Search Results for "gene regulatory networks" - Page 2
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Showing 56 open source projects for "gene regulatory networks"
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PANDA
Passing Attributes between Networks for Data Assimilation
PANDA (Passing Attributes between Networks for Data Assimilation), is a message-passing model to gene regulatory network reconstruction. PANDA integrates multiple sources of biological data, including protein-protein interaction, gene expression, and sequence motif information, in order to reconstruct genome-wide, condition-specific regulatory networks. PANDA is also available in other programming languages, including: MATLAB/Octave: (1) https://drive.google.com/a/channing.harvard.edu... -
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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PRUNET is a user-friendly software tool designed to address the contextualization of a prior knowledge gene regulatory networks (PKN) to specific experimental conditions. As the input, the algorithm takes a PKN and the expression profile of two given stable states or cellular phenotypes.
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budden2014predictive
Scripts and supplementary data for budden2014predictive manuscript
Scripts and supplementary data for the manuscript "Predictive modeling of gene expression from transcriptional regulatory elements" -
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grn_inference_multigpu
This project is a exhaustive search algoritm for multiple GPUs
Gene regulatory networks (GRN) inference is an important bioinformatics problem in which the gene interactions need to be deduced from gene expression data, such as microarray data. <br> Feature selection methods can be applied to this problem. A feature selection technique is composed by two parts: a search algorithm and a criterion function. Among the search algorithms already proposed, there is the exhaustive search where the best feature subset is returned, although its computational... -
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VariabilityAnalysisInNetworks
An R package for identifying biologically perturbed networks
The VAN package enables an integrative analysis of (i) gene expression data with protein-protein interaction networks or (ii) gene and microRNA expression data with microRNA-gene interaction networks to identify biologically perturbed networks. -
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rTRM
Identification of transcriptional regulatory modules (TRMs)
This R package can be used to identify TRMs using experimental evidence from a single ChIP-seq experiment. It combines computational predicted transcription factor (TF) binding sites, gene expression and protein-protein interaction (PPI) data and use it to predict TRMs. -
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Kinsolver
A simulator for biochemical and gene regulatory networks
Research Article: http://www.sciencedirect.com/science/article/pii/S0898122108006287 -
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Genet_Package
Identifying Gene Signatures with Implication Networks
Identifying Gene Signatures with Implication Networks -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
IMPORTANT: Since publication of the AMBIENT method in BMC Sys Bio, several updates have been made. If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have... -
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GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.
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NetDS is provided to easily observe the dynamic behaviors of signaling, regulatory as well as random Boolean networks by two types of mutaion. Otherwise, some structural properties can also be found to understand more about those dynamic behaviors.
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BioNetwork Bench is a flexible interactive database querying system for storing and manipulating gene expression data and genetic networks, constructing networks from expression data and iteratively querying multiple networks and expression datasets.
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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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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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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.