Suppr超能文献

phraSED-ML:SED-ML的一种经过释义的、人类可读的改编形式。

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.

作者信息

Choi Kiri, Smith Lucian P, Medley J Kyle, Sauro Herbert M

机构信息

1 University of Washington, Department of Bioengineering, Seattle, WA, USA.

出版信息

J Bioinform Comput Biol. 2016 Dec;14(6):1650035. doi: 10.1142/S0219720016500359. Epub 2016 Sep 30.

Abstract

MOTIVATION

Model simulation exchange has been standardized with the Simulation Experiment Description Markup Language (SED-ML), but specialized software is needed to generate simulations in this format. Text-based languages allow researchers to create and modify experimental protocols quickly and easily, and export them to a common machine-readable format.

RESULTS

phraSED-ML language allows modelers to use simple text commands to encode various elements of SED-ML (models, tasks, simulations, and results) in a format easy to read and modify. The library can translate this script to SED-ML for use in other softwares.

AVAILABILITY

phraSED-ML language specification, libphrasedml library, and source code are available under BSD license from http://phrasedml.sourceforge.net/ .

摘要

动机

模型模拟交换已通过模拟实验描述标记语言(SED-ML)实现标准化,但需要专门的软件来生成这种格式的模拟。基于文本的语言使研究人员能够快速轻松地创建和修改实验方案,并将其导出为通用的机器可读格式。

结果

phraSED-ML语言允许建模人员使用简单的文本命令以易于阅读和修改的格式对SED-ML的各种元素(模型、任务、模拟和结果)进行编码。该库可以将此脚本转换为SED-ML以供其他软件使用。

可用性

phraSED-ML语言规范、libphrasedml库和源代码可在BSD许可下从http://phrasedml.sourceforge.net/获取。

相似文献

1
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.
J Bioinform Comput Biol. 2016 Dec;14(6):1650035. doi: 10.1142/S0219720016500359. Epub 2016 Sep 30.
2
SED-ED, a workflow editor for computational biology experiments written in SED-ML.
Bioinformatics. 2012 Apr 15;28(8):1180-1. doi: 10.1093/bioinformatics/bts101. Epub 2012 Feb 25.
3
Antimony: a modular model definition language.
Bioinformatics. 2009 Sep 15;25(18):2452-4. doi: 10.1093/bioinformatics/btp401. Epub 2009 Jul 3.
4
SED-ML web tools: generate, modify and export standard-compliant simulation studies.
Bioinformatics. 2017 Apr 15;33(8):1253-1254. doi: 10.1093/bioinformatics/btw812.
5
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.
J Integr Bioinform. 2021 Oct 5;18(3):20210021. doi: 10.1515/jib-2021-0021.
6
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).
J Integr Bioinform. 2018 Mar 19;15(1):20170086. doi: 10.1515/jib-2017-0086.
7
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.
J Integr Bioinform. 2024 Apr 15;21(1). doi: 10.1515/jib-2024-0008. eCollection 2024 Mar 1.
9
Stochastic simulation GUI for biochemical networks.
Bioinformatics. 2007 Jul 15;23(14):1859-61. doi: 10.1093/bioinformatics/btm231. Epub 2007 Jun 22.
10
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.
J Integr Bioinform. 2015 Sep 4;12(2):262. doi: 10.2390/biecoll-jib-2015-262.

引用本文的文献

1
Using SED-ML for reproducible curation: Verifying BioModels across multiple simulation engines.
bioRxiv. 2025 Jan 20:2025.01.16.633337. doi: 10.1101/2025.01.16.633337.
2
Curating models from BioModels: Developing a workflow for creating OMEX files.
PLoS One. 2024 Dec 5;19(12):e0314875. doi: 10.1371/journal.pone.0314875. eCollection 2024.
3
Curating models from BioModels: Developing a workflow for creating OMEX files.
bioRxiv. 2024 Nov 6:2024.03.15.585236. doi: 10.1101/2024.03.15.585236.
4
Adapting modeling and simulation credibility standards to computational systems biology.
J Transl Med. 2023 Jul 26;21(1):501. doi: 10.1186/s12967-023-04290-5.
5
A Practical Guide to Reproducible Modeling for Biochemical Networks.
Methods Mol Biol. 2023;2634:107-138. doi: 10.1007/978-1-0716-3008-2_5.
6
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.
Funct Integr Genomics. 2022 Feb;22(1):3-26. doi: 10.1007/s10142-021-00810-y. Epub 2021 Oct 18.
7
PEtab-Interoperable specification of parameter estimation problems in systems biology.
PLoS Comput Biol. 2021 Jan 26;17(1):e1008646. doi: 10.1371/journal.pcbi.1008646. eCollection 2021 Jan.
8
Best Practices for Making Reproducible Biochemical Models.
Cell Syst. 2020 Aug 26;11(2):109-120. doi: 10.1016/j.cels.2020.06.012.
9
Publishing reproducible dynamic kinetic models.
Brief Bioinform. 2021 May 20;22(3). doi: 10.1093/bib/bbaa152.
10
Recent advances in biomedical simulations: a manifesto for model engineering.
F1000Res. 2019 Mar 5;8. doi: 10.12688/f1000research.15997.1. eCollection 2019.

本文引用的文献

1
libRoadRunner: a high performance SBML simulation and analysis library.
Bioinformatics. 2015 Oct 15;31(20):3315-21. doi: 10.1093/bioinformatics/btv363. Epub 2015 Jun 17.
2
The systems biology simulation core algorithm.
BMC Syst Biol. 2013 Jul 5;7:55. doi: 10.1186/1752-0509-7-55.
3
SED-ED, a workflow editor for computational biology experiments written in SED-ML.
Bioinformatics. 2012 Apr 15;28(8):1180-1. doi: 10.1093/bioinformatics/bts101. Epub 2012 Feb 25.
5
Controlled vocabularies and semantics in systems biology.
Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77.
6
Antimony: a modular model definition language.
Bioinformatics. 2009 Sep 15;25(18):2452-4. doi: 10.1093/bioinformatics/btp401. Epub 2009 Jul 3.
7
LibSBML: an API library for SBML.
Bioinformatics. 2008 Mar 15;24(6):880-1. doi: 10.1093/bioinformatics/btn051. Epub 2008 Feb 5.
8
COPASI--a COmplex PAthway SImulator.
Bioinformatics. 2006 Dec 15;22(24):3067-74. doi: 10.1093/bioinformatics/btl485. Epub 2006 Oct 10.
9
CellML: its future, present and past.
Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):433-50. doi: 10.1016/j.pbiomolbio.2004.01.004.
10

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验