Curator Dashboard

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

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• SciCrunch
• 16 years ago - by Anonymous

An infrastructure to allow Quebec researchers to have at their disposal tumor banks and the services that support large scale research in genomics and proteomics. The database and the tissue bank of the research network was created to allow rapid access to biological samples and their clinical data. It is spread out over many hospital institutions (in Montreal, Quebec and Sherbrooke). The members of the RRCancer-BTD supply normal, benign and malignant samples from routine surgeries and blood tests. Blood and tissue samples are collected by the provincial biobanks on a regular basis and are coded, classified and stored. The samples can be supplied to a researcher either fresh or frozen or blocks of paraffin or on slices. The sharing of information and biological material is managed according to ethical rules and contributes to increasing the value of research in Quebec. The network has mobilized a significant number of researchers in the area of cancer that unite their efforts to pursue high caliber multidisciplinary research. They are a group of researchers from many different Qu��bec Universities all working in the branch of cancer research. They are located in four hospital centers in Quebec, namely the University of Montreal Hospital Centre (CHUM), the University of Quebec Hospital Centre (CHUQ), the University of Sherbrooke Hospital Centre (CHUS) and the McGill University Hospital Centre (CUSM), as well as in the affiliated research and university centers (Sacr��-Coeur, Maisonneuve-Rosemont and the Montreal Jewish Hospital). The collaborative efforts created and maintained in this network have allowed transfer of knowledge and the sharing of cutting edge technologies. RRCancer favors multidisciplinary cancer research in both fundamental and clinical scopes. The network is based on the desire researchers to work together to prevent cancer and improve therapeutic strategies, all the while continuing the very important task of raining new specialists and graduate students.

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• SciCrunch
• 16 years ago - by Anonymous

The Alberta Cancer Foundation is more than a charity. It''s a movement for cancer-free lives today, tomorrow and forever. It''s a movement of those who know a cancer-free future is possible and who won''t settle for some day. It''s a movement of those who stand with Albertans who have no choice but to stand up to cancer. It''s a movement of those who know something can be done and are willing to do it. For those facing cancer today, in honour of those lost to cancer, and for generations to come, we promise progress. Our mission is to deliver progress in cancer research, prevention, treatment and care by generating community investment for Alberta''s coordinated research strategy, the Cross Cancer Institute, Tom Baker Cancer Centre and 15 other cancer centres throughout the province. The Alberta Cancer Foundation is a Registered Charity - Business Number 11878 0477 RR0001. Your dollar fights cancer on every front: research, prevention, screening, early diagnosis, education, treatment and care.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

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• SciCrunch
• 13 years ago - by Anonymous

The Tissue Procurement Shared Facility (TPSF) of the Comprehensive Cancer Center operates as a prospective service to collect, from UAB associated hospitals, normal, malignant, benign, and diseased fresh human tissues and fluids which are then preserved appropriate to protocol. The TPSF can provide normal, malignant, benign, or diseased remnant human tissues and/or fluids from surgical resections, autopsies, or clinical procedures for IRB-approved researchers. The preservation can include fresh storage in media or saline, snap-frozen storage in liquid nitrogen, freezing in OCT for frozen section preparation, or preservation in a fixative of choice. The TPSF can also provide procurement of control tissues including uninvolved tissues or matched tissues from patients with benign disease processes. The histology laboratory can provide paraffin blocks and/or stained or unstained slides. In addition, investigators can obtain access to rare tissues through the national Cooperative Human Tissue Network (CHTN). Although the facility operates as a prospective service specializing in the preparation of samples to protocol, limited banked frozen and paraffin-embedded samples may be available. Investigators are required to complete an application and provide a copy of their IRB approval as well as a brief description of the project for which the requested samples will be utilized. Samples are provided for research purposes only. Processing fees are to offset processing costs and should be included in all grant applications.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. The mission of the Canadian Virtual Brain Tumour Bank (CVBTB) is to facilitate clinical, molecular and translational research through the provision of well-characterized tissue linked to clinical data and to become a standardized national tissue resource whereby scientific needs are met, addressed and accelerated through a common public accessible core the CVBTB. Recognizing the need to encourage systemic banking of brain tumor tissues throughout the country and to link banks of brain tumor tissue samples with academic and scientific institutions that require these samples, the CVBTB was established. Under the sponsorship of Schering Plough Canada Inc. and in association with the Canadian Brain Tumour Consortium (CBTC), the CVBTB looks to act as a resource for all researchers to provide them with information on the types of brain tumor tissue samples available and to direct them to the tumor tissue banking sites holding these samples. The CVBTB also looks to provide information on standard operating procedures regarding aspects of tumor tissue banking such as tissue accrual, storage and shipment and the processing of blood samples such as serum and lymphocytes. The CVBTB currently consists of four brain tumour tissue banking sites (Toronto Western Hospital - Toronto, Ontario; London Health Sciences Centre - London, Ontario; McGill University - Montreal, Quebec; University of Calgary - Calgary, Alberta) and is continuously looking for more institutions to be a part of the CVBTB. If your institution would like to become a part of the CVBTB, please contact the CVBTB coordinator.

