Search Results for "disease" - Page 3
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Showing 151 open source projects for "disease"
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MutAid
MutAid: Sanger and NGS based pipeline for mutation screening.
... mapping, variant calling, variant annotation and co-analyze Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as deletions and insertions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms (Sanger, Illumina, 454 and Ion Torrent) and five read mappers including BWA,TMAP, Bowtie,Bowtie2 and GSNAP and four variant... -
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ppienergy
Compute Protein Protein Interaction Energy Profile
Protein-protein interactions (PPIs) are crucial for understanding the signaling and disease mechanisms in a cell. In the present work, we have developed a new approach to explore the energy landscape of protein-protein interactions by employing a rapid modified DFT-D approach using the atomic coordinates obtained from X-ray and NMR spectroscopy data. The distance energy plots of contact residues in the interacting regions of several experimentally validated protein-protein complexes were... -
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Brucellosis Ontology (IDOBRU) is an extension ontology of the Infectious Disease Ontology (IDO) with a focus on brucellosis, a zoonotic infectious disease caused by Brucella spp.
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Health Care Management System
Health care management and reporting.
This software will be used to manage hospitals (patient registration, drug management), and provide reporting capabilities which will enable decision makers to take proper and swift actions; especially with regards to outbreaks and drug mismanagement. -
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LargeDEL
A tool for finding possible large deletions in whole genome
DNA deletions are one of the main genetic reasons of disease. Currently there are many tools which are capable of detecting structural variations. However, these tools usually require long running time and lack ease of use. It is generally not possible to restrict the search to a region of interest. The programs also yield excessive number of results which makes further investigation troublesome. In this work, we present LargeDEL, a tool which quickly scans aligned paired-end next generation... -
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BiRW
Bi-random Walks for Phenome-Genome Association Prediction
... for unveiling human and mouse phenome-genome association. The processed OMIM human disease phenotype-gene association network and MGI mouse phentoype-gene association network are also released together with the source code. -
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ExSTraCS
Extended Supervised Tracking and Classifying System
... to address problems in epidemiological data mining to identify complex patterns relating predictive attributes in noisy datasets to disease phenotypes of interest. ExSTraCS combines a number of recent advancements into a single algorithmic platform. It can flexibly handle (1) discrete or continuous attributes, (2) missing data, (3) balanced or imbalanced datasets, and (4) binary or many classes. A complete users guide for ExSTraCS is included. Coded in Python 2.7. -
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ExAM-Exome_Analysis_And_Mining
A whole exome sequencing analysis package and its graphical interface
... to the limited bioinformatics resources that are currently freely available for their analysis and the partial information that they provide. Here, we present an interactive and free analysis package, ExAM, dedicated to whole exome sequencing data analysis. It is accessible to non-computer scientists and provides a complete set of information, as well as decision support to prioritize candidate disease causing variants. -
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The NEDSS Base System (NBS) is a web-based integrated public health disease surveillance system sponsored by the Center for Disease Control and Prevention(CDC). It was developed to provide a NEDSS-standards based system for the secure, accurate, and efficient collection, transmission, and analysis of public health data. It also provides a platform upon which program-specific modules can be built to meet state and program area requirements. State health departments use the NBS...
