues. The systems provides a user with efficient means of control over data exchange process and at the same time helps to format the metadata in compliance with the standards accepted in functional genomics. Since SIMBioMS is an open source project, source files can be downloaded and changed by the user if needed.

Proper citation: SIMBioMS (RRID:SCR_005745) Copy   

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

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.

Proper citation: BovMap Database (RRID:SCR_008145) 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://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

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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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://comgen.pl/mirex/

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window.

Proper citation: mirEX (RRID:SCR_006060) Copy   

•   Source: SciCrunch Registry