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首页> 外文期刊>Source Code for Biology Medicine >BioFlow: a web based workflow management software for design and execution of genomics pipelines
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BioFlow: a web based workflow management software for design and execution of genomics pipelines

机译：BioFlow：基于Web的工作流管理软件，用于设计和执行基因组学管道

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Background Bioinformatics data analysis is usually done sequentially by chaining together multiple tools. These are created by writing scripts and tracking the inputs and outputs of all stages. Writing such scripts require programming skills. Executing multiple pipelines in parallel and keeping track of all the generated files is difficult and error prone. Checking results and task completion requires users to remotely login to their servers and run commands to identify process status. Users would benefit from a web-based tool that allows creation and execution of pipelines remotely. The tool should also keep track of all the files generated and maintain a history of user activities. Results A software tool for building and executing workflows is described here. The individual tools in the workflows can be any command line executable or script. The software has an intuitive mechanism for adding new tools to be used in workflows. It contains a workflow designer where workflows can be creating by visually connecting various components. Workflows are executed by job runners. The outputs and the job history are saved. The tool is web based software tool and all actions can be performed remotely. Conclusions Users without scripting knowledge can utilize the tool to build pipelines for executing tasks. Pipelines can be modeled as workflows that are reusable. BioFlow enables users to easily add new tools to the database. The workflows can be created and executed remotely. A number of parallel jobs can be easily controlled. Distributed execution is possible by running multiple instances of the application. Any number of tasks can be executed and the output will be stored making it is easy to correlate the outputs to the jobs executed.
机译：背景生物信息学数据分析通常是通过将多个工具链接在一起来顺序进行的。这些是通过编写脚本并跟踪所有阶段的输入和输出来创建的。编写此类脚本需要编程技能。并行执行多个管道并跟踪所有生成的文件既困难又容易出错。检查结果和完成任务需要用户远程登录其服务器并运行命令以标识进程状态。用户将从基于Web的工具中受益，该工具允许远程创建和执行管道。该工具还应该跟踪所有生成的文件，并保持用户活动的历史记录。结果这里描述了用于构建和执行工作流程的软件工具。工作流中的各个工具可以是任何命令行可执行文件或脚本。该软件具有直观的机制，可以添加要在工作流程中使用的新工具。它包含一个工作流设计器，可以在其中通过可视化连接各个组件来创建工作流。工作流由工作执行者执行。输出和作业历史已保存。该工具是基于Web的软件工具，所有操作都可以远程执行。结论不具备脚本知识的用户可以使用该工具来构建执行任务的管道。可以将管道建模为可重用的工作流程。 BioFlow使用户可以轻松地将新工具添加到数据库。可以远程创建和执行工作流程。可以轻松控制许多并行作业。通过运行应用程序的多个实例，可以执行分布式执行。可以执行任意数量的任务，并且可以存储输出，从而可以轻松地将输出与执行的作业相关联。

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