Galaxy 相關文獻

Galaxy是一套運用來協助進行基因體研究的開放源碼的網頁介面平台,提供了許多的分析工具,包含諸多的序列分析比對工具,以及近年來最熱門的次世代基因體序列分析,此軟體具有下列三項特性:

  1. 容易使用的:使用者無需程式編寫經驗,就能輕易的設定參數來執行分析工具或流程.
  2. 可再現性:此軟體紀錄了所有的資訊,所以任何使用者都可以輕易地重複或是了解整個計算分析的過程.
  3. 透明的:使用者可以經由網頁或是創建頁面來分享以及發佈分析過程,並且有一個描述整個分析的網頁互動式文件說明.

Galaxy software has been cited by following papers:

  1. ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia.
    Arnaiz O, Sperling L
    Nucleic Acids Res 2011 Jan, 39:D632-6 [連結至NCBI]
  2. The uniqueome: a mappability resource for short-tag sequencing.
    Koehler R, Issac H, Cloonan N, Grimmond SM
    Bioinformatics 2011 Jan 15, 27:272-4 [連結至NCBI]
  3. X-MATE: a flexible system for mapping short read data.
    Wood DL, Xu Q, Pearson JV, Cloonan N, Grimmond SM
    Bioinformatics 2011 Feb 15, 27:580-1 [連結至NCBI]
  4. A sustained dietary change increases epigenetic variation in isogenic mice.
    Li CC, Cropley JE, Cowley MJ, Preiss T, Martin DI, Suter CM
    PLoS Genet 2011 Apr, 7:e1001380 [連結至NCBI]
  5. Ten simple rules for providing a scientific Web resource.
    Schultheiss SJ
    PLoS Comput Biol 2011 May, 7:e1001126 [連結至NCBI]
  6. The Strategies WDK: a graphical search interface and web development kit for functional genomics databases.
    Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, Pennington C, Treatman C, Kissinger JC, Roos DS, Stoeckert CJ
    Database (Oxford) 2011, 2011:bar027 [連結至NCBI]
  7. The BioExtract Server: a web-based bioinformatic workflow platform.
    Lushbough CM, Jennewein DM, Brendel VP
    Nucleic Acids Res 2011 Jul, 39:W528-32 [連結至NCBI]
  8. PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.
    Muiño JM, Hoogstraat M, van Ham RC, van Dijk AD
    Nucleic Acids Res 2011 Jul, 39:W524-7 [連結至NCBI]
  9. Making whole genome multiple alignments usable for biologists.
    Blankenberg D, Taylor J, Nekrutenko A, The Galaxy Team
    Bioinformatics 2011 Sep 1, 27:2426-2428 [連結至NCBI]
  10. The real cost of sequencing: higher than you think!
    Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB
    Genome Biology 2011, 12:125 (25 August 2011) [連結至NCBI]
  11. Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011
    Rouchka EC, Flight RM, Homayouni R
    BMC Bioinformatics 2011, 12(Suppl 7):A1 (5 August 2011) [連結至BioMed Central]
  12. ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
    Friedman BA, Maniatis T
    Genome Biology 2011, 12:R69 (28 July 2011) [連結至NCBI]
  13. Applications of the pipeline environment for visual informatics and genomics computations
    Dinov ID, Torri F, Macciardi F, Petrosyan P, Liu Z, Zamanyan A, Eggert P, Pierce J, Genco A, Knowles JA, Clark AP, Van Horn JD, Ames J, Kesselman C, Toga AW
    BMC Bioinformatics 2011, 12:304 (26 July 2011) [連結至NCBI]
  14. An integrated ChIP-seq analysis platform with customizable workflows
    Giannopoulou EG, Elemento O
    BMC Bioinformatics 2011, 12:277 (7 July 2011) [連結至NCBI]
  15. Metagenomic biomarker discovery and explanation
    Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C
    Genome Biology 2011, 12:R60 (24 June 2011) [連結至NCBI]
  16. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study
    Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A
    Genome Biology 2011, 12:R59 (23 June 2011) [連結至NCBI]
  17. Microarrays, deep sequencing and the true measure of the transcriptome
    Malone JH, Oliver B
    BMC Biology 2011, 9:34 (31 May 2011) [連結至NCBI]
  18. A framework and workflow system for virtual screening and molecular docking
    Schumann M, Röttig M, Fischer NM, Kohlbacher O
    Journal of Cheminformatics 2011, 3(Suppl 1):P15 (19 April 2011) [連結至BioMed Central]
  19. BiologicalNetworks 2.0 - an integrative view of genome biology data
    Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M
    BMC Bioinformatics 2010, 11:610 (29 December 2010) [連結至NCBI]
  20. The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
    Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H
    BMC Bioinformatics 2010, 11(Suppl 12):S12 (21 December 2010) [連結至NCBI]
  21. Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)
    Tan TW, Tong JC, Khan AM, de Silva M, Lim KS, Ranganathan S
    BMC Genomics 2010, 11(Suppl 4):S27 (2 December 2010) [連結至NCBI]




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