Search Results for "disease"
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Showing 14 open source projects for "disease"
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1
Virmid
Virtual Microdissection for SNP calling
...The important features of Virmid are: •Estimation of accurate proporation of control sample in a (mixed) disease sample •Improved SNP and somatic mutation calling with regard to the estimated proportion -
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gametes
Generate complex SNP models and heterogeneous datasets
Genetic Architecture Model Emulator for Testing and Evaluating Software (GAMETES) is an algorithm for the generation of complex single nucleotide polymorphism (SNP) models for simulated association studies. GAMETES is designed to generate epistatic models which we refer to as pure and strict, that constitute the worst-case in terms of detecting disease associations, since such associations may only be observed if all n-loci are included in the disease model. User friendly GAMETES software rapidly and precisely generates epistatic multi-locus models, and can generate simulated datasets based on these models. Version 2.0, adds the ability to generate heterogeneous datasets by applying multiple independent models to different subsets of the simulated data. ... -
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GESPA
Accurately predicts disease association of single nucleotide mutations
...Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. The software can be used clinically to determine if observed nsSNPs are associated with disease. A host of annotations are provided: orthologous and paralogous multiple sequence alignments, UCSC annotations, reports detailing conservation of a nsSNP in alignments, and links to external nsSNP and gene information such as relevant publications. GESPA is connected to a constantly updating SQL server allowing for fast data retrieval. ... -
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HHS Digital Media API Platform
Syndicate text and multimedia content with this API and storefront.
...The APIs allow content reuse and reduce development costs and product time-to-market. The APIs are available as .NET or Java instances. For more information, see the ReadMe.txt file in the downloadable zip archive. The Centers for Disease Control and Prevention (CDC) and the Department of Health and Human Services (HHS) Assistant Secretary for Public Affairs office (ASPA) developed these APIs in collaboration with the Food and Drug Administration’s (FDA) Center for Tobacco Products (CTP). The CDC, FDA/CTP, HHS/ASPA, and the National Institute of Health’s National Institute for Allergy and Infectious Diseases (NIH/NIAID) use these platforms. ... -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
...This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation and several recessive disease genes have been discovered with the help of this technique in consanguineous families. The researchers typically use SNP arrays to determine the homozygous regions and then search for the disease gene by sequencing the genes within this candidate disease loci. Recently, the advent of next generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. ... -
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VarImpact
Extracting effects of mutations on molecular properties from text.
...VarImpact extracts experimentally observed changes from the literature. This allows to annotate sequencing results with observed impacts, gather information about the mutational landscape observed in disease populations, and to study disease mechanisms. Check our Wiki for more! -
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MendelScan
Variant scoring and linkage mapping for family exome sequencing
MendelScan is a tool for prioritizing candidate variants in family-based studies of inherited disease. -
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RODS (Real-time Outbreak and Disease Surveillance) is a real-time computer-based public health surveillance system initially developed at the RODS Laboratory, University of Pittsburgh for the early detection of disease outbreaks .
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PathMEN
A Java tool for mining pathway mentions from literature
...Using PathNER, you can identify all occurrences of informative pathway names (e.g. 'the Wnt pathway'). PathNER can be used to assist studies that aim at uncovering associations between disease and pathways. -
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10
GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
...It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein interactions, gene expression, disease-causing probabilities, genomic context). GEPETTO is written in Java/Python and supported by an advanced modular architecture, which means that it can easily be modified and extended by the user, in order to include alternative scoring methods and new data sources. We intend to extend the system from gene-level to variant-level prioritization, by exploiting the variant data in the MSV3D database. ... -
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Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.
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Global Epidemic Simulator
A platform for modelling influenza-like epidemics and containment
The Global Epidemic Simulator is a platform for modelling directly transmissible human diseases such as influenza, and testing intervention policies that may reduce the duration or severity of an outbreak of such a disease. Building on previous work, this model is spatial and individual-based, using various geographical and demographic data sources to place households at absolute locations, populated with individuals of specific ages who each attend schools or workplaces situated in their vicinity. The significant advance of this project over previous work is the global nature of simulation, the memory and performance requirements of which motivate us towards a multi-core, multi-computer solution. -
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The Disease Simulation Framework (DiSiF) represents a spatial simulation environment for infectious viral disease spread. The framework currently embodies a very simple framework for simulation in 2D space with focus on SARS and the Common Flu.
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14
OpenClinics is a software platform for the collection, maintainance and analysis of medical, (primarily disease-based), information for use by medical clinics worldwide.
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