LXtoo: an integrated live Linux distribution for the bioinformatics community

BMC Research Notes

Qing-Yu He¹  Xiao-Hua Meng²  Li-Gen Wang²  Guangchuang Yu¹ 

[1] Institute of Life and Health Engineering and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, China;College of Information Science and Technology, Jinan University, Guangzhou, 510632, China

关键词: Operating system;    Linux;    Software;    Bioinformatics;   

Others  :  1166133
DOI  :  10.1186/1756-0500-5-360

 received in 2012-03-31, accepted in 2012-07-19,  发布年份 2012

【 摘 要 】

Background

Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis.

Findings

Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing.

Conclusions

LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo webcite.

【 授权许可】

   
2012 Yu et al.;

【 参考文献 】

• [1]Watson JD: The human genome project: past, present, and future. Science 1990, 248:44-49.
• [2]Metagenomics versus Moore’s law Nat Methods 2009, 6:623-623.
• [3]Thomson RC: PhyLIS: a simple GNU/Linux distribution for phylogenetics and phyloinformatics. Evol Bioinforma 2009, 5:91-95.
• [4]Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M: Open software for biologists: from famine to feast. Nat Biotechnol 2006, 24:801-803.
• [5]Geeleher P, Morris D, Hinde JP, Golden A: BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server. Bioinformatics 2009, 25:1438-1439.
• [6]Bassi S, Gonzalez V: DNALinux virtual desktop edition. Nature Precedings 2007.
• [7]Ihaka R, Gentleman R: R: a language for data analysis and graphics. J Comput Graph Stat 1996, 5:299-314.
• [8]Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC: GROMACS: fast, flexible, and free. J Comput Chem 2005, 26:1701-1718.
• [9]Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
• [10]Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29.
• [11]Osborne J, Flatow J, Holko M, Lin S, Kibbe W, Zhu L, Danila M, Feng G, Chisholm R: Annotating the human genome with disease ontology. BMC Genomics 2009, 10:S6.
• [12]Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M: KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-D360.
• [13]Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. BioMed Central Full Text
• [14]Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S: GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 2010, 26:976-978.
• [15]Yu G, Wang L-G, Han Y, He Q-Y: clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: J Integr Biol 2012, 16:284-287.
• [16]Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16:276-277.
• [17]Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE: UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 2004, 25:1605-1612.
• [18]Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
• [19]Gatto L, Lilley KS: MSnbase – an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, Processing and quantitation. Bioinformatics 2012, 28:288-289.
• [20]Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E: The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39:1278-1284.
• [21]Suzuki R, Shimodaira H: Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 2006, 22:1542-1540.
• [22]Yu G, He Q-Y: Functional similarity analysis of human virus-encoded miRNAs. J Clin Bioinforma 2011, 1:15. BioMed Central Full Text
• [23]Powers S: The second-string desktop. Linux J 2011, 202:2.
• [24]Elmendorf D: Economy size geek: installation toolkit. Linux J 2010, 191:10.
• [25]Tchantchaleishvili V, Schmitto JD: Preparing a scientific manuscript in Linux: today’s possibilities and limitations. BMC Res Notes 2011, 4:434. BioMed Central Full Text