Search Results for "pathway" - Page 4
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Showing 105 open source projects for "pathway"
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ChiBE
Chisio BioPAX Editor
ChiBE (Chisio BioPAX Editor) is an open source pathway editor for biological pathways in BioPAX format. ChiBE converts BioPAX graphs into process diagrams where complexes and compartments are represented with compound nodes. !!! For latest version, please see !!! http://code.google.com/p/chibe -
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This project is aimed at providing useful thermodynamic tools for biochemists, including formation energy estimation of virtually every biochemical compound and metabolic pathway analysis and profiling.
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The Edinburgh Pathway Editor (EPE) is a tool and framework that allows the drawing and manipulation of Biological Networks, such as signalling or matabolic pathways. The editor supports several notations including SBGN and Cytoscape notations.
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We are developing MIRACH, a Statistical Online Model Checker for Biological Pathway Models, based on the PLTLs formalism for expressing the rules/properties to be checked. MIRACH can currently check pathways models written either in CSML or SBML.
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Data Assimilation (DA) is a computational approach that estimates unknown parameters in a pathway model using time-course data. Here, we developed a Java software with an intuitive interface to allow users to carry out parameters estimation using DA.
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SBMLforge is a tool that enables the user to convert and merge KEGG metabolic and signaling pathways (KGML format) to create a single SBML pathway model.
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We propose a metabolic pathway drawing algorithm for reducing the number of edge crossings by considering the fact that metabolic pathway graph is scale-free network.
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J2dPathway project are composed of several packages: J2dPathway(biological pathway viewer), Pyrus Pathway Editor (biological CAD), and DNASequenceViewer (platform-independent sequence viewer).
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The goal of this project is to make a biologic pathway simulation / emulation application. The ultimate goal is to feed different file types to the application and configure a pathway and its behaviour.
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EMMA 2 is web-based server application for management, annotation, and analysis of microarray data. It provides mapping of gene expression data onto pathway data extensible analysis and visualization functions and MAGE-ML support.
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The SIGMOID project is a persistent object model for storing cellular signaling pathway information.
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Genome Expression Pathway Analysis Tool - Analysis and Visualization of Microarray Gene Expression Data under Genomic, Proteomic and Metabolic Context
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Access your windows based database from any platform using a powerful XML based communication protocol.
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GSCope3 performs microarray data analysis to find correlations between BLSOM clusters and any form of omic knowledge expressed in OSML. Includes example metabolic pathway, gene ontology, genome position, transcription and PPI knowledge in OSML format.
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PathwayAnalyser is a software for systems biologists who want to perform flux based analyses and simulations on SBML Models. PA affords FBA as well as interfacing with Taylor software for high precision simulations of ODEs.
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Cyclone aims at facilitating the use of BioCyc, a biological pathway tool. Cyclone provides a comprehensive library of Java classes.
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GeXpert is an expert system that can be used for genetics and metabolic pathway analysis. GeXpert can help Biotechnologists do their work faster, reducing the time required for performing, analyzing and storing the results of Bioinformatics research.
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Tundra is an extensible, open-source game engine which replicates Lemmings (written originally by DMA Design). Players must save thousands of adorable, tiny rodents from certain death by helping them create a pathway to the exit.
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This project use the open source Protege knowledge base tool to create knowledge base version of the main public database of genomic data available on the internet (GO, Kegg, Entrez) to draw biological pathway.
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runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.
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World Foundry is a 3D level game engine and asset production pathway with over 170,000 lines of code. Originally a commercial product, now released under the GPL. Designed from the beginning to be cross-platform, runs on windows, working on linux port.
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PNE provides an environment for modeling, simulating, and optimizing biological networks including regulatory and metabolic networks.
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