Biopipe: A flexible framework for protocol-based bioinformatics analysis
Biopipe: A flexible framework for protocol-based bioinformatics analysis
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DOI：
10.1101/gr.1363103
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发表时间：
2003-08-01
期刊：
影响因子：
7
通讯作者：
Stupka, E
中科院分区：
文献类型：
--
作者：
Hoon, S;Ratnapu, KK;Stupka, E
我们确定了当今生物信息学分析面临的几个挑战。首先，为了实现比较研究的承诺，生物信息学分析将需要容纳驻留在数据库联盟中的不同数据源，这些数据库反过来又具有不同的格式和可访问性模式。其次，需要处理的海量数据将需要强有力的系统，使生物信息学分析能够以并行方式进行。第三，生物信息学不断发展的状态提出了新的算法和范式进行分析。这意味着任何生物信息学框架都必须足够灵活和通用，以适应这种变化。此外，我们确定需要引入一个明确的协议为基础的方法，生物信息学分析，将借给严谨的分析。这使得外部各方更容易进行实验和复制结果。Biopipe就是为了实现这些目标而设计的。它旨在让研究人员专注于协议设计。同时，它被设计为在计算场上工作，从而提供高吞吐量性能。一个通用的交换格式，封装整个协议的分析模块，参数和数据版本已被开发，以提供一个强大的方式来分发和复制结果。这将使研究人员能够更好地讨论和解释数据，因为曾经隐含的假设现在在Biopipe框架中明确定义。
We identify several challenges facing bioinformatics analysis today. Firstly, to fulfill the promise of comparative studies, bioinformatics analysis will need to accommodate different sources of data residing in a federation of databases that, in turn, come in different formats and modes of accessibility. Secondly, the tsunami of data to be handled will require robust systems that enable bioinformatics analysis to be carried out in a parallel fashion. Thirdly, the ever-evolving state of bioinformatics presents new algorithms and paradigms in conducting analysis. This means that any bioinformatics framework must be flexible and generic enough to accommodate such changes. In addition, we identify the need for introducing an explicit protocol-based approach to bioinformatics analysis that will lend rigorousness to the analysis. This makes it easier for experimentation and replication of results by external parties. Biopipe is designed in an effort to meet these goals. It aims to allow researchers to focus on protocol design. At the same time, it is designed to work over a compute farm and thus provides high-throughput performance. A common exchange format that encapsulates the entire protocol in terms of the analysis modules, parameters, and data versions has been developed to provide a powerful way in which to distribute and reproduce results. This will enable researchers to discuss and interpret the data better as the once implicit assumptions are now explicitly defined within the Biopipe framework.