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Galaxy, a web-based framework for the integration of genome analysis.

机译：Galaxy，一个基于网络的基因组分析集成框架。

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摘要

The standardization and sharing of data and tools are among the biggest challenges facing large collaborative projects and small individual labs alike. Here a compact web application, Galaxy, is described which effectively addresses these issues. It provides an intuitive interface for the deposition and access of data and features a vast number of analysis tools including operations on genomic intervals, utilities for manipulation of multiple sequence alignments and molecular evolution algorithms. By providing a direct link between data and analysis tools, Galaxy allows addressing biological questions that are beyond the reach of existing software. Available both as (1) a publicly available web service providing tools for the analysis of genomic, comparative genomic and functional genomic data and (2) a downloadable package that can be deployed in individual labs, Galaxy attempts to serve both sides of the user distribution: experimental biologists and bioinformaticians.;For experimental biologists, it provides an intuitive interface for data deposition and access, features a large number of tools and makes analysis transparent by documenting every step in the Galaxy history system. Most importantly, it streamlines the path from data to analysis, as even complex tools can be applied to genomic data directly without manual parsing or preprocessing.;For bioinformaticians, Galaxy is a software system that provides informatics support through a platform that gives biologists simple interfaces to powerful tools, while automatically managing the computational details. Galaxy provides a framework that can integrate command-line tools with almost no effort. For each tool, Galaxy generates the interface and provides all computational housekeeping.;A prime example of a remarkable disconnect between genomic data and analysis tools is in the case of multiple-species whole genome alignments. Continuingly expanding collections of freely downloadable multiple-species whole genome alignments have been made available to the scientific community, however, several issues exist which prevent experimental biologists from utilizing these important datasets. Simply put, these alignments are not only large enough to cause significant logistical problems just to download and store, but there are no tools available that allow command-line averse biologists to manipulate these alignments. Furthermore, current genome analysis packages, such as the phylogenetic software HyPhy, do not accept the Multiple Alignment Format (MAF) as input. A set of tools designed to address these challenges has been integrated into the Galaxy framework and is included as part of the standard software distribution. Short examples of tool usage as well as an in-depth sample analysis are presented along with descriptions of the individual tools. The step-by-step sample analysis and toolset integration provide real-life examples of the utility of Galaxy both as (1) an effective and intuitive analysis platform for experimental biologists and (2) a tool and data source integration framework for bioinformaticians.
机译：数据和工具的标准化和共享是大型协作项目和小型个体实验室面临的最大挑战之一。这里描述了一个紧凑的Web应用程序Galaxy，它可以有效解决这些问题。它为存储和访问数据提供了一个直观的界面，并具有大量的分析工具，包括对基因组间隔的操作，用于操纵多个序列比对的实用程序以及分子进化算法。通过提供数据和分析工具之间的直接链接，Galaxy可以解决现有软件无法解决的生物学问题。可作为（1）提供用于分析基因组，比较基因组和功能基因组数据的工具的公共可用Web服务以及（2）可在各个实验室中部署的可下载软件包来提供，Galaxy尝试为用户分发的双方提供服务：实验生物学家和生物信息学家。；对于实验生物学家，它为数据的存储和访问提供了一个直观的界面，具有大量工具，并通过记录Galaxy历史系统中的每个步骤来使分析变得透明。最重要的是，它简化了从数据到分析的路径，因为即使复杂的工具也可以直接应用于基因组数据而无需人工解析或预处理。对于生物信息学家来说，Galaxy是一个软件系统，它通过一个平台为生物学家提供了信息支持，该平台为生物学家提供了简单的界面强大的工具，同时自动管理计算细节。 Galaxy提供了一个可以毫不费力地集成命令行工具的框架。对于每种工具，Galaxy都会生成界面并提供所有计算内务处理。；在多物种全基因组比对的情况下，基因组数据与分析工具之间明显脱节的一个典型例子。可供免费下载的多物种全基因组比对的集合不断扩大，已为科学界所用，但是，存在一些问题阻止了实验生物学家利用这些重要的数据集。简而言之，这些对齐方式不仅大到足以引起严重的后勤问题，而不仅仅是下载和存储，而且没有可用的工具允许命令行反生物学家操纵这些对齐方式。此外，当前的基因组分析软件包（例如系统发育软件HyPhy）不接受多重比对格式（MAF）作为输入。旨在解决这些挑战的一组工具已集成到Galaxy框架中，并作为标准软件分发的一部分包含在内。给出了工具用法的简短示例以及深入的样本分析以及各个工具的说明。循序渐进的样本分析和工具集集成提供了Galaxy实用程序的真实示例，它们既是（1）实验生物学家有效且直观的分析平台，又是（2）生物信息学家使用的工具和数据源集成框架。

著录项

  • 作者

    Blankenberg, Daniel James.;

  • 作者单位

    The Pennsylvania State University.;

  • 授予单位 The Pennsylvania State University.;
  • 学科 Biology Genetics.;Biology Evolution and Development.;Biology Bioinformatics.
  • 学位 Ph.D.
  • 年度 2009
  • 页码 130 p.
  • 总页数 130
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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