SysMO-DB2

系统生物学是以生物学为基础的交叉学科研究领域，它将实验研究和计算建模相结合，以发现生物系统中复杂相互作用的涌现特性。SYSMO是一个欧洲跨国资助和研究项目，其主题是“微生物系统生物学”。该倡议的目标是以全面的方式记录和描述微生物中发生的动态分子过程，并以计算机数学模型的形式呈现这些过程。每个项目由一个欧洲机构联盟组成，每个项目都致力于各种微生物的不同研究成果，包括细菌、古生菌(单细胞微生物)和酵母。每种生物的环境条件各不相同，生长在培养物、土壤、水和动物宿主中。这种多样性意味着有许多不同类型的模型和收集的许多不同类型的数据。SYSMO倡议分为两个阶段：SysMO1资助了11个项目和91个机构；SysMO2将资助7个项目，其中5个是第2阶段的延续项目(因此有6个项目已经结束)，其中2个是新项目。研究成果(模型、数据、程序)以及科学家开发的技术诀窍和最佳做法将得到管理和汇集，以便：在项目运行期间使方案成员受益；向更广泛的科学界传播和发表成果；并在项目完成后保护成果，使SYSMO产生的数据的‘保质期’和效用最大化。Sysmo-DB是一个项目，旨在构建和管理一个逐步开发的基于Web的软件平台来实现这一点。在第一阶段得到资助的Sysmo-DB1开始开发一个名为Seek的网络平台，用于编目项目的不同成果，存档数据、程序和模型，并与不同项目的本地数据管理系统相结合，包括用于描述数据和模型的信息的标准化以及项目电子表格的处理。Seek还包括一个供Sysmo成员使用的社交网络，并与数据、模型、分析和出版物的公共存储库相结合，如JWS Online(用于模型)、Sabio-RK(用于数据)、MyExperient(用于生物信息学数据分析管道)和PubMed(用于出版物)。Sysmo-DB还制定了与Sysmo科学家合作的有效做法，建立了一个PALS研究人员重点小组，他们制定了汇集所需的发展、数据标准和协议，并促进在他们自己的项目中寻求采用。Sysmo-DB1的重点是支持当前的项目。Sysmo-DB2继续并扩展工作，以应对Sysmo阶段的变化以及在Sysmo之后和之后的生活：新的和终止的项目、人员变动、联盟外的发布以及结果的长期保存。Sysmo-DB2还计划将软件和方法打包，以便它们可以被EraSysBio+等其他程序采用和支持。EraSysBio+是一个泛欧洲计划，涉及16个系统生物学项目。它在组织上与Sysmo相似，但在范围上截然不同。因此，它在所需的数据、模型和处理能力方面有所不同。作为扩大采用Sysmo-DB方法的一部分，该项目将在头18个月支持EraSysBio+。EraSysBio+的两个侧重于微生物的项目将完全纳入Sysmo-DB工作方案。对于所有EraSysBio+项目，Sysmo-DB2将实例化Seek的新实例，提供建议并帮助启动PALS方案。

Systems biology is a biology-based inter-disciplinary study field combining experimental investigations and computational modeling to discover emergent properties of complex interactions in biological systems. SysMO is a European trans-national funding and research initiative on 'Systems Biology of Microorganisms'. The initiative's goal is to record and describe the dynamic molecular processes that occur in microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models. Each project is made up of a consortium of European institutions and each works towards different research outcomes on a variety of microorganisms, including bacteria, archaea (single-celled microorganisms) and yeast. The environmental conditions for each organism vary, growing in culture, soil, water and animal hosts. This diversity means that there are many different kinds of models and many different types of data collected. The SysMO initiative has been divided into two phases: SysMO1 funded eleven projects and 91 institutions; SysMO2 will fund seven projects, five of which are project continuations from phase 2 (so six projects are concluded) and two of which are new. The research outcomes (models, data, procedures), and the know-how and best practice developed by the scientists, are to be managed and pooled in order to: benefit the members of the programme during the running of the projects; disseminate and publish the results to the wider scientific community; and safeguard the results after the completion of the projects that maximises the 'shelf life' and utility of data generated by SysMO. SysMO-DB is a project to build and manage an incrementally developed web-based software platform to achieve this. SysMO-DB1, funded during the first phase, begun the development of a web-based platform - called the SEEK - for cataloguing the different outcomes of the projects, archiving data, procedures and models and integrating with the different project's local data management systems, including the standardisation of the information used to describe the data and models and the handling of project spreadsheets. The SEEK also includes a social network for the SysMO members and integrates with public repositories for data, models, analyses and publications such as JWS Online (for models); SABIO-RK (for data), myExperiment (for bioinformatics data analysis pipelines) and PubMed (for publications). SysMO-DB has also developed effective practices for working with SysMO scientists through the founding of a PALs focus group of researchers who shape the developments, data standards and protocols necessary for pooling and promote SEEK adoption in their own projects. The focus of SysMO-DB1 is on supporting the current projects. SysMO-DB2 continues and extends the work to cope with SysMO-phase changes and life after beyond and after SysMO: new and terminating projects, personnel change, publication outside the consortium and long-term preservation of results. SysMO-DB2 also plans to package up the software and methods so that they can be adopted and sustained by other programmes such as EraSysBio+. EraSysBio+ is a pan-European programme for 16 Systems Biology projects. It is similar in organisation to SysMO but radically different in terms of scope. Hence it differs in the data, model and process capabilities needed. As part of widening the adoption of the SysMO-DB approach the project will support EraSysBio+ in its first 18 months. The two projects from EraSysBio+ that focus on microorganisms will be fully integrated into the SysMO-DB work programme. For the full range of EraSysBio+ projects SysMO-DB2 will instantiate a new instance of the SEEK, provide advice and help launch a PALs scheme.