共查询到20条相似文献,搜索用时 515 毫秒
1.
Background
Boolean network (BN) modeling is a commonly used method for constructing gene regulatory networks from time series microarray data. However, its major drawback is that its computation time is very high or often impractical to construct large-scale gene networks. We propose a variable selection method that are not only reduces BN computation times significantly but also obtains optimal network constructions by using chi-square statistics for testing the independence in contingency tables. 相似文献2.
Wei Tan Ravi Madduri Alexandra Nenadic Stian Soiland-Reyes Dinanath Sulakhe Ian Foster Carole A Goble 《BMC bioinformatics》2010,11(1):542
Background
In biological and medical domain, the use of web services made the data and computation functionality accessible in a unified manner, which helped automate the data pipeline that was previously performed manually. Workflow technology is widely used in the orchestration of multiple services to facilitate in-silico research. Cancer Biomedical Informatics Grid (caBIG) is an information network enabling the sharing of cancer research related resources and caGrid is its underlying service-based computation infrastructure. CaBIG requires that services are composed and orchestrated in a given sequence to realize data pipelines, which are often called scientific workflows. 相似文献3.
Anna Maria Masci Cecilia N Arighi Alexander D Diehl Anne E Lieberman Chris Mungall Richard H Scheuermann Barry Smith Lindsay G Cowell 《BMC bioinformatics》2009,10(1):70
Background
Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal rigor of ontologies to better support computation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL's utility for computation and for cross-species data integration. 相似文献4.
Daniel Wegmann Christoph Leuenberger Samuel Neuenschwander Laurent Excoffier 《BMC bioinformatics》2010,11(1):116
Background
The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. 相似文献5.
Unitsa Sangket Surakameth Mahasirimongkol Wasun Chantratita Pichaya Tandayya Yurii S Aulchenko 《BMC bioinformatics》2010,11(1):217
Background
Genome-Wide Association (GWA) analysis is a powerful method for identifying loci associated with complex traits and drug response. Parts of GWA analyses, especially those involving thousands of individuals and consuming hours to months, will benefit from parallel computation. It is arduous acquiring the necessary programming skills to correctly partition and distribute data, control and monitor tasks on clustered computers, and merge output files. 相似文献6.
Background
In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. 相似文献7.
Background
Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. 相似文献8.
Background
With the advent of high throughput genomics and high-resolution imaging techniques, there is a growing necessity in biology and medicine for parallel computing, and with the low cost of computing, it is now cost-effective for even small labs or individuals to build their own personal computation cluster. 相似文献9.
Background
Flux variability analysis is often used to determine robustness of metabolic models in various simulation conditions. However, its use has been somehow limited by the long computation time compared to other constraint-based modeling methods. 相似文献10.
Background
Scientists striving to unlock mysteries within complex biological systems face myriad barriers in effectively integrating available information to enhance their understanding. While experimental techniques and available data sources are rapidly evolving, useful information is dispersed across a variety of sources, and sources of the same information often do not use the same format or nomenclature. To harness these expanding resources, scientists need tools that bridge nomenclature differences and allow them to integrate, organize, and evaluate the quality of information without extensive computation. 相似文献11.
Erich J Baker Guan N Lin Huadong Liu Ravi Kosuri 《Source code for biology and medicine》2007,2(1):1-11
Background
Advances in Internet technologies have allowed life science researchers to reach beyond the lab-centric research paradigm to create distributed collaborations. Of the existing technologies that support distributed collaborations, there are currently none that simultaneously support data storage and computation as a shared network resource, enabling computational burden to be wholly removed from participating clients. Software using computation-enable logistical networking components of the Internet Backplane Protocol provides a suitable means to accomplish these tasks. Here, we demonstrate software that enables this approach by distributing both the FASTA algorithm and appropriate data sets within the framework of a wide area network. 相似文献12.
Yoichiro Azuma Yoshinori Kumazawa Masaki Miya Kohji Mabuchi Mutsumi Nishida 《BMC evolutionary biology》2008,8(1):215
Background
Recent advances in DNA sequencing and computation offer the opportunity for reliable estimates of divergence times between organisms based on molecular data. Bayesian estimations of divergence times that do not assume the molecular clock use time constraints at multiple nodes, usually based on the fossil records, as major boundary conditions. However, the fossil records of bony fishes may not adequately provide effective time constraints at multiple nodes. We explored an alternative source of time constraints in teleostean phylogeny by evaluating a biogeographic hypothesis concerning freshwater fishes from the family Cichlidae (Perciformes: Labroidei). 相似文献13.
