Molecular Dynamics Data Bank. The European Repository for Biosimulation Data

经过几十年的发展和诺贝尔奖，分子动力学（MD）已经成熟。它不再是一种由一小群理论家使用的外来技术，而是一种被非常大的用户社区广泛使用的方法。数以百万计的超级计算机小时致力于收集轨迹，从而产生了社区无法处理的大量模拟数据。数据共享的不良传统和缺乏适当的基础设施导致在有限的分析之后数据丢失，这些分析很可能只揭示了所包含信息的一小部分。建立轨迹存储库的稀疏倡议遇到了以下困难：i)社区对存储数据的可靠性缺乏信任；Ii)缺乏可互操作的标准和模拟本体；Iii)所需数据库技术的不确定性；V)使用者难以以公开方式与资料互动；(6) md场与邻近社区的脱节。MDDB项目打算设计一个欧洲规模的MD模拟存储库（以及相关的分析工具），这将：i)优化计算资源；Ii)支持对许多不同视角和领域的轨迹进行分析（和荟萃分析）；Iii)保证小组之间快速有效的信息交换；iv)促进MD仿真领域与邻近社区的整合。总体结果将是更有效地利用生物化学，并将生物化学领域整合到主流生物学和化学研究中。

After decades of development and a Nobel prize, Molecular Dynamics(MD) hasreached maturity. It is no longer an exotic technique used by a small group of theoreticians but rather a method extensively used by a very large community of users. Millions of supercomputer hours are devoted to collecting trajectories, thus producing a deluge of simulation data that the community is unable to handle. A poor tradition of data sharing and the lack of appropriate infrastructures to do so lead to the loss of data after limited analysis that most likely revealed only a small fraction of the information contained. Sparse initiativesto build trajectory repositories have encountered difficulties related to: i) the lack of trust of the community in the reliability of the data deposited; ii) the lack of interoperable standards and simulation ontologies; iii) uncertainties regarding the database technology required; v) difficulties of the users to interact in an open manner with the data; and vi) disconnection of the MD-field with neighboring communities. The MDDB projects intends to design a European-scale repository of MD simulation (and associated analysis tools), which will: i) optimize computational resources; ii) favor the analysis (and meta-analysis) of trajectories for many different perspectives and fields; iii) guarantee a fast and efficient interchange of information between groups; and iv) facilitate the integration of the MD simulation field into neighboring communities. The overall result will be a more efficient use of MD and the integration of the MD field into mainstream biology and chemistry research.