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THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. It is a dataset of structurally dissimilar proteins. This dataset has been compiled by selecting well resolved representatives from the Topology level of the CATH database which hierarchically classifies all protein structures. These have been been pruned to remove: i) domains that may contain homologous elements (by pairwise sequence comparison and structural superposition of aligned residues) ii) internal duplications (by repeat detection) iii) regions with high B-Factor The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfill minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here a reference dataset of non-homologous protein domains is provided, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted. The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. Even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%. Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB.

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• SciCrunch
• 17 years ago - by Anonymous

Research center in Greece, supervised by the Ministry for Education through its General Secretariat for Research and Technology.

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• SciCrunch
• 13 years ago - submitted by Andrea Stagg

IBIS Microscopy platform offers sample preparation and acces to TEM, SEM, STED, confocals and other microscopes.

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• RRID
• 11 months ago - by Anonymous

Open Library is a project of the non-profit Internet Archive, and is funded in part by a grant from the California State Library. They have a small team of fantastic programmers who have accomplished a lot, but we can''t do it alone! This is an Open project - the software is open, the data is open, the documentation is open, and the site is open. To build it, they need hundreds of millions of book records, a brand new database infrastructure for handling huge amounts of dynamic information, a wiki interface, multi-language support, and people who are willing to contribute their time, effort, and book data. To date, they have gathered about 30 million records (20 million are available through the site now), and more are on the way. They have built the database infrastructure and the wiki interface, and you can search millions of book records, narrow results by facet, and search across the full text of 1 million scanned books. Sponsors: Open Library is funded by a grant from the California State Library.

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• SciCrunch
• 17 years ago - by Anonymous

Provides assistance with consulting on experimental design, training on bioinformatics tools and databases, data quality assessment, data processing, data visualization, data interpretation, data mining of published datasets, and assistance with preparation of manuscripts and grant proposals.

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• SciCrunch
• 14 years ago - submitted by Andrea Stagg

Core provides collaborative process development support to investigators across the Center engaged in new Biotherapeutics initiatives. Core staff are responsible for converting research-lab processes into GMP-compliant manufacturing processes. This includes establishing Standard Operating Procedures (SOPs) and batch records for cell processing, cell engineering, and vector production. Provides full support for cGMP manufacturing of cell products: handling patient cells in cGMP environment, from purification and transduction to expansion and formulation, for use in phase 1 and phase 2 clinical trials. Manufactures vector stocks, oversees biosafety and releases testing of generated projects for human use. This includes analysis of patient cells and vector stocks, assessing characteristics such as phenotype, potency, purity, and stability. Gene transfer and expression analyses are also performed. Core performs analytical post-infusion monitoring. For each trial, the Core develops a comprehensive set of analytical tests to ensure quality and safety of the manufactured drug products.

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• RRID
• 11 months ago - submitted by Patrick Badua

Neuroptikon is a tool for visualizing and interacting with neural circuits. Sponsors: This resource is supported by Janelia Farms.

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• SciCrunch
• 17 years ago - by Anonymous

NHLBI provides leadership for a national program in diseases of the heart, blood vessels, lung, and blood; blood resources; and sleep disorders. Since October 1997, the NHLBI has also had administrative responsibility for the NIH Woman''s Health Initiative. The Institute plans, conducts, fosters, and supports an integrated and coordinated program of basic research, clinical investigations and trials, observational studies, and demonstration and education projects. The National Heart, Lung, and Blood Institute (NHLBI) provides global leadership for a research, training, and education program to promote the prevention and treatment of heart, lung, and blood diseases and enhance the health of all individuals so that they can live longer and more fulfilling lives. The NHLBI stimulates basic discoveries about the causes of disease, enables the translation of basic discoveries into clinical practice, fosters training and mentoring of emerging scientists and physicians, and communicates research advances to the public. It creates and supports a robust, collaborative research infrastructure in partnership with private and public organizations, including academic institutions, industry, and other government agencies. The Institute collaborates with patients, families, health care professionals, scientists, professional societies, patient advocacy groups, community organizations, and the media to promote the application of research results and leverage resources to address public health needs. The NHLBI also collaborates with international organizations to help reduce the burden of heart, lung, and blood diseases worldwide.

