The missing graphical user interface for genomics.
The missing graphical user interface for genomics.
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DOI：
10.1186/gb-2010-11-8-128
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发表时间：
2010
期刊：
影响因子：
12.3
通讯作者：
Schatz MC
中科院分区：
文献类型：
--
作者：
Schatz MC
Galaxy软件包使普通用户能够通过急需的用户友好的图形Web界面执行丰富的DNA序列分析。http://genomebiology.com/2010/11/8/R86随着经济实惠和高通量DNA测序的出现，测序正在成为几乎每个遗传学实验室的重要组成部分。生成这些数据是为了探测序列变异，了解转录、调节或甲基化的DNA元件，并探索生命树和一系列环境和条件下的许多其他生物学特征。鉴于如此大量的数据，新手和专家都面临着试图通过计算分析原始序列数据的艰巨挑战。有这么多可用的工具和这么多的分析，如何能期望一个保持最新的最先进的？如何才能学习使用每种工具并构建强大的端到端分析管道，同时确保正确设置输入格式，命令行选项，序列数据库和程序库？最后，一旦分析完成，如何确保结果是可重复的和透明的，以供其他人仔细检查和研究？在一篇发表在《基因组生物学》上的文章中，杰里米·戈恩、安东·内克鲁坚科、詹姆斯·泰勒和银河团队的其他成员（戈恩等人）通过他们的银河项目的最新更新，在解决这些关键问题方面取得了很大的进展。Galaxy的宏伟目标是使普通用户能够进行自己的计算分析，而不必成为计算生物学或计算机科学的专家。Galaxy为基因组学研究添加了一个迫切需要的图形用户界面，使数据分析在Web浏览器中普遍可用，并将用户从古老的命令行参数，数据格式和脚本语言的细节中解放出来。从动态图形菜单中选择数据输入和计算步骤，并以直观的图表和摘要显示结果，鼓励交互式工作流程和探索假设。底层的数据分析工具几乎可以是任何软件，用任何语言编写，但它们所有的复杂性都巧妙地隐藏在Galaxy中，使用户能够专注于科学而不是技术问题。
The Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface. See research article http://genomebiology.com/2010/11/8/R86 With the advent of affordable and high-throughput DNA sequencing, sequencing is becoming an essential component in nearly every genetics lab. These data are being generated to probe sequence variations, to understand transcribed, regulated or methylated DNA elements, and to explore a host of other biological features across the tree of life and across a range of environments and conditions. Given this deluge of data, novices and experts alike are facing the daunting challenge of trying to analyze the raw sequence data computationally. With so many tools available and so many assays to analyze, how can one be expected to stay current with the state of the art? How can one be expected to learn to use each tool and construct robust end-to-end analysis pipelines, all while ensuring that input formats, command-line options, sequence databases and program libraries are set correctly? Finally, once the analysis is complete, how does one ensure the results are reproducible and transparent for others to scrutinize and study? In an article published in Genome Biology, Jeremy Goecks, Anton Nekrutenko, James Taylor and the rest of the Galaxy Team (Goecks et al.) make a great advance towards resolving these critical questions with the latest update to their Galaxy Project. The ambitious goal of Galaxy is to empower regular users to carry out their own computational analysis without having to be an expert in computational biology or computer science. Galaxy adds a desperately needed graphical user interface to genomics research, making data analysis universally accessible in a web browser, and freeing users from the minutiae of archaic command-line parameters, data formats and scripting languages. Data inputs and computational steps are selected from dynamic graphical menus, and the results are displayed in intuitive plots and summaries that encourage interactive workflows and the exploration of hypotheses. The underlying data analysis tools can be almost any piece of software, written in any language, but all their complexity is neatly hidden inside of Galaxy, allowing users to focus on scientific rather than technical questions.
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影响因子：
12.3
作者：
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 JY;Zhang J
通讯作者：
Zhang J
人类胰岛中的开放染色质图。
影响因子：
30.8
作者：
Gaulton, Kyle J.;Nammo, Takao;Pasquali, Lorenzo;Simon, Jeremy M.;Giresi, Paul G.;Fogarty, Marie P.;Panhuis, Tami M.;Mieczkowski, Piotr;Secchi, Antonio;Bosco, Domenico;Berney, Thierry;Montanya, Eduard;Mohlke, Karen L.;Lieb, Jason D.;Ferrer, Jorge
通讯作者：
Ferrer, Jorge
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
56.9
作者：
Peleg, Shahaf;Sananbenesi, Farahnaz;Fischer, Andre
通讯作者：
Fischer, Andre
影响因子：
12.3
作者：
Goecks J;Nekrutenko A;Taylor J;Galaxy Team
通讯作者：
Galaxy Team