Bioinformatics (Oxford, England)
1367-4811
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Haplotype inference by maximum parsimony Abstract
Motivation: Haplotypes have been attracting increasing attention because of their importance in analysis of many fine-scale molecular-genetics data. Since direct sequencing of haplotype via experimental methods is both time-consuming and expensive, haplotype inference methods that infer haplotypes based on genotype samples become attractive alternatives.
Results: (1) We design and implement an algorithm for an important computational model of haplotype inference that has been suggested before in several places. The model finds a set of minimum number of haplotypes that explains the genotype samples. (2) Strong supports of this computational model are given based on the computational results on both real data and simulation data. (3) We also did some comparative study to show the strength and weakness of this computational model using our program.
Availability: The software HAPAR is free for non-commercial uses. Available upon request ([email protected]).
Tập 19 Số 14 - Trang 1773-1780 - 2003
How frugal is mother nature with haplotypes? Abstract
Motivation: Inference of haplotypes from genotype data is crucial and challenging for many vitally important studies. The first, and most critical step, is the ascertainment of a biologically sound model to be optimized. Many models that have been proposed rely partially or entirely on reducing the number of unique haplotypes in the solution.
Results: This article examines the parsimony of haplotypes using known haplotypes as well as genotypes from the HapMap project. Our study reveals that there are relatively few unique haplotypes, but not always the least possible, for the datasets with known solutions. Furthermore, we show that there are frequently very large numbers of parsimonious solutions, and the number increases exponentially with increasing cardinality. Moreover, these solutions are quite varied, most of which are not consistent with the true solutions. These results quantify the limitations of the Pure Parsimony model and demonstrate the imperative need to consider additional properties for haplotype inference models. At a higher level, and with broad applicability, this article illustrates the power of combinatorial methods to tease out imperfections in a given biological model.
Contact: [email protected]
Tập 25 Số 1 - Trang 68-74 - 2009
A graphical interface for the FoldX forcefield Abstract
Summary: A graphical user interface for the FoldX protein design program has been developed as a plugin for the YASARA molecular graphics suite. The most prominent FoldX commands such as free energy difference upon mutagenesis and interaction energy calculations can now be run entirely via a windowed menu system and the results are immediately shown on screen.
Availability and Implementation: The plugin is written in Python and is freely available for download at http://foldxyasara.switchlab.org/ and supported on Linux, MacOSX and MS Windows.
Contact: [email protected]; [email protected]; [email protected]
Tập 27 Số 12 - Trang 1711-1712 - 2011
J-Express: exploring gene expression data using Java Abstract
Summary: J-Express is a Java application that allows the user to analyze gene expression (microarray) data in a flexible way giving access to multidimensional scaling, clustering, and visualization methods in an integrated manner. Specifically, J-Express includes implementations of hierarchical clustering, k-means, principal component analysis, and self-organizing maps. At present, it does not include methods for comparing two or more experiments for differentially expressed genes. The application is completely portable and requires only that a Java runtime environment 1.2 is installed on the system. Its efficiency allows interactive clustering of thousands of expression profiles on standard personal computers.
Availability: http://www.ii.uib.no/~bjarted/jexpress/
Contact: [email protected]
* To whom correspondence should be addressed.
Tập 17 Số 4 - Trang 369-370 - 2001
A multi-algorithm, multi-timescale method for cell simulation Abstract
Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models.
Results: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a ‘composite’ heat-shock response model that combines the Gillespie–Gibson stochastic algorithm and deterministic differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multi-timescale demonstration of coupled harmonic oscillators is also shown.
Availability: An implementation of the method is available as part of E-Cell Simulation Environment Version 3 downloadable from http://www.e-cell.org/software. Benchmark models are included in the package, and also available upon request.
Supplementary information: Complete lists of reactions and parameters of the heat-shock model, and more results are available at http://www.e-cell.org/bioinfo/takahashi03-1-supp.pdf
Tập 20 Số 4 - Trang 538-546 - 2004
E-CELL: software environment for whole-cell simulation. Abstract
MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.
Tập 15 Số 1 - Trang 72-84 - 1999
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data Abstract
Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of ‘widgets’ performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages.
Availability: Freely available from http://www.intermine.org under the LGPL license.
Contact: [email protected]
Supplementary information: Supplementary data are available at Bioinformatics online.
Tập 28 Số 23 - Trang 3163-3165 - 2012
The CellML Model Repository Abstract
Summary: The CellML Model Repository provides free access to over 330 biological models. The vast majority of these models are derived from published, peer-reviewed papers. Model curation is an important and ongoing process to ensure the CellML model is able to accurately reproduce the published results. As the CellML community grows, and more people add their models to the repository, model annotation will become increasingly important to facilitate data searches and information retrieval.
Availability: The CellML Model Repository is publicly accessible at http://www.cellml.org/models
Contact: [email protected]
Tập 24 Số 18 - Trang 2122-2123 - 2008
Integrating metabolic, transcriptional regulatory and signal transduction models in<i>Escherichia coli</i> Abstract Motivation: The effort to build a whole-cell model requires the development of new modeling approaches, and in particular, the integration of models for different types of processes, each of which may be best described using different representation. Flux-balance analysis (FBA) has been useful for large-scale analysis of metabolic networks, and methods have been developed to incorporate transcriptional regulation (regulatory FBA, or rFBA). Of current interest is the integration of these approaches with detailed models based on ordinary differential equations (ODEs). Results: We developed an approach to modeling the dynamic behavior of metabolic, regulatory and signaling networks by combining FBA with regulatory Boolean logic, and ordinary differential equations. We use this approach (called integrated FBA, or iFBA) to create an integrated model of Escherichia coli which combines a flux-balance-based, central carbon metabolic and transcriptional regulatory model with an ODE-based, detailed model of carbohydrate uptake control. We compare the predicted Escherichia coli wild-type and single gene perturbation phenotypes for diauxic growth on glucose/lactose and glucose/glucose-6-phosphate with that of the individual models. We find that iFBA encapsulates the dynamics of three internal metabolites and three transporters inadequately predicted by rFBA. Furthermore, we find that iFBA predicts different and more accurate phenotypes than the ODE model for 85 of 334 single gene perturbation simulations, as well for the wild-type simulations. We conclude that iFBA is a significant improvement over the individual rFBA and ODE modeling paradigms. Availability: All MATLAB files used in this study are available at http://www.simtk.org/home/ifba/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.
Tập 24 Số 18 - Trang 2044-2050 - 2008
E-Cell 2: Multi-platform E-Cell simulation system Abstract
Summary: A new version of the E-Cell simulation system, which runs on Windows as well as Linux, has been released as free software under the terms of the GNU General Public License.
Availability: Downloadable from http://www.E-Cell.org
Tập 19 Số 13 - Trang 1727-1729 - 2003