The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows.
The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows.
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DOI：
10.3389/fninf.2012.00007
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发表时间：
2012
影响因子：
3.5
通讯作者：
Evans AC
中科院分区：
文献类型：
--
作者：
Bellec P;Lavoie-Courchesne S;Dickinson P;Lerch JP;Zijdenbos AP;Evans AC
神经影像数据库的分析通常涉及大量相互关联的步骤，称为管道。Octave和MatLab的管道系统(PSOM)是以Octave或MatLab脚本的形式实现管道的灵活框架。PSOM没有引入新的语言结构来指定工作流的步骤和结构。相反，所有分析步骤都由常规的MatLab数据结构描述，记录了它们的相关命令和选项，以及它们的输入、输出和清理文件。PSOM执行引擎提供了许多自动化服务：(1)只要作业之间的依赖关系允许并且有足够的资源可用，它就在本地计算设施上并行执行作业；(2)它生成流水线阶段和执行历史的全面记录，该记录足够详细，足以完整地再现分析；(3)如果分析被多次启动，它只执行流水线中需要重新处理的部分。PSOM是在MIT开源许可下分发的，可以不受限制地用于学术或商业项目。除了MatLab或Octave外，该软件包没有外部依赖，安装简单，支持多种操作系统(Linux、Windows、Mac)。我们在一个包括200名受试者的公共数据库上进行了几个基准实验，使用了一条用于功能磁共振图像(FMRI)预处理的管道。基准测试结果表明，对于使用本地或分布式计算资源的大型数据库的分析，PSOM是一个强大的解决方案。
The analysis of neuroimaging databases typically involves a large number of inter-connected steps called a pipeline. The pipeline system for Octave and Matlab (PSOM) is a flexible framework for the implementation of pipelines in the form of Octave or Matlab scripts. PSOM does not introduce new language constructs to specify the steps and structure of the workflow. All steps of analysis are instead described by a regular Matlab data structure, documenting their associated command and options, as well as their input, output, and cleaned-up files. The PSOM execution engine provides a number of automated services: (1) it executes jobs in parallel on a local computing facility as long as the dependencies between jobs allow for it and sufficient resources are available; (2) it generates a comprehensive record of the pipeline stages and the history of execution, which is detailed enough to fully reproduce the analysis; (3) if an analysis is started multiple times, it executes only the parts of the pipeline that need to be reprocessed. PSOM is distributed under an open-source MIT license and can be used without restriction for academic or commercial projects. The package has no external dependencies besides Matlab or Octave, is straightforward to install and supports of variety of operating systems (Linux, Windows, Mac). We ran several benchmark experiments on a public database including 200 subjects, using a pipeline for the preprocessing of functional magnetic resonance images (fMRI). The benchmark results showed that PSOM is a powerful solution for the analysis of large databases using local or distributed computing resources.
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影响因子：
1.3
作者：
COLLINS, DL;NEELIN, P;EVANS, AC
通讯作者：
EVANS, AC
影响因子：
3.4
作者：
Carbonell, Felix;Bellec, Pierre;Shmuel, Amir
通讯作者：
Shmuel, Amir
影响因子：
3.5
作者：
Gorgolewski K;Burns CD;Madison C;Clark D;Halchenko YO;Waskom ML;Ghosh SS
通讯作者：
Ghosh SS
影响因子：
5.7
作者：
Fonov V;Evans AC;Botteron K;Almli CR;McKinstry RC;Collins DL;Brain Development Cooperative Group
通讯作者：
Brain Development Cooperative Group
DOI：
10.1073/pnas.0908073106
发表时间：
2009-12-01
影响因子：
11.1
作者：
Liu, Hesheng;Stufflebeam, Steven M.;Buckner, Randy L.
通讯作者：
Buckner, Randy L.