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Featureextraction
Feature Extraction: Fractal, Statistical, Geostatistical, Succolarity
The objective of this project is to find in the literature the best feature extractors related to the detection and diagnosis of disease in the breast, and implement them in order to make it open to research groups worldwide. The features will be available as an API (Application Programming Interface) in Java. -
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FMFilter
Fast Model Based Variant Filtering Tool
Filtering out the prominent portion through the excessive amount of information produced by next generation techniques is a challenging task. Current tools enable to analyze next generation sequencing data in various methods. However, there is still need for fast, easy to use and efficacious tools. We provide an efficient filtering tool for next generation sequencing data produced by genetic disease studies. FMFilter allows to choose one of the inheritance models (recessive, dominant, compound... -
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Virmid
Virtual Microdissection for SNP calling
NEWS: 11-07-2013 A new version Virmid 1.1.0 has been uploaded. 08-29-2013 Virmid paper is now published in Genome Biology. Kim S et al, "Virmid: accurate detection of somatic mutations with sample impurity inference", Genome Biology 2013, 14:R90 http://genomebiology.com/2013/14/8/R90/abstract Virmid (Virtual Microdissection for SNP calling) is a Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual... -
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O2 pathway and ROS generation model
Multi-scale Modeling of Skeletal Muscle ROS Generation
The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of many fundamental processes governing the balance between health and disease. It is well known that ROS are necessary signaling molecules in gene expression, yet when expressed at high levels, ROS may cause oxidative stress and cell damage. Both hypoxia and hyperoxia may alter ROS production by changing mitochondrial PO2 (PmO2). This graphical user interface facilitates to parameterize and simulate... -
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... of clinical care information systems with clinical research information systems and drug and disease knowledge databases, as well as the appliance of advanced data mining techniques and enhanced learning algorithms.
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CPAG
Cross-Phenotype Analysis of GWAS
CPAG (Cross-Phenotype Analysis of GWAS) can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks. -
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GESPA
Accurately predicts disease association of single nucleotide mutations
... 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. NOTE: REQUIRES Java 1.7.0+. Port 1433 cannot be blocked by firewall, network, or antivirus program. Please cite: http://tinyurl.com/oj7p84a -
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vcfhacks
simple to use commandline programs for VCF filtering and manipulation
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/vcfhacks) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/vcfhacks/releases/latest). (relatively) Simple to use commandline tools for the manipulation and analysis of VCF files, geared towards the identification of pathogenic mutations in Mendelian disease. -
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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... -
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RGD Vocabularies
Rat Genome Database Disease Vocabulary
This project involves maintenance and updates of the Rat Genome Database Vocabularies, as driven by the users of the vocabularies. -
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HHS Digital Media API Platform
Syndicate text and multimedia content with this API and storefront.
Use this suite of Application Programming Interface (API) platforms to share web content across multiple channels. Mobile and tablet applications, widgets, and web pages may use the APIs to deliver and update content. 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... -
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outbreaker
outbreaker
A R package for disease outbreak reconstruction using epidemiological and genetic data. -
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SEM_bestShortestPath
A SEM-based method for disease module detection
SEM_bestShortestPath is a Structural Equation Modeling (SEM)-based methodology to evaluate the most important shortest paths between differentially expressed genes in biological interaction networks, with absolutely no need of user-defined parameters or heuristic rules, enabling a free-of-bias discovery and overcoming common issues affecting recent network-based algorithms. SEM-bsp is based on Structural Equation Modeling techniques to detect significantly perturbed sub-networks (disease... -
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SEM_bestShortestPath
A SEM-based method for disease module detection
SEM_bestShortestPath is a Structural Equation Modeling (SEM)-based methodology to evaluate the most important shortest paths between differentially expressed genes in biological interaction networks, with absolutely no need of user-defined parameters or heuristic rules, enabling a free-of-bias discovery and overcoming common issues affecting recent network-based algorithms. SEM-bsp is based on Structural Equation Modeling techniques to detect significantly perturbed sub-networks (disease... -
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epimetric
Modelling the spread of disease and medical conditions in a population
Using open data sets (e.g. on drug prescription and healthcare provision) to produce tie-series models of the incidence of disease and other medical conditionsto enable more effective planning of medical service delivery and preventative interventions. -
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SoloDel
Somatic Low-frequent Deletion Caller Model
SoloDel (Somatic Low-frequent Deletion call model) is a Java based somatic deletion caller designed for whole-genome sequencing data from unmatched samples. SoloDel is specialized for identifying somatic deletions with frequently existing sampling issues : low mutational frequency in cell population and absence of the matched control samples. The important features of SoloDel are: • Estimation of mutational frequency in a mixed disease sample without matched control • Improved somatic...