Continued Support and Development of SBML

描述（由申请人提供）：系统生物学标记语言（SBML）是用于生物系统中的生化网络的计算模型的流行存储和交换格式。本申请的补助金是对SBML语言和一些相关软件工具的基础研究和开发的补充（1 R 01 GM 070923 -01）。为了响应用户社区的频繁请求，我们建议开发一个新的相关资源：带注释的模型数据库。该数据库（我们称之为“biomodels.net“，以我们保留供其使用的网站名称命名）将是一个免费提供的资源，具有浏览、搜索、可视化和导出功能，可通过网络浏览器界面和远程API（应用程序编程界面）访问。它将专门面向生物系统中生化网络的计算模型。该系统将提供以SBML以外的多种格式导出模型的能力，最大限度地提高其对使用各种软件工具的建模者的效用。 这里提出的工作有三个主要方面：（a）开发数据库/网络系统的软件基础设施，（B）开发SBML扩展，以支持在数据库环境中对模型及其组成部分进行更好的分类，以及（c）对提交给数据库的模型进行人工检查和注释（策展）。为了实现这些目标，我们将扩大我们目前工作地点的团队规模，并在英国的欧洲生物信息学研究所（EBI）增加合作者。 计算建模在生物学中变得越来越重要，它可以帮助我们科普自然生物的巨大规模和复杂性。实验科学家使用定量模型有望为更严格的生物功能分析铺平道路，从而加深对疾病的理解，并最终找到新的更好的疾病治疗方法。但要做到这一点，计算模型本身必须覆盖更广泛的受众。我们相信，biomodels.net将成为一个重要的社区资源，促进模型、思想和研究成果的交流，加速生物学中计算建模的发展。

DESCRIPTION (provided by applicant): The Systems Biology Markup Language (SBML) is a popular storage and exchange format for computational models of biochemical networks in biological systems. The grant to which this application is a supplement (1 R01 GM070923-01) funds basic research and development on the SBML language and some associated software tools. In response to frequent requests from the user community, we propose to develop a new, related resource: an annotated model database. The database (which we call "biomodels.net", after the website name we have reserved for its use) will be a freely available resource and will feature browsing, searching, visualization and exporting capabilities, accessible from both a web browser interface and remote API (application programming interface). It will be oriented specifically to computational models of biochemical networks in biological systems. The system will provide the ability to export models in a number of formats besides SBML, maximizing its utility to modelers using a variety of software tools. There are three main aspects to the work proposed here: (a) developing the software infrastructure of the database/web system, (b) developing SBML extensions for supporting better categorization of models and their components in a database context, and (c) performing manual examination and annotation (curation) of models submitted to the database. In order to achieve these aims, we will expand the size of our team at our current work sites and also add collaborators at the European Bioinformatics Institute (EBI) in the UK. Computational modeling is becoming increasingly important in biology for helping us cope with the vast size and complexity of natural organisms. The use of quantitative models by experimental scientists promises to pave the way for more rigorous analyses of biological functions, leading to deeper understanding and ultimately to new and better treatments for diseases. But for this to happen, the computational models themselves must reach a wider audience. We believe biomodels.net will act as a crucial community resource enabling greater exchange of models, ideas and research results, accelerating the uptake of computational modeling in biology.