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• SciCrunch
• 16 years ago - by Anonymous

Diabetes Wiki is a wiki where people with diabetes share personal stories, and build a database of helpful information. Categories include News, What is Diabetes?, Managing Diabetes, Impact of Diabetes, and more. Additionally, contribute to blog posts and the forum.

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• SciCrunch
• 16 years ago - by Anonymous

Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis.

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• SciCrunch
• 16 years ago - by Anonymous

Database of three-dimensional structures of macromolecules that allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH''''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAssay, and PCCompound. The PubChem data are linked to other data types (illustrated example) in the Entrez system, making it possible, for example, to retrieve information about a compound and then Link to its biological activity data, retrieve 3D protein structures bound to the compound and interactively view their active sites, and find biosystems that include the compound as a component. * Biological Systems: A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The NCBI BioSystems Database provides centralized access to biological pathways from several source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system. BioSystem records list and categorize components (illustrated example), such as the genes, proteins, and small molecules involved in a biological system. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems.

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• SciCrunch
• 16 years ago - by Anonymous

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• SciCrunch
• 13 years ago - submitted by Andrea Stagg

A biorepository for HIV-infected human biospecimens from a wide spectrum of HIV-related or associated diseases, including cancer, and from appropriate HIV-negative controls. The ACSR has formalin-fixed paraffin embedded biospecimens, fresh frozen biospecimens, malignant cell suspensions, fine needle aspirates, and cell lines from patients with HIV-related malignancies. It also contains serum, plasma, urine, bone marrow, cervical and anal specimens, saliva, semen, and multi-site autopsy speicmens from patients with HIV-related malignancies including those who have participated in clinical trials. The ACSR has an associated databank that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. The ACSR database contains more than 300,000 individual biospecimens with associated clinical information. Biospecimens are entered into the ACSR database by processing type, disease category, and number of cases defined by disease category.

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• SciCrunch
• 16 years ago - by Anonymous

The Canadian Breast Cancer Foundation is the leading national volunteer-based organization in Canada dedicated to creating a future without breast cancer. Established in 1986 by a dedicated group of volunteers, the Foundation works collaboratively to fund, support and advocate for: * Relevant and innovative research, * Meaningful education and awareness programs, * Early diagnosis and effective treatment * A positive quality of life for those living with breast cancer. Our fundraising through our annual Canadian Breast Cancer Foundation CIBC Run for the Cure, special events, corporate sponsorship and donations has enabled the Foundation to allocate millions of dollars in grants for breast cancer projects and services since our inception. Addressing the needs of Canadians from coast to coast, the Canadian Breast Cancer Foundation has regional offices in British Columbia/Yukon Territory, Prairies/NWT, Ontario and the Atlantic Region. The Foundation''s central office is located in Toronto. Charitable Registration No. 12799 3608 RR0001

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 18, 2022. A tumor bank that provides a large collection of cancer specimens, from breast and other cancers, annotated with clinical information. The CBCF TB enables researchers to address unanswered questions concerning the prognosis and treatment of breast cancer and other cancers. The CBCF TB website is also directed to participants interested in donating tumor tissue or blood. Biological specimens such as blood, urine, bone marrow, and ascites (fluid that sometimes collects in the abdomen) contain genetic information, just as tumor tissue does. These samples can be used in studies that may help researchers see how people with certain genetic make-ups respond to certain treatments. It can also explain why different people have different health problems. CBCF TB, formerly ARTB, was created by a merger of components of two existing Tumor-banking initiatives, the CLS Repository in Calgary and the Tumor bank of the PolyomX Program in Edmonton.

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• SciCrunch
• 16 years ago - by Anonymous

Biosample processing, management, storage and retrieval infrastructure that operates on a cost-recovery basis to investigators. Services are available to Research Ethics Board (REB) approved studies. They accept any human tissue from appropriately consented subjects for processing to DNA, RNA, serum, plasma, peripheral blood cells, fixed tissue, and tissue blocks. Once your samples have been collected and processed, CBSR will provide short and long-term sample storage, and retrieval(typically within 24hrs) upon request. Their storage services include robust robotic systems for sample aliquoting, tracking, storage, and retrieval to ensure chain of custody on all samples. Their temperature monitoring system ensures that all samples are maintained at the chosen temperature, and provides regulatory-grade audit trail for all samples.

