Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new features-Custom Node graphics and Attribute Equations-which can be used ...
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Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new features-Custom Node graphics and Attribute Equations-which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities. Custom Node graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties.
computer simulation models can be useful in exploring the efficacy of HIV therapy regimens in preventing the evolution of drug-resistant viruses. Current modeling programs, however, were designed by researchers with e...
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computer simulation models can be useful in exploring the efficacy of HIV therapy regimens in preventing the evolution of drug-resistant viruses. Current modeling programs, however, were designed by researchers with expertise in computational biology, limiting their accessibility to those who might lack such a background. We have developed a user-friendly graphical program, HIV Therapy Simulator (HIVSIM), that is accessible to nontechnical users. The program allows clinicians and researchers to explore the effectiveness of various therapeutic strategies, such as structured treatment interruptions, booster therapies and induction-maintenance therapies. We anticipate that HIVSIM will be useful for evaluating novel drug-based treatment concepts in clinical research, and as an educational tool.
The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To...
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The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those.
We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally re...
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We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods.
Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to calculate statistics or to explore parameter space is a common means for analysing these models and can be computati...
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Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to calculate statistics or to explore parameter space is a common means for analysing these models and can be computationally intensive. However, in many cases, the simulations are easily parallelizable. graphics processing units (GPUs) are capable of efficiently running highly parallel programs and outperform CPUs in terms of raw computing power. Despite their computational advantages, their adoption by the systems biology community is relatively slow, since differences in hardware architecture between GPUs and CPUs complicate the porting of existing code. Results: We present a Python package, cuda-sim, that provides highly parallelized algorithms for the repeated simulation of biochemical network models on NVIDIA CUDA GPUs. Algorithms are implemented for the three popular types of model formalisms: the LSODA algorithm for ODE integration, the Euler-Maruyama algorithm for SDE simulation and the Gillespie algorithm for MJP simulation. No knowledge of GPU computing is required from the user. Models can be specified in SBML format or provided as CUDA code. For running a large number of simulations in parallel, up to 360-fold decrease in simulation runtime is attained when compared to single CPU implementations. Availability: http://***/ Contact: ***@***;***@*** Supplementary Information: Supplementary data are available at Bioinformatics online.
Motivation: As disease loci are rapidly discovered, an emerging challenge is to identify common pathways and biological functionality across loci. Such pathways might point to potential disease mechanisms. One strateg...
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Motivation: As disease loci are rapidly discovered, an emerging challenge is to identify common pathways and biological functionality across loci. Such pathways might point to potential disease mechanisms. One strategy is to look for functionally related or interacting genes across genetic loci. Previously, we defined a statistical strategy, Gene Relationships Across Implicated Loci (GRAIL), to identify whether pair-wise gene relationships defined using PubMed text similarity are enriched across loci. Here, we have implemented VIZ-GRAIL, a software tool to display those relationships and to depict the underlying biological patterns. Results: Our tool can seamlessly interact with the GRAIL web site to obtain the results of analyses and create easy to read visual displays. To most clearly display results, VIZ-GRAIL arranges genes and genetic loci to minimize intersecting pair-wise gene connections. VIZ-GRAIL can be easily applied to other types of functional connections, beyond those from GRAIL. This method should help investigators appreciate the presence of potentially important common functions across loci.
Data processing, analysis and visualization (datPAV) is an exploratory tool that allows experimentalist to quickly assess the general characteristics of the data. This platform-independent software is designed as a ge...
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Data processing, analysis and visualization (datPAV) is an exploratory tool that allows experimentalist to quickly assess the general characteristics of the data. This platform-independent software is designed as a generic tool to process and visualize data matrices. This tool explores organization of the data, detect errors and support basic statistical analyses. Processed data can be reused whereby different step-by-step data processing/analysis workflows can be created to carry out detailed investigation. The visualization option provides publication-ready graphics. Applications of this tool are demonstrated at the web site for three cases of metabolomics, environmental and hydrodynamic data analysis.
Summary: We present an improved version of our Protein Peeling web server dedicated to the analysis of protein structure architecture through the identification of protein units produced by an iterative splitting algo...
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Summary: We present an improved version of our Protein Peeling web server dedicated to the analysis of protein structure architecture through the identification of protein units produced by an iterative splitting algorithm. New features include identification of structural domains, detection of unstructured terminal elements and evaluation of the stability of protein unit structures.
We consider the problem of a particle subject to Brownian motion in a 2D circular domain with reflecting boundaries except for an absorbing gate. An exact solution for the mean first escape time is given for a gate of...
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We consider the problem of a particle subject to Brownian motion in a 2D circular domain with reflecting boundaries except for an absorbing gate. An exact solution for the mean first escape time is given for a gate of any size. Also obtained is the exact probability density of the location of an exiting particle. Numerical simulations of the stochastic process with finite step size are compared with the exact solution to the Brownian motion (the limit of zero step size). The difference between the two appears to decrease with diminishing step size. (C) 2010 Academic des sciences. Published by Elsevier Masson SAS. All rights reserved.
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