Groupe Logiciels et Banques de Données, Institut Pasteur, 28, rue du Dr Roux, 75724 Paris Cedex, France.
Bioinformatics. 2009 Nov 15;25(22):3005-11. doi: 10.1093/bioinformatics/btp493. Epub 2009 Aug 17.
For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally, given that scientific tools can be difficult to install, it is particularly helpful for biologists to be able to use these tools through a web user interface. However, providing a web interface for a set of tools raises the problem that a single web portal cannot offer all the existing and possible services: it is the user, again, who has to cope with data copy among a number of different services. A framework enabling portal administrators to build a network of cooperating services would therefore clearly be beneficial.
We have designed a system, Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software. While being focused on the end user, the Mobyle system also addresses the need, for the bioinfomatician, to automate remote services execution: PlayMOBY is a companion tool that automates the publication of BioMOBY web services, using Mobyle program definitions.
The Mobyle system is distributed under the terms of the GNU GPLv2 on the project web site (http://bioweb2.pasteur.fr/projects/mobyle/). It is already deployed on three servers: http://mobyle.pasteur.fr, http://mobyle.rpbs.univ-paris-diderot.fr and http://lipm-bioinfo.toulouse.inra.fr/Mobyle. The PlayMOBY companion is distributed under the terms of the CeCILL license, and is available at http://lipm-bioinfo.toulouse.inra.fr/biomoby/PlayMOBY/.
对于生物学家来说，运行生物信息学分析涉及到数据和工具的耗时管理。用户需要支持来组织他们的工作，检索参数并重现他们的分析。他们还需要能够使用安全的数据流程软件机制来组合他们的分析工具。最后，由于科学工具可能难以安装，生物学家能够通过网络用户界面使用这些工具是特别有帮助的。然而，为一组工具提供网络界面会带来一个问题，即单个门户不能提供所有现有的和可能的服务：用户仍然需要处理多个不同服务之间的数据复制。因此，一个能够使门户管理员构建合作服务网络的框架显然是有益的。
我们设计了一个系统，名为 Mobyle，为定义和运行生物信息学分析提供了一个灵活且易用的 Web 环境。它嵌入了简单而强大的数据管理功能，允许用户使用分层类型系统重现分析并组合工具。Mobyle 提供了对分布在远程 Mobyle 服务器上