Construction and characterization of a rock-cluster-based EST analysis pipeline
Cancer Biology Research Center, TongJi Hospital, TongJi Medical School, Huazhong University of Science and Technology, WuHan, Hubei 430030, PR China. Computational Biology and Chemistry
(Impact Factor: 1.12).
03/2006; 30(1):81-6. DOI: 10.1016/j.compbiolchem.2005.10.003
Open access to vast amount of expression sequence tags (ESTs) data in the public databases has provided a powerful platform for gene identification, gene expression studies and comparative/functional genomic studies. To facilitate management of large-scale EST data, high performance cluster and analysis softwares, especially parallel softwares, are fundamentally essential. We reported herein a convenient approach to construct a high performance computating (HPC) cluster based on popular Rocks and a perl-scripted analysis pipeline for EST pre-processing, clustering, assembling and annotation and any other desired analysis modules through parallel computing. We tested the system using different datasets on increasing nodes. Our present results showed that the cluster and pipeline accelerate the EST analysis without artificial interference.
Available from: Bilal Wajid
- "do address to a broad set of users, however, as there is no 'one size fits all' solution, scientists have come with other solutions each tailored for a specific problem. For instance, BioBrew provided an 'over-the-counter' cluster functionality   . DNALinux   provided a preconfigured virtual machine that runs on top of the free VMWare Player on Windows XP and Vista, meaning that one could use Windows in parallel with running one's bioinformatics application in DNALinux  . "
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ABSTRACT: Research in Life Sciences has moved a from purely hypothesis driven science to a data-hypothesis driven science. Huge volumes of data requires powerful systems, intelligent algorithms and a group of people maintaining and improving the infrastructure associted with the software environments. These software environments need to be constantly maintained, configured and updated to suit the researchers ever changing needs and goals. To address these challenges engineers and computer scientists have proposed multiple solutions built on Linux systems that include within them all the necessary software needed by the research group. Therefore, this paper presents a review of the major Life Sciences driven customized Linux distributions (henceforth referred to as 'Life-Linux distros') used in the academia and industry.
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ABSTRACT: Bax inhibitor-1 (BI1) family contains six known genes in human. Some members of BI1 family have been proved to play important roles in cell death. Here we discuss the similarities and differences among the members of BI1 family by comparative genomics and proteomics, and report here the discovery of a novel member, tmbim1b, in Bos taurus. BI1 family is evolutionarily conserved as integral membrane proteins containing multiple membrane-spanning segments and predominantly localized to intracellular membranes, similar to Bcl-2 family proteins. They share multiple motifs and transcriptional factors within the promoter and the coding regions. They may represent regulators of cell death pathways, which are concluded from structure conservation of BI1 family.
Computational Biology and Chemistry 07/2008; 32(3):159-62. DOI:10.1016/j.compbiolchem.2008.01.002 · 1.12 Impact Factor
Available from: Michael James C Crabbe
Computational Biology and Chemistry 12/2008; 32(6):469. DOI:10.1016/j.compbiolchem.2008.07.028 · 1.12 Impact Factor
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