BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
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DOI：
10.1186/1752-0509-4-92
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发表时间：
2010-06-29
影响因子：
--
通讯作者：
Laibe C
中科院分区：
文献类型：
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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
生化和细胞系统的定量模型被用于回答生物科学中的各种问题。由于人们对模型使用的兴趣日益增加，以及改进的软件系统的开发和更好、更便宜的计算机硬件的普及，已发表的定量模型数量在稳步增长。为了最大限度地发挥这一不断增长的模型库的优势，该领域需要集中式的模型库，以鼓励、促进和推动模型的传播和再利用。理想情况下，存储在这些库中的模型应该经过广泛测试，并以社区支持的标准化格式进行编码。此外，模型及其组件应该与其他资源相互参照，以便能够明确识别。
BioModels数据库（http://www.ebi.ac.uk/biomodels/）正是为了满足这些需求而设立的。它是一个可免费访问的在线资源，用于存储、查看、检索和分析已发表的、经过同行评审的生化和细胞系统定量模型。BioModels数据库所发布的每个模拟模型的结构和行为都经过彻底检查；此外，模型元素使用受控词汇表中的术语进行注释，并与相关数据资源相链接。模型可以在线查看，也可以以多种格式下载。由模型生成的反应网络图也有多种格式可供使用。BioModels数据库还提供诸如在线模拟以及从大规模模型中提取组件以形成较小子模型等功能。最后，该系统提供了一系列网络服务，外部软件系统可以利用这些服务从数据库中获取最新数据。
BioModels数据库已成为系统生物学公认的参考资源。它被该领域以多种方式使用；例如，它被用于对不同的模拟系统进行基准测试，以及根据模型的注释研究模型的聚类。如今，一些科学期刊的出版商建议将模型提交到该数据库。BioModels数据库中的模型可免费分发和再利用；其底层软件基础设施也可根据GNU通用公共许可证从SourceForge（https://sourceforge.net/projects/biomodels/）获取。
Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License.
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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
Miriam Resources：生成和解决系统生物学中强大的交叉引用的工具。
影响因子：
--
作者：
Laibe, Camille;Le Novere, Nicolas
通讯作者：
Le Novere, Nicolas
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
5.8
作者：
Bornstein, Benjamin J.;Keating, Sarah M.;Hucka, Michael
通讯作者：
Hucka, Michael
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J