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0) 总被引:1,自引:0,他引:1
Background
Approximate Bayesian computation (ABC) is a recent flexible class of Monte-Carlo algorithms increasingly used to make model-based inference on complex evolutionary scenarios that have acted on natural populations. The software DIYABC offers a user-friendly interface allowing non-expert users to consider population histories involving any combination of population divergences, admixtures and population size changes. We here describe and illustrate new developments of this software that mainly include (i) inference from DNA sequence data in addition or separately to microsatellite data, (ii) the possibility to analyze five categories of loci considering balanced or non balanced sex ratios: autosomal diploid, autosomal haploid, X-linked, Y-linked and mitochondrial, and (iii) the possibility to perform model checking computation to assess the "goodness-of-fit" of a model, a feature of ABC analysis that has been so far neglected. 相似文献14.
Background
Mathematical models for revealing the dynamics and interactions properties of biological systems play an important role in computational systems biology. The inference of model parameter values from time-course data can be considered as a "reverse engineering" process and is still one of the most challenging tasks. Many parameter estimation methods have been developed but none of these methods is effective for all cases and can overwhelm all other approaches. Instead, various methods have their advantages and disadvantages. It is worth to develop parameter estimation methods which are robust against noise, efficient in computation and flexible enough to meet different constraints. 相似文献15.
Akito Taneda 《BMC bioinformatics》2008,9(1):521
Background
Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA) discovery. 相似文献16.
Background
The preprocessing of gene expression data obtained from several platforms routinely includes the aggregation of multiple raw signal intensities to one expression value. Examples are the computation of a single expression measure based on the perfect match (PM) and mismatch (MM) probes for the Affymetrix technology, the summarization of bead level values to bead summary values for the Illumina technology or the aggregation of replicated measurements in the case of other technologies including real-time quantitative polymerase chain reaction (RT-qPCR) platforms. The summarization of technical replicates is also performed in other "-omics" disciplines like proteomics or metabolomics. 相似文献17.
Background
The question of how a circle or line segment becomes covered when random arcs are marked off has arisen repeatedly in bioinformatics. The number of uncovered gaps is of particular interest. Approximate distributions for the number of gaps have been given in the literature, one motivation being ease of computation. Error bounds for these approximate distributions have not been given. 相似文献18.
Yu-Chiao Chiu Tzu-Hung Hsiao Li-Ju Wang Yidong Chen Yu-Hsuan Joni Shao 《BMC systems biology》2018,12(8):124
Background
Single-cell RNA sequencing (scRNA-Seq) is an emerging technology that has revolutionized the research of the tumor heterogeneity. However, the highly sparse data matrices generated by the technology have posed an obstacle to the analysis of differential gene regulatory networks.Results
Addressing the challenges, this study presents, as far as we know, the first bioinformatics tool for scRNA-Seq-based differential network analysis (scdNet). The tool features a sample size adjustment of gene-gene correlation, comparison of inter-state correlations, and construction of differential networks. A simulation analysis demonstrated the power of scdNet in the analyses of sparse scRNA-Seq data matrices, with low requirement on the sample size, high computation efficiency, and tolerance of sequencing noises. Applying the tool to analyze two datasets of single circulating tumor cells (CTCs) of prostate cancer and early mouse embryos, our data demonstrated that differential gene regulation plays crucial roles in anti-androgen resistance and early embryonic development.Conclusions
Overall, the tool is widely applicable to datasets generated by the emerging technology to bring biological insights into tumor heterogeneity and other studies. MATLAB implementation of scdNet is available at https://github.com/ChenLabGCCRI/scdNet.19.
Background
The automated annotation of biological sequences (protein, DNA) relies on the computation of hits (predicted features) on the sequences using various algorithms. Public databases of biological sequences provide a wealth of biological "knowledge", for example manually validated annotations (features) that are located on the sequences, but mining the sequence annotations and especially the predicted and curated features requires dedicated tools. Due to the heterogeneity and diversity of the biological information, it is difficult to handle redundancy, frequent updates, taxonomic information and "private" data together with computational algorithms in a common workflow. 相似文献20.
K El Emam S Samet J Hu L Peyton C Earle GC Jayaraman T Wong M Kantarcioglu F Dankar A Essex 《PloS one》2012,7(7):e39915