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The PDGene database aims to provide a comprehensive, unbiased and regularly updated collection of genetic association studies performed on Parkinson's disease (PD) phenotypes. Eligible publications are identified following systematic searches of scientific literature databases, as well as the table of contents of journals in genetics, neurology, and psychiatry. The database can be searched either by a variety of dropdown menus or by specific keywords. For each gene, summary overviews are provided displaying key characteristics for each publication, including links to genotype distributions of the polymorphisms studied, random-effects allelic meta-analyses, and funnel plots for an assessment of publication bias. The PDGene database, developed by Massachusetts General Hospital/Harvard Medical School, The Michael J. Fox Foundation and the Alzheimer Research Forum, is supported by a grant from The Michael J. Fox Foundation in partnership with the Alzheimer Research Forum.

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• SciCrunch
• 16 years ago - by Anonymous

Core facility that provides the following services: Energy Expenditure Assessment, Body Composition Assessment, Physical Activity Assessment. This component of the core utilizes existing institutional resources for measurement of energy balance and provides personnel support that permit assessment of research in energy balance and nutrition assessment.

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• SciCrunch
• 13 years ago - by Anonymous

The Breast Cancer Family Registry (Breast CFR) and the Colon Cancer Family Registry (Colon CFR) were established by the National Cancer Institute (NCI) as a unique resource for investigators to use in conducting studies on the genetics and molecular epidemiology of breast and colon cancer. Known collectively as the CFRs, they share a central goal: the translation of research to the clinical and prevention settings for the benefit of Registry participants and the general public. The CFRs are particularly interested in: * Identifying and characterizing cancer susceptibility genes; * Defining gene-gene and gene-environment interactions in cancer etiology; and * Exploring the translational, preventive, and behavioral implications of research findings. The CFRs do not provide funding for studies; however, researchers can apply to access CFR data and biospecimens contributed by thousands of families from across the spectrum of risk for these cancers and from population-based or relative controls. Special features of the CFRs include: * Population-based and clinic-based ascertainment; * Systematic collection of validated family history; * Epidemiologic risk factor , clinical, and followup data; * Biospecimens (including tumor blocks and Epstein-Barr virus (EBV)-transformed cell lines); * Ongoing molecular characterization of the participating families; and * A combined informatics center.

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• SciCrunch
• 16 years ago - by Anonymous

Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes

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• SciCrunch
• 17 years ago - by Anonymous

A versatile web-server application for the analysis and visualization of array-CGH data.

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• SciCrunch
• 13 years ago - by Anonymous

The Cooperative Human Tissue Network- Western Division at Vanderbilt University Medical Center is one of six institutions throughout the country funded by the National Cancer Institutes to procure and distribute remnant human tissues to biomedical researchers throughout the United States and Canada. CHTN operates through a shared networking system which allows investigators greater access to available research specimens. CHTN offers a variety of preparation and preservation techniques to ensure investigators are receiving the quality specimens needed for research. Remnant tissues are obtained from surgical resections and autopsies and are procured to the specifications of the investigator.

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• SciCrunch
• 16 years ago - by Anonymous

Brain Innovation B.V. is developing scientific software in the field of human and animal brain imaging, neural network simulation and computer-based experimental control. Our current major product, BrainVoyager QX, is a commercially available cross-platform neuroimaging tool, which is used in hundreds of labs across the planet. Turbo-BrainVoyager is an easy to use program for real-time data analysis, which allows to observe a subject''s or patient''s brain activity during an ongoing functional MRI scanning session. TMS Neuronavigator provides the hard- and software to navigate a TMS coil to desired anatomical or functionally defined brain regions. We also provide free software products. BrainVoyager Brain Tutor allows to learn about brain areas by clicking on rotatable 3D brain models. StimulDX is a powerful stimulation software based on Microsofts DirectX API, which we will make available for free download in the near future.

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• SciCrunch
• 17 years ago - by Anonymous

Public research university in Pittsburgh, Pennsylvania. Pitt was founded by Hugh Henry Brackenridge in 1787 as the Pittsburgh Academy.

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• SciCrunch
• 13 years ago - submitted by Timothy Tsui

Ontology that assigns a grade to a tumor starting from the 3 criteria of the NGS

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• SciCrunch
• 13 years ago - by Anonymous

Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.

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• SciCrunch
• 13 years ago - by Anonymous

DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses. The public sequence databases contain vast amounts of data on virus genomes but accessing and comparing the data, except for relatively small sets of related viruses can be very time consuming. The procedure is made difficult because some of the sequences on these databases are incorrectly named, poorly annotated or redundant. The NCBI Reference Sequence project (1) provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) and protein products, for major research organisms. This now includes curated information for a single sequence of each fully sequenced virus species. While this is a welcome development, it can only deal with complete sequences. An important feature of DPV is the opportunity to access genes (and other features) of multiple sequences quickly and accurately. Thus, for example, it is easy to obtain the nucleotide or amino acid sequences of all the available accessions of the coat protein gene of a given virus species or for a group of viruses. To increase its usefulness further, DPVweb also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA (ssDNA) genome. Sponsors: This site is supported by the Association of Applied Biologists and the Zhejiang Academy of Agricultural Sciences, Hangzhou, People''s Republic of China.

