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As a basis for the experimental cluster projects, and for further future projects a collection of various biological specimens of cancer patients shall be established. All participating Ludwig Boltzmann Institutes (LBIs) are supplying biological specimens from tumor patients and clinical documentation. At the LBI for Gynecology and Gynecologic Oncology a tumor bank for biological specimens from gynecologic cancer patients already exists. All the procedures for sample processing and storage are well established. Existing equipment for storing tissue specimens at -196 degrees C can be used. Materials from the following malignant diseases are collected: Breast cancer Colorectal cancer Neuroendocrine tumors (NET) (Small cell lung cancer (SCLC) and Carcinoid tumors) Types of biological materials: Tissue (fresh frozen) Bone marrow Blood (serum/plasma/cell fractions) Pleural effusions Ascitic fluids Sputum Bronchial lavage Stool The biological specimens are initially processed at the respective LBIs or at their connected lab facilities. Enrichment of blood samples for disseminated tumor cells is done at the LBI for Gynecology and Gynecologic oncology. Long time storage of all materials is done at appropriate temperatures at the same institution. This LBI also coordinates the logistics. All relevant sample-specific and clinical data are surveyed at the respective LBIs and stored centralized in an on-line data bank in anonymized form, respecting all relevant regulations on data protection and security.

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• SciCrunch
• 16 years ago - by Anonymous

Database containing information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug-target relations. The SIDER Side Effect Resource represents an effort to aggregate dispersed public information on side effects. To our knowledge, no such resource exist in machine-readable form despite the importance of research on drugs and their effects. The creation of this resource was motivated by the many requests for data that we received related to our paper (Campillos, Kuhn et al., Science, 2008, 321(5886):263-6.) on the utilization of side effects for drug target prediction. Inclusion of side effects as readouts for drug treatment should have many applications and we hope to be able to enhance the respective research with this resource. You may browse the drugs by name, browse the side effects by name, download the current version of SIDER, or use the search interface.

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• SciCrunch
• 16 years ago - by Anonymous

Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers.

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• SciCrunch
• 16 years ago - by Anonymous

Established in 1990 as a long term storage cryobank, ReproTech, Ltd. is dedicated to offering safe and effective shipment and long term storage of reproductive tissue that has been originally cryopreserved at another laboratory or cryobank. It is the intent of RTL to provide the physician and client depositors with quality services that fully comply with industry and government Standards and/or Regulations. Our Locations: Florida, Minnesota, Nevada, US Network Administration ReproTech, Ltd. (RTL) is a one-stop resource specializing in effective solutions to the challenges faced in today''s ever changing field of Reproductive Medicine. ReproTech''s experienced staff provides expert consultation services for long term storage of reproductive tissues and donor program management to assist in compliance with regulatory agencies.

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• SciCrunch
• 16 years ago - by Anonymous

This Core at the University of Virginia employs state-of-the-art methods to quantitate peptide and steroid reproductive hormones in blood and tissue. It also develops new methodology, prepares labeled reagents for immunoassays, immunocytochemistry and binding studies and assists in the transfer of technology to participating investigators. Available services: AMH ELISA, 3-ALPHA DIOL G ELISA (ON HOLD), ANDROSTENEDIONE RIA, CORTISOL HUMAN IMMULITE, CORTICOSTERONE RIA, DHEA ELISA, DHEA-SO4 HUMAN IMMULITE, DHT NON EXTRACTION RIA (ON HOLD), ESTRADIOL HUMAN & MOUSE BECKMAN COULTER RIA, ESTRADIOL RAT SIEMENS RIA, ESTRONE- RIA, FSH HUMAN IMMULITE, IGF-1 HUMAN IMMULITE, INHIBIN-A ELISA, INHIBIN-B ELISA, INSULIN HUMAN IMMULITE, LH HUMAN IMMULITE, MOUSE FSH RIA, MOUSE LH SANDWICH IRMA, PROGESTERONE RIA, PROINSULIN RIA, PROLACTIN HUMAN IMMULITE, 17a-OH-PROGESTERONE RIA, RAT FSH RIA, RAT LH SANDWICH IRMA, SHBG HUMAN IMMULITE, TESTOSTERONE RIA, SENSITIVE ESTRADIOL HUMAN & RAT RIA, SENSITIVE PROGESTERONE RIA, SENSITIVE TESTOSTERONE - RIA

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• SciCrunch
• 17 years ago - by Anonymous

The Center for Organ Recovery & Education (CORE) is one of 58 federally designated agencies in the United States known as a not-for-profit organ procurement organization (OPO). CORE is dedicated to promoting donation, education and research for the purpose of saving and improving the quality of life through organ, tissue and corneal transplantation. An innovative, responsive OPO, CORE plays a pivotal role between potential donors and patients awaiting transplantation. In addition to talking with families about the opportunity to donate, CORE coordinates the surgical recovery of organs, tissue and corneas, as well as the computerized matching of donated organs and placement of corneas. In 1995, CORE created the first donor card database in Pennsylvania. In 1996, the organization added tissue recovery and eye banking services to its organ recovery component. It enhanced its line of services by opening an internal laboratory in 1997, where CORE performs the necessary tests to help determine if the organs, tissue and corneas are healthy for transplantation. Since its inception more than 30 years ago, CORE has helped to provide more than 300,000 organs, tissue and corneas for transplantation. The chances for renewed health provided through CORE would not be possible without those who have said yes to donation.

