COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
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DOI：
10.1186/s12859-014-0369-z
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发表时间：
2014-12-14
影响因子：
3
通讯作者：
Le Novère N
中科院分区：
文献类型：
--
作者：
Bergmann FT;Adams R;Moodie S;Cooper J;Glont M;Golebiewski M;Hucka M;Laibe C;Miller AK;Nickerson DP;Olivier BG;Rodriguez N;Sauro HM;Scharm M;Soiland-Reyes S;Waltemath D;Yvon F;Le Novère N
随着计算模型在生物科学中的使用越来越多，共享模型并有效和轻松地复制已发表研究结果的需求变得越来越重要。为此，已经提出了各种标准，这些标准可以用于以一致的方式描述模型、模拟、数据或其他基本信息。这些构成了复制给定的已发表科学结果所需的各种独立组件。我们描述了开放建模交换格式（OMEX）。OMEX与生物学计算建模网络（联合收割机）的其他标准格式一起使用，是联合收割机Archive的基础，COMBINE Archive是一个支持交换生物学建模和模拟实验所需的所有信息的单一文件。OMEX文件是一个ZIP容器，它包括一个清单文件，列出归档文件的内容，一个可选的元数据文件，添加有关归档文件及其内容的信息，以及描述模型的文件。联合收割机档案的内容包括尽可能以联合收割机标准编码的文件，但可能包括由Internet媒体类型定义的其他文件。有几个支持联合收割机Archive的工具可以作为独立的库或嵌入到建模软件中。联合收割机Archive通过将所有相关信息嵌入到一个文件中，促进了生物学建模和模拟实验的再现。同时存储和交换所有信息也有助于构建活动日志和审计跟踪。我们预计，联合收割机Archive将成为建模者的重要帮助，因为该领域转向更大，更复杂的实验，如器官，数字生物和生物工程的多尺度模型。本文的在线版本（doi：10.1186/s12859-014-0369-z）包含补充材料，可供授权用户使用。
With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software. The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering. The online version of this article (doi:10.1186/s12859-014-0369-z) contains supplementary material, which is available to authorized users.
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影响因子：
46.9
作者：
Le Novère, N;Finney, A;Wanner, BL
通讯作者：
Wanner, BL
影响因子：
3.7
作者：
Mattioni M;Le Novère N
通讯作者：
Le Novère N
影响因子：
5.8
作者：
Olivier, BG;Rohwer, JM;Hofmeyr, JHS
通讯作者：
Hofmeyr, JHS
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
--
作者：
Li C;Donizelli M;Rodriguez N;Dharuri H;Endler L;Chelliah V;Li L;He E;Henry A;Stefan MI;Snoep JL;Hucka M;Le Novère N;Laibe C
通讯作者：
Laibe C