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• SciCrunch
• 16 years ago - by Anonymous

International Biologics is a fully accredited American Association of Tissue Banks (����??AATB����??) Tissue Bank and Processing Facility --- Accreditation #00162. It receives 100% of it''s donor tissue from federally licensed Organ Procurement Organizations (OPO����??s) and other AATB accredited donor sources. International Biologics provides multitudinous bone and soft tissue allografts. Clinical applications for these products include: Orthopedic, Spine, Joint Restoration, Oral Maxillofacial, Podiatry, Periodontal, Urology, Trauma The collection and distribution of donated tissue including soft tissue, bone tissue and organ donation of kidneys, livers and hearts (collectively tissue) are controlled by the Government. Organ Procurement Organizations (OPOs) have long been established in every state to recover tissue from donors. Because there is a very short period following death before tissue breaks down rendering it useless for implantation, OPOs maintain round-the-clock presences in hospitals including grief counseling through procurement personnel. OPO tissue is heavily federally regulated and is therefore the most highly sought tissue because it is universally understood to be the safest tissue for transplant. International Biologics has long-term high-volume OPO tissue supply contracts making it one of the largest recipients of cadaveric bone and soft tissue in the world. International Biologics processes its tissue within a state-of-the-art facility located in Scottsdale, Arizona. The facility includes nine -86C ultra low temperature freezers, 14 tray lyophilization, and four validated class 1000 clean rooms including CNC.

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• SciCrunch
• 16 years ago - by Anonymous

An independent, not-for-profit biobanking and biotechnology foundation designed to facilitate new, high quality medical research. The IBBL collects, stores, and analyzes biological samples and associated data, which are then made available to research organizations investigating new treatments for diseases. It houses a biospecimen collection and biorepository that contains high quality tissues and maintains quality control of the specimens and the clinical data associated with the tissue samples, while maintaining biobanking ethical standards. It also provides biorefinery analyses and research services that can make analytes from tissues (e.g. DNA, RNA and protein), maintains technology for high throughput gene sequencing and gene expression, and conducts biospecimen research. An informatics platform maintains the clinical and biospecimens data in a secure fashion for additional analysis. Samples are collected by IBBL personnel from hospitals in a targeted manner. The IBBL collaborates with research and health organizations in North America, Europe and the Middle East, and with the major international biobanking societies.

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• SciCrunch
• 16 years ago - by Anonymous

This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers: * Segal et al., A Genomic Code for Nucleosome Positioning, Nature 2006 * Field et al., Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals, PLoS Comp Biol. 2008 * Kaplan et al., The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome, Nature 2008 We recommend using the latest version of the model (Version 3), which is applicable to all species. Paste in a sequence to analyze or upload file. You can provide multiple sequences in fasta format (separate sequences by lines starting with ''>'' followed by the sequence name). The length of each sequence must be between 147bp and 40kb bp. Note: Due to boundary effects, we highly recommend that you add at least 5000 bp of flanking sequence around your sequence of interest. You can generate the nucleosomes positioning predictions on your own machine using our executable and wrapping Perl scripts.

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• SciCrunch
• 16 years ago - by Anonymous

Software that implements the full regularization path optimization algorithm for training a support vector machine. The support vector machine algorithm has a single hyperparameter C that regularizes the learned model. Recently, Hastie et al. (2004) described an algorithm for finding the SVM solution for all possible values of this regularization parameter. An efficient C++ implementation of this algorithm is presented. For large values of C, it is often faster to find the entire regularization path than to train a single model.

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• SciCrunch
• 16 years ago - by Anonymous

A repository of biological samples and data from people with multiple sclerosis, selected other demyelinating diseases, and unaffected controls. The repository not only provides much-needed samples and data to researchers studying MS and other diseases, but also aggregates the results from all of these studies so that they can be analyzed collectively, leading to new findings and breakthroughs. The repository collects blood, DNA, and imaging once per year. The repository currently includes samples and data from over 2,700 subjects with Multiple Sclerosis, Neuromyelitis Optica, Acute Disseminated Encephalomyelitis, Transverse Myelitis, Optic Neuritis, and Clinically Isolated Syndromes, as well as controls. Blood samples are provided as aliquots as serum, plasma, DNA, RNA, and lymphocytes and each sample is accompanied by more than 40 pages of clinical and epidemiological data contributed by the subject and the enrolling neurologist.

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• SciCrunch
• 16 years ago - by Anonymous

A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

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• SciCrunch
• 16 years ago - by Anonymous