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• SciCrunch
• 16 years ago - by Anonymous

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

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• SciCrunch
• 13 years ago - by Anonymous

Charge Czar is a software tool that uses a support vector machine to discriminate between +2- and +3-charged tandem mass spectra, with the goal of reducing database search time by eliminating the need to search twice with each spectrum. Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded after you have agreed to the license agreement. Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current charge-state-determination algorithms only discriminate singly- from multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiply-charged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra.

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• SciCrunch
• 16 years ago - by Anonymous

A provider for commercial products for analyzing neuronal morphology, stereology, etc.

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• SciCrunch
• 17 years ago - by Anonymous

UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. There are 10 categories of keywords: Biological process Cellular component Coding sequence diversity Developmental stage Disease Domain Ligand Molecular function Post-translation modification Technical term You may browse by hierarchy, search in Keywords, or list all keywords. By default, searching the keywords will look for matches in both name and definition.

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• SciCrunch
• 16 years ago - by Anonymous

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.

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• SciCrunch
• 16 years ago - by Anonymous

Biorepository promoting the safe handling, receipt, processing, storage, inventory control, packaging and distribution for all types of infectious and non-infectious biological specimens and reagents. The facility houses ultra-low mechanical freezers, vapor-phase liquid nitrogen freezers and mechanical walk-in freezer and cold rooms. A multi-purpose computerized security system provides around-the-clock secure access, intrusion and fire detection, and electronic monitoring of all freezers and critical building functions. In the past, KamTek managed NIH-NIAID Reference reagent Repository that stored and distributed over 2000 different reagent products including antisera against a wide variety of viruses and other infectious organisms, as well as viral antigens, allergenic, mycoplasma, and immunologic reagents. The NIAID Repository was designated World Health Organization (WHO) Collaborating Center for Antiviral Drugs and Interferon and responsible for the international distribution of the WHO Interferon reference standards. In addition, other government agencies and private sector clients use our repository and there is provision to accommodate new clients as well. BIO-SPECIMEN REPOSITORY SERVICES: * Bio-specimen Acquisition * Bio-specimen Processing * Cryo-preservation * Cryo-storage and Maintenance of Bio-Repository * Shipments * Inventory of stored biological samples * Database management of inventory for each project

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• SciCrunch
• 16 years ago - by Anonymous

As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis.

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• SciCrunch
• 16 years ago - by Anonymous

qvality estimates q-values and posterior error probabilities directly from score distributions. The method can be accessed via a web interface or downloaded as stand-alone software (C++ source code and binaries are available under MIT license). The qvality web server allows you to use qvality to compute posterior error probability and q-values for your data. There are two input modes: *Input the empirical score distribution and a corresponding null score distribution. The two inputs do not have to contain the same numbers of scores. *Input only the empirical p-value distribution. In this case, you must use p-values rather than raw scores. In either mode, the output is the same: a three-column file in which the first column contains sorted observed scores, the second column contains estimated q-values, and the third column contains estimated posterior error probabilities. Qvality is a C++ program for estimating two types of standard statistical confidence measures: the q-value, which is an analog of the p-value that incorporates multiple testing correction, and the posterior error probability (PEP, also known as the local false discovery rate), which corresponds to the probability that a given observation is drawn from the null distribution. In computing q-values, qvality employs a standard bootstrap procedure to estimate the prior probability of a score being from the null distribution; for PEP estimation, qvality relies upon non-parametric logistic regression. Relative to other tools for estimating statistical confidence measures, qvality is unique in its ability to estimate both types of scores directly from a null distribution, without requiring the user to calculate p-values.

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• SciCrunch
• 16 years ago - by Anonymous

Favorite and most desired neuroscience books, and books in fields related to neuroscience, listed by Neuroscience News staff members. You may search for books or browse by category. If you don''t see your favorite neuroscience books, or related science books for sale on the site, they want you to let them know which neuroscience books they should include.