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• SciCrunch
• 15 years ago - submitted by Andrea Stagg

Facility offers traditional data acquisition, analysis, and cell sorting as well as imaging cytometry. Provided equipment includes: BD FACSAria Fusion: A cell sorter that can also be used as an analyzer, it is equipped with 488nm, 640nm, and 405nm excitation sources and is equipped to analyze up to fifteen parameters simultaneously. The Fusion is capable of processing up to 70,000 events per second and sorting up to four different cell populations at once. It is also equipped with an Automatic Cell Deposition Unit (ACDU) that allows sorting of cells into plates or onto slides; Amnis ImageStream MarkII: this imaging cytometer combines the speed and objectivity of flow cytometry with the detailed imagery of microscopy to allow you to objectively and quantitatively describe biological processes based on cell size, shape, and fluorescence location, texture, and signal intensity.This open platform enables new methods of research and improves traditional flow and imaging based applications. It is equipped with 405nm, 488nm, and 642nm excitation sources and is able to analyze up to twelve parameters simultaneously. It has 20X, 40X, and 60X objective lenses and Enhanced Depth of Field technology. It can process several thousand cells per second.

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• SciCrunch
• 11 months ago - submitted by Edyta Vieth

This database is a public resource for inference of large phylogenetic trees. It is designed to provide all researchers with access to large computational resources of the NSF TeraGrid through a simple browser interface. The CIPRES Science Gateway provides new hybrid parallel versions of RAxML (7.2.7) and MrBayes (3.1.2), as well as parallel GARLI (1.0) code to insure the fastest possible run times for submitted jobs. Through a collaboration with Alexandros Stamatakis and Wayne Pfeiffer, they now offer the fastest hybrid versions of RAxML and MrBayes currently available. Sponsors: The CIPRES project is a multi-site collaboration funded by the NSF Information Technology Research (ITR) program grant entitled BUILDING THE TREE OF LIFE: A National Resource for Phyloinformatics and Computational Phylogenetics.

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• SciCrunch
• 14 years ago - by Anonymous

A collaborative institute of the bioinformatics groups in the Netherlands that perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. They aim to build and maintain a strong bioinformatics and e-bioscience community that meets the (growing) demand for bioinformatics expertise, infrastructure and personnel in the Dutch life sciences field and provides a stimulating force for advanced research in biology. The NBIC grants aim to support the NBIC projects and (the visibility of) the NBIC community. Therefore, only people working in NBIC partner organizations can apply for sponsoring by NBIC. Positions for postdocs and others are available and there is a yearly conference.

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• SciCrunch
• 14 years ago - submitted by Andrea Stagg

Department of Medical Illustration’s Medical Sculpture Core advances education and research capabilities in medical sculpture. The space serves as an AU Core Research Lab to provide expertise in medical sculpture, volumetric visualization, and 3D printing. This lab space will offer educational and research opportunities for students to develop medical models such as surgical simulation models and patient education models. The research will improve surgical and medical training and provide insight into materials and technology to improve patient care.

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• RRID
• 10 months ago - submitted by Amanda Behr

Welcome to the EMQN website. EMQN is a not-for-profit organisation promoting quality in molecular genetic testing through the provision of external quality assessment (proficiency testing schemes) and the organisation of best practice meetings and publication of guidelines. The European Molecular Genetics Quality Network (EMQN) started in October 1998 after a successful pilot trial. From January 1999 to March 2002, the network was supported by a grant from the European Commission under the Standards Measurement and Testing Programme (contract number SMT4-CT98-7515). From April 2002, the network is supported by subscriptions from it users. External Quality Assessment (EQA): There are 26 EQA schemes being offered in 2010. To participate you must be a registered member of the network. For more information on EQA schemes, click the link here. Best Practice: EMQN is actively promoting ''best practice'' meetings on individual diseases. To assist in this process, EMQN will be organising best practice meetings. To participate you must be a registered member of the network. Following the meeting, draft best practice guidelines are produced and publised on this and other related websites, for example, the web site of the UK Clinical Molecular Genetics Society (CMGS). To find out more about best practice click here. Administration: The EMQN is based at the National Genetics Reference Laboratory (Manchester), St Mary''s Hospital, Manchester, The United Kingdom. The Network is co-ordinated and administered by Dr''s Rob Elles and Simon Patton. A management group is responsible for the activities and direction of the network. National partners in different countries help to disseminate information about the network. Quality Policy The EMQN provides a comprehensive range of quality assurance programs for molecular genetics to laboratories and industry worldwide. The European Molecular Genetics Quality Network (EMQN) is committed to helping ensure diagnostic molecular genetic laboratory test results are accurate, reliable and comparable wherever they are produced. The EMQN will provide a high quality and timely service which takes into account the needs and requirements of its users. Objectives To help to raise and maintain the standards of diagnostic clinical molecular genetic testing. To undertake and promote educational activities. To be a leading authority in quality assurance . To design and provide the best possible materials and data management. To design and provide quality reports that are timely and valid. To provide professional support and consultation. To develop new programs as required. To participate in peer review. To strive for continual improvement of the quality system. Sponsor. the network was supported by a grant from the European Commission under the Standards Measurement and Testing Programme (contract number SMT4-CT98-7515