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• SciCrunch
• 17 years ago - by Anonymous

This site is intended primarily to provide information on IUPAC nomenclature recommendations (Organic & Biochemical Nomenclature, Symbols & Terminology etc.). As the author has been primarily involved in the preparation of organic and biochemical material most work will be in that field. Other material will be provided as it becomes available, either from this site or by links to other locations.

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• SciCrunch
• 16 years ago - by Anonymous

The European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) is the central source of comprehensive information on drugs and drug addiction in Europe. It was set up to provide factual, objective, reliable and comparable information concerning drugs, drug addiction and their consequences. Mission and work programme Just over a decade ago, Europes capacity for monitoring its drug problem was extremely limited. National approaches to the topic varied greatly and there was a lack of reliable and comparable information at European level concerning drugs, drug addiction and their consequences. In other words, it was impossible to talk with confidence about patterns and trends in drug use across the EU. The European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) was founded in 1993 to change that. Inaugurated in Lisbon in 1995, the EMCDDA is the hub of drug-related information in the European Union. It exists to provide the EU and its Member States with a factual overview of European drug problems and a common information framework to support the drugs debate. The EMCDDA consists of a 90-strong team of specialists representing some 20 nationalities. Today it offers policy-makers the scientific evidence base they need for drawing up drug laws and strategies and helps professionals and researchers pinpoint best practice and new areas for analysis. Improving the comparability of drug information in the EU is central to the agencys work. To achieve this, the EMCDDA coordinates and relies on a network of some 30 national monitoring centres (Reitox network) to gather and analyse country data according to common data-collection standards and tools. The results of this national monitoring process are fed to the Lisbon centre for analysis and are ultimately released in the Annual report on the state of the drugs problem in Europe one of its many outputs. The EMCDDA has many working partners in Portugal. These include technical bodies primarily the Instituto da droga e da toxicodependncia which furnish the agency with the Portuguese drugs picture, and political bodies which use EMCDDA information when taking decisions on drug-related issues. In addition to cooperating with partners at national level, the EMCDDA also collaborates with its peers worldwide, having signed agreements with European and international organisations working in the drugs field. Over time, the EMCDDA has become not only Europes central reference point on drugs but also a respected authority globally. This interest has been reflected in visits by Heads of State and high-ranking politicians from all world regions and in requests from several non-EU countries for cooperation, whether in the area of technical assistance or the exchange of data and expertise. While the EMCDDA monitors the drug situation today, it is ever vigilant for new drugs and emerging trends that may pose a threat to Europes citizens tomorrow. With the production of cocaine and heroin at historically high levels and with around 7,000 Europeans dying every year of drug overdoses, constant monitoring is imperative. Public access to documents Citizens of the European Union and natural or legal persons residing or having their registered office in a Member State have the right of access to EMCDDA documents under Article 255(1) of the EC Treaty and Article 2(1) of Regulation (EC) No 1049/2001 in accordance with detailed rules laid out in the implementing rules adopted by the Management Board on 24 February 2006. This right to access concerns documents held by the EMCDDA, that is to say, documents drawn up or received by it and in its possession. Pursuant to article 2(2) of Regulation (EC) No 1049/2001, citizens of third countries not residing in a Member State and legal persons not having their registered office in one of the Member States shall enjoy the right of access to EMCDDA documents on the same terms as the beneficiaries referred to in Article 255(1) of the EC Treaty and Article 2(1) of Regulation (EC) No 1049/2001. All applications for access to a document should be sent by mail, fax or email, clearly stating the reference Application for access to EMCDDA documents. Funding The EMCDDA receives stable funding under Commission budget line B3-441 of the general budget of the European Union. Each year, a preliminary draft budget is presented by the Centre''s Director to the Management Board which may modify the draft before adopting it and submitting it to the European Commission. On this basis, the Commission presents its proposal for the annual funding to the EMCDDAs budget, to be adopted by the European Parliament and the Council. The implementation of the EMCDDA budget is subject to the external audit of the European Court of Auditors. The political responsibility for the execution of the budget rests with the EMCDDA''s Management Board, which adopts its own internal financial rules, based on the financial regulation applicable to the general budget of the European Communities.

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• SciCrunch
• 17 years ago - by Anonymous

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

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• SciCrunch
• 13 years ago - by Anonymous

A simple interface to simulate Brownian motion in arbitrary, complex environments. The analysis routines enable visualization of these models with DTI, q-space, and higher order diffusion weighted MRI.

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• SciCrunch
• 13 years ago - by Anonymous

Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver.

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• SciCrunch
• 13 years ago - by Anonymous

Software to estimate transcript isoform abundances from RNA-Seq data by variational Bayesian inference. The statistical method can handle gapped alignments of reads against reference sequences so that it allows insertion or deletion errors within reads.

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• SciCrunch
• 13 years ago - by Anonymous

Founded in 1973, the American Brain Tumor Association (ABTA) was the first national nonprofit organization dedicated solely to brain tumors. For nearly 40 years, the Chicago-based ABTA has provided critical funding to researchers working toward breakthroughs in brain tumor diagnosis, treatment and care, and is the only national organization providing comprehensive resources and serving the complex supportive care needs of brain tumor patients and caregivers from diagnosis through treatment and beyond.

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• SciCrunch
• 15 years ago - by Anonymous

A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays.

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• SciCrunch
• 14 years ago - by Anonymous