MR-Tandem：在亚马逊网络服务（Amazon Web Services）上使用 Hadoop MapReduce 的并行 X!Tandem。
MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.
机构信息
Insilicos LLC, Seattle WA, USA.
出版信息
Bioinformatics. 2012 Jan 1;28(1):136-7. doi: 10.1093/bioinformatics/btr615. Epub 2011 Nov 8.
SUMMARY
MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows.
AVAILABILITY AND IMPLEMENTATION
MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL.
CONTACT
摘要
MR-Tandem 对流行的 X!Tandem 肽搜索引擎进行了改编，使其能够与 Hadoop MapReduce 配合使用，以可靠地并行执行大型搜索。MR-Tandem 可以在任何 Hadoop 集群上运行，但为创建廉价按需 Hadoop 集群提供了对 Amazon Web Services 的特殊支持，从而能够进行可能无法使用手头研究人员计算资源完成的搜索量。MR-Tandem 旨在随时替代 X!Tandem 的使用，并且不需要对现有的 X!Tandem 参数文件进行任何修改，并且只需对基于 X!Tandem 的工作流程进行最小的修改。
可用性和实现
MR-Tandem 作为一个经过轻微修改的 X!Tandem C++可执行文件和一个 Python 脚本实现，该脚本驱动包括 Amazon Web Services (AWS) Elastic Map Reduce (EMR)在内的 Hadoop 集群，使用修改后的 X!Tandem 程序作为 Hadoop Streaming 的映射器和归约器。修改后的 X!Tandem C++源代码采用艺术许可证，支持可插拔评分，并作为 Sashimi 项目的一部分，可在 http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/ 上获得。MR-Tandem Python 脚本采用 Apache 许可证，可作为 Insilicos Cloud Army 项目的一部分在 http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/ 上获得。完整的文档和配置 MR-Tandem、Python 和所有必要包的 Windows 安装程序都可在同一 URL 上获得。
Zotero 插件