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• SciCrunch
• 17 years ago - by Anonymous

Public research university in Newark, New Jersey. Founded in 1881 with the support of local industrialists and inventors especially Edward Weston

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• SciCrunch
• 13 years ago - submitted by Andrea Stagg

Electron microscopy core provides microscopy and image analysis, applications development, and services.

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• SciCrunch
• 10 months ago - submitted by Edyta Vieth

WDIN is a collaborative project working to develop a Web-based monitoring and reporting system to provide state and federal resource managers, animal disease specialists, veterinary diagnostic laboratories, physicians, public health workers, educators, and the general public with access to data on wildlife diseases, mortality events, and other critical related information. Data are contributed voluntarily, with partners deciding which data they choose to share.

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• SciCrunch
• 17 years ago - by Anonymous

A cancer research center whose goal is to offer innovative technoligies to spur the develpment of new methods of diagnosing and treating cancer. CNIO contains a variety of programs of investigation, including a biotechnology program, a clinical research program, and a molecular oncology program. CNIO also provides services that allow researchers to access and use technologies and tools such as cytogenetics and monoclonal antibodies, and hosts a biomedical biobank.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

SBSR core consists of the Protein Purification unit and the Structure Determination unit. Protein Purification unit produces homogeneous, high-quality proteins well suited for downstream biophysical studies and structure determination. Structure Determination unit employs X-ray crystallography, Cryo-EM, and advanced AI-assisted analytical tools for structure determination and imaging.

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• SciCrunch
• 9 months ago - submitted by Edyta Vieth

The data for the smoking challenge consisted exclusively of discharge summaries from Partners HealthCare which were preprocessed and converted into XML format, and separated into training and test sets. I2B2 is a data warehouse containing clinical data on over 150k patients, including outpatient DX, lab results, medications, and inpatient procedures. ETL processes authored to pull data from EMR and finance systems Institutional review boards of Partners HealthCare approved the challenge and the data preparation process. The data were annotated by pulmonologists and classified patients into Past Smokers, Current Smokers, Smokers, Non-smokers, and unknown. Second-hand smokers were considered non-smokers. Other institutions involved include Massachusetts Institute of Technology, and the State University of New York at Albany. i2b2 is a passionate advocate for the potential of existing clinical information to yield insights that can directly impact healthcare improvement. In our many use cases (Driving Biology Projects) it has become increasingly obvious that the value locked in unstructured text is essential to the success of our mission. In order to enhance the ability of natural language processing (NLP) tools to prise increasingly fine grained information from clinical records, i2b2 has previously provided sets of fully deidentified notes from the Research Patient Data Repository at Partners HealthCare for a series of NLP Challenges organized by Dr. Ozlem Uzuner. We are pleased to now make those notes available to the community for general research purposes. At this time we are releasing the notes (~1,000) from the first i2b2 Challenge as i2b2 NLP Research Data Set #1. A similar set of notes from the Second i2b2 Challenge will be released on the one year anniversary of that Challenge (November, 2010).

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• SciCrunch
• 17 years ago - by Anonymous

United States Army's medical materiel developer, with responsibility for medical research, development, and acquisition and medical logistics management.

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• SciCrunch
• 15 years ago - submitted by Andrea Stagg