Center for Integrated Fungal Research, Department of Plant Pathology and Bioinformatics Research Center, North Carolina State University, NC 27695, USA.
Bioinformatics. 2014 May 15;30(10):1488-90. doi: 10.1093/bioinformatics/btu055. Epub 2014 Jan 30.
Previously we developed the stand-alone SNAP Workbench toolkit that integrated a wide array of bioinformatics tools for phylogenetic and population genetic analyses. We have now developed a web-based portal front-end, using the Mobyle portal framework, which executes all of the programs available in the stand-alone SNAP Workbench toolkit on a high-performance Linux cluster. Additionally, we have expanded the selection of programs to over 189 tools, including population genetic, genome assembly and analysis tools, as well as metagenomic and large-scale phylogenetic analyses. The Mobyle SNAP Workbench web portal allows end users to (i) execute and manage otherwise complex command-line programs, (ii) launch multiple exploratory analyses of parameter-rich and computationally intensive methods and (iii) track the sequence of steps and parameters that were used to perform a specific analysis. Analysis pipelines or workflows for population genetic, metagenomic and genome assembly provide automation of data conversion, analysis and graphical visualization for biological inference.
The Mobyle SNAP Workbench portal is freely available online at http://snap.hpc.ncsu.edu/. The XMLs can be downloaded at http://carbonelab.org/system/files/snap_xmls.tgz. Each XML provides links to help files, online documentation and sample data.
Supplementary data are available at Bioinformatics online.
我们之前开发了独立的 SNAP Workbench 工具包，该工具包集成了用于系统发育和群体遗传学分析的各种生物信息学工具。现在，我们使用 Mobyle 门户框架开发了一个基于网络的门户前端，该门户前端在高性能 Linux 集群上执行独立的 SNAP Workbench 工具包中提供的所有程序。此外，我们还扩展了程序选择，增加了 189 多种工具，包括群体遗传学、基因组组装和分析工具，以及宏基因组和大规模系统发育分析工具。Mobyle SNAP Workbench 网络门户允许最终用户：(i) 执行和管理原本复杂的命令行程序；(ii) 启动对参数丰富和计算密集型方法的多次探索性分析；(iii) 跟踪执行特定分析时使用的步骤和参数序列。用于群体遗传学、宏基因组和基因组组装的分析流程或工作流程提供了数据转换、分析和图形可视化的自动化功能，以进行生物学推断。
Mobyle SNAP Workbench 门户可免费在线使用，网址为 http://snap.hpc.ncsu.edu/。XML 可在 http://carbonelab.org/system/files/snap_xmls.tgz 下载。每个 XML 都提供了指向帮助文件、在线文档和示例数据的链接。
补充数据可在 Bioinformatics 在线获取。
