论文标题
路径工具软件与Reactome软件的比较
A Comparison of the Pathway Tools Software with the Reactome Software
论文作者
论文摘要
本文档将SRI的途径工具（PTools）软件与Reactome软件进行了比较。这两个软件系统都服务于途径生物信息学领域，包括代谢途径和信号通路的表示和分析。该比较涵盖了途径生物信息学能力，但不涵盖Reactome软件完全不存在的其他主要途径工具：途径工具基因组信息学功能，法规信息学功能和基于表格的分析工具（SmartTables）。 我们的总体发现如下。 （1）ptools在其基本信息页面中明显领先于Reactome。例如，几十年来，Ptools路径布局布局算法已开发到高级状态，而Reactome途径的布局是难以辨认的，省略了重要的信息，并且是手动创建的，因此无法扩展到成千上万的基因组。 （2）Ptools在OMICS分析中远远领先于Reactome。 Ptools包括所有反应组提供的OMICS-分析方法，并包括多种反应组缺乏的方法。 （3）Ptools包含一个代谢路线搜索工具（通过代谢网络搜索路径），该工具缺乏。 （4）在基因组信息的代谢途径推断以创建新的代谢数据库的代谢途径推断方面，ptools明显领先于反应组。 （5）Ptools具有广泛的代谢模型工具的补充，而Reactome则没有。 （6）Ptools比Reactome更可扩展，处理18,000个基因组与90个基因组的反应组。 （7）Ptools的用户群比Reactome更大。 Ptools为17个网站提供权力，而两个网站则为Reactome。 Ptools已获得10,800名用户许可（Reactome许可用户数量未知）。
This document compares SRI's Pathway Tools (PTools) software with the Reactome software. Both software systems serve the pathway bioinformatics area, including representation and analysis of metabolic pathways and signaling pathways. The comparison covers pathway bioinformatics capabilities, but does not cover other major facets of Pathway Tools that are completely absent from the Reactome software: Pathway Tools genome-informatics capabilities, regulatory informatics capabilities, and table-based analysis tools (SmartTables). Our overall findings are as follows. (1) PTools is significantly ahead of Reactome in its basic information pages. For example, PTools pathway layout algorithms have been developed to an advanced state over several decades, whereas Reactome pathway layouts are illegible, omit important information, and are created manually and therefore cannot scale to thousands of genomes. (2) PTools is far ahead of Reactome in omics analysis. PTools includes all of the omics-analysis methods that Reactome provides, and includes multiple methods that Reactome lacks. (3) PTools contains a metabolic route search tool (searching for paths through the metabolic network), which Reactome lacks. (4) PTools is significantly ahead of Reactome in inference of metabolic pathways from genome information to create new metabolic databases. (5) PTools has an extensive complement of metabolic-modeling tools whereas Reactome has none. (6) PTools is more scalable than Reactome, handling 18,000 genomes versus 90 genomes for Reactome. (7) PTools has a larger user base than Reactome. PTools powers 17 websites versus two for Reactome. PTools has been licensed by 10,800 users (Reactome licensed user count is unknown).
