MAMMOTh: A new database for curated mathematical models of biomolecular systems

Kazantsev Fedor; Akberdin Ilya; Lashin Sergey; Ree Natalia; Timonov Vladimir; Ratushny Alexander; Khlebodarova Tamara; Likhoshvai Vitaly

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MAMMOTh: A new database for curated mathematical models of biomolecular systems

机译：庞大：用于生物分子系统的策划数学模型的新数据库

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Motivation: Living systems have a complex hierarchical organization that can be viewed as a set of dynamically interacting subsystems. Thus, to simulate the internal nature and dynamics of the entire biological system, we should use the iterative way for a model reconstruction, which is a consistent composition and combination of its elementary subsystems. In accordance with this bottom-up approach, we have developed the MAthematical Models of bioMOlecular sysTems (MAMMOTh) tool that consists of the database containing manually curated MAMMOTh fitted to the experimental data and a software tool that provides their further integration.

机译：动机：生存系统具有复杂的分层组织，可以被视为一组动态交互的子系统。因此，为了模拟整个生物系统的内部性质和动态，我们应该使用迭代方式进行模型重建，这是一种一致的组成和其基本子系统的组合。根据这种自下而上的方法，我们开发了由包含装配到实验数据的手动策划的数据库和提供其进一步集成的软件工具的数据库系统（Mammoth）工具的数学模型。

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来源
《Journal of Bioinformatics and Computational Biology》 |2018年第1期|共16页
作者
Kazantsev Fedor; Akberdin Ilya; Lashin Sergey; Ree Natalia; Timonov Vladimir; Ratushny Alexander; Khlebodarova Tamara; Likhoshvai Vitaly;
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作者单位

RAS SB Inst Cytol &

Genet Lavrentyev Ave 10 Novosibirsk 630090 Russia;

RAS SB Inst Cytol &

Genet Lavrentyev Ave 10 Novosibirsk 630090 Russia;

RAS SB Inst Cytol &

Genet Lavrentyev Ave 10 Novosibirsk 630090 Russia;

RAS SB Inst Cytol &

Genet Lavrentyev Ave 10 Novosibirsk 630090 Russia;

Novosibirsk State Univ Pirogova Str 2 Novosibirsk 630090 Russia;

Ctr Infect Dis Res Seattle WA 98109 USA;

RAS SB Inst Cytol &

Genet Lavrentyev Ave 10 Novosibirsk 630090 Russia;

RAS SB Inst Cytol &

Genet Lavrentyev Ave 10 Novosibirsk 630090 Russia;

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原文格式 PDF
正文语种 eng
中图分类细胞生物学;
关键词
Mathematical models; generalized Hill functions; respiration; de novo nucleotide synthesis; gene network; gene expression;

机译：数学模型;广义山功能;呼吸;De Novo核苷酸合成;基因网络;基因表达;

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专利

1. MAMMOTh: A new database for curated mathematical models of biomolecular systems [J] . Kazantsev Fedor, Akberdin Ilya, Lashin Sergey, Journal of Bioinformatics and Computational Biology . 2018,第1期

机译：庞大：用于生物分子系统的策划数学模型的新数据库
2. Bookshelf: a simple curation system for the storage of biomolecular simulation data [J] . Benjamin A. Hall, Daniel A. Holdbrook, Philip C. Biggin, Database . 2010,第1期

机译：书架：用于存储生物分子模拟数据的简单策展系统
3. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models [J] . Chen Li, Marco Donizelli, Nicolas Rodriguez, BMC Systems Biology . 2010,第1期

机译：生物模型数据库：发布的定量动力学模型的增强，精选和批注资源
4. The Emergence of biological coding theory as a mathematical framework for modeling, monitoring, and modulating biomolecular systems [C] . May E. Information Sciences and Systems, 2009. CISS 2009 . 2009

机译：生物编码理论作为一种用于建模，监测和调节生物分子系统的数学框架的出现
5. Mathematical and computational modeling of biomolecular systems. [D] . Baker, Nathan Andrew. 2001

机译：生物分子系统的数学和计算模型。
6. BioModels Database: a free centralized database of curated published quantitative kinetic models of biochemical and cellular systems [O] . Nicolas Le Novère, Benjamin Bornstein, Alexander Broicher, 2006

机译：BioModels数据库：免费的集中式数据库其中包含生化和细胞系统的精选已发布的定量动力学模型
7. MAMMOTh: a new database for curated MAthematical Models of bioMOlecular sysTems [O] . Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, 2016

机译：庞大：一个新数据库，用于生物分子系统的策划数学模型
8. Quantitative Developments of Biomolecular Databases, Measurement Methodology, and Comprehensive Transport Models for Bioanalytical Microfluidics [R] . Santiago, J. G. , Sundaram, S. , Krishnamoorthy, S. , 2006

机译：生物分析微流体生物分子数据库，测量方法和综合运输模型的定量开发

MAMMOTh: A new database for curated mathematical models of biomolecular systems

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