Search Results for "gene regulatory networks" - Page 3
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Showing 75 open source projects for "gene regulatory networks"
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regnann
Reverse Engineering Gene Network using ANN
RegnANN is a method for reverse engineering gene networks based on an ensemble of multilayer perceptrons. The algorithm is a multi-variable regressor (one to many) trained using an input expression matrix to learn the relationships (correlations) among a target gene and all the other genes. The overall network is obtained by joining all the neighborhoods. RegnANN makes no assumptions about the nature of the relationships between the variables, potentially capturing high-order and non linear... -
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GenePrioritization is a program to prioritize disease genes based on the random walk with restart algorithm for any kind of gene/protein networks. Putative genes can be verified through evidences found in PubMed, OMIM, and GeneRIF databases.
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GeneNetwork is an open source bioinformatics software resource for systems genetics used to study gene networks that link sequence variants to differences in gene and protein expression and to differences in traits such as health and disease risk.
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BIL++ is a set of standalone C++ packages for data processing in Bioinformatics (Graph mining, Bayesian networks, Genetic algorithm, Discretization, Gene expression data analysis, Hypothesis testing).
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A data mining tool for finding frequent motifs in DNA regulatory area that may play significant role in gene regulation. It makes the search more efficient by using different data like conservation and binding scores about relevant promoter areas. It is implemented as a part of Barchelor thesis work of Timo Petmanson available here: http://comserv.cs.ut.ee/forms/ati_report/downloader.php?file=0701eb033c3bad8d3be4a79a29c70107c1cad745
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Reliability Oriented Bioinformatic Networks Visualization
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FormFunction is software used to identify the degree to which the form of a three-gene regulatory network constrains or determines its function.
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HiNO is an open source project that allows to extract the hierarchical organization from directed regulatory networks. It is implemented as Netbeans Project and ready to use. Programming Language: Java License: Q Public License (QPL)
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GRaPe - a platform-independent software tool for building integrative gene-reaction-protein (GRP) networks. It generates the kinetic equations for each reaction and outputs a SBML document. It also implements two methods for parameter estimation.
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LocalMotif is a bioinformatics tool for discovering nucleotide motifs in a set of gene regulatory sequences. It takes into account the positional distribution of the motifs relative to a biological landmark. Look out for an updated version in May.
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This is a C library for using genetic algorithms to evolve biological networks, specifically metabolic, signaling, and gene regulatory networks. Users must specify the fitness function and may override the other default functions.
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Genome Data Visualization Toolkit (GDVTK) is a Java library for building bioinformatics visualization application. See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations.
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A simple Java application for the analysis and identification of gene networks. ProPesca takes as input shorts temporal series of realtime-PCR expression levels and it clusters genes that exhibit either similar or specular behaviors.
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RENCO is a C++ based software for automatic generation of ordinary differential equations for gene and protein expression dynamics in artificial regulatory networks.
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NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues.
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The complexity project will be a home for various tools and libraries associated with modelling complex systems. Initially featured will be the Central Dogma set of gene regulatory network simulation libraries, which have been recently open sourced.
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Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID.
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A user-friendly interface for running simulations of the gene networks comprising the circadian clock. Modules allow the simulation of experimental protocols with just a few mouse clicks. Users can fine-tune simulations to suit their particular interests.
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Gene Set and Gene Network Analysis are a set of bioinformatics tools designed to manipulate gene sets that function in biological networks. WebGestalt, BatchSequenceAnalysis, GeneNetWorkFlow, and other tools will be created.
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Cis-Regulatory analysis modules. Includes frequenc/weight matrices scanning at genome level, annotation by using DB access to ensembl, genekeydb, etc. and visualization (through Bioperl or as custom UCSC tracks). May include gene set analysis in future.
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GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work
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Trelis is a graphical Monte Carlo simulation tool for modeling the time evolution of chemical reaction systems involving small numbers of reactant molecules, such as occur in subcellular biological processes like genetic regulatory networks.
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PD_BiochemicalSystemsTheory
Major pathways involving in Parkinson's disease (PD) such as alphasynuclein aggregation, dopamine synthesis, lewy body formation, tau phosphorylation, parkin, and apoptosis were modeled using stochastic differential equations. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. The model allows a qualitative analysis of PD...
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Extensible simulation engine for the intra-cellular and inter-cellular dynamics of genetic regulatory networks and biological systems.
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PNE provides an environment for modeling, simulating, and optimizing biological networks including regulatory and metabolic networks.