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• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

The Duke Institute for Genome Sciences & Policy (IGSP), in partnership with the Duke University School of Medicine Research Foundation and Department of Pathology (SOMRF), has established the Duke IGSP Biospecimen Repository as a centralized and accessible biological resource for Duke Investigators and research programs. The Repository is a standardized, regulatory-compliant and privacy protected repository for fluid and tissue biospecimens, and enables Duke investigators to reduce costs, and eliminate redundancies and significant risks associated with alternative biobanking practices, while facilitating integration of clinical trials and translational research programs with molecular profiling technologies. In order to ensure sample and data integrity and comparability, the Biorepository is developing, evaluating, and implementing evidence-based biobanking ''best practices''. Centralization of activities to a dedicated and expert staff and facility allows small and large research programs to reduce costs through elimination of redundancies and achieving efficiencies and economies of scale. The Duke-IGSP Biorepository is committed to ensuring appropriate consent, approved use, and protection of privacy through compliance with HIPAA regulations and IRB guidelines. The Duke-IGSP Biospecimen Repository will facilitate the integration of clinical research programs with molecular profiling technologies, enabling large-scale ''omic'' research programs that will inform and drive the development of new generations of targeted diagnostics, therapies, and preventions, which in turn will transform clinical outcomes.

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• 16 years ago - by Anonymous

The UAB Alzheimer's Disease Center provides comprehensive treatment for Alzheimer's patients while also promoting research for the prevention and cure of Alzheimer's disease and related disorders. The ADC is an interdisciplinary program of scientists working in areas including neurology, psychiatry, genetics, and psychology. The Center provides comprehensive treatment and promotes research for the prevention and/or cure of Alzheimer's disease and other related disorders with memory loss and impaired cognition. A major emphasis of research is the maintenance of a clinical research database comprised of neurological, medical, and neuropsychological test data from participants seen in the ADRC Clinical study since 1999, many of whom have been followed for several years in the study.

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• SciCrunch
• 16 years ago - by Anonymous

The Duke Biobank is an institutional resource that combines well-annotated clinical data with a standardized, regulation compliant, cost efficient repository for both fluid and tissue, connected via information systems to a large scale, long-term biobank in Kannapolis, in order to foster breakthroughs in research; while ensuring the strictest adherence to ethical standards and regulations. Our goal is to work with investigators to maintain biorepository collections which are in compliance with all relevant local, regional and national and IRB biobanking standards. Capabilities * Provide expert consultation in planning and design of biobanking programs * Access, process, aliquot, store and distribute a wide array of liquid and tissue biological samples * Maintain informatics capabilities to accurately and efficiently track samples and link to clinical and laboratory assay data * Use the Duke Biobanking Guidelines document (in development) as guidance on scientific, ethical/legal, and operational to ensure quality and standardization of biospecimen collection * Minimize redundancy of infrastructure, as appropriate, across Duke Medicine. Duke University offers both on- and off-campus options for investigators seeking biobanking services. Our biobanking facilities are: * The Center for Human Genetics (CHG). Serves as the primary on-campus biobank for liquid sample storage for Duke Medicine, and as a portal between Duke and the LabCorp Biobank. * Duke Hospital South Tissue Bank. Serves as a sample portal for the Duke Biobank, and as the primary facility for tissue storage for Duke Medicine. ** DCCC Tissue & Blood Procurement ** IGSP Biospecimen Repository * LabCorp Biorepository. Located in Kannapolis, NC, this is the preferred storage center for large-scale, infrequently accessed sample collections

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• SciCrunch
• 16 years ago - by Anonymous

Alzheimer''s Disease International (ADI) believes that the key to winning the fight against dementia lies in a unique combination of Global Solutions and local knowledge. As such, it works locally, by empowering Alzheimer associations to promote and offer care and support for people with dementia and their carers, while working globally to focus attention on dementia. Our board is composed of people from around the world, and our staff team is based in London. ADI is the international federation of Alzheimer associations around the world, in official relations with the World Health Organization. Each member is the Alzheimer association in their country who support people with dementia and their families. ADI''s vision is an improved quality of life for people with dementia and their families throughout the world. ADI runs the Alzheimer University, a series of practical workshops aimed at helping the staff and volunteers of Alzheimer associations build and strengthen their organisations. ADI holds an annual international conference which is the longest running international conference on dementia. The conference is a unique multi-disciplinary event which unites people with an interest in dementia from around the world. World Alzheimer''s Day, celebrated on September 21 each year, is an opportunity to raise global awareness about dementia and its impact on families and the important work of our members throughout the world. Medical research is also important, and some of ADI''s member Alzheimer associations actively support research in their own countries. More information about research can be found on the web sites of Alzheimer''s Association (USA), Alzheimer''s Society (UK), Alzheimer Society of Canada, or the association in your country. For the fourth year, the Fondation M��d��ric Alzheimer and ADI are running Alzheimer''s Awards for evidence-based psychosocial interventions for people with dementia and their carers.

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• SciCrunch
• 16 years ago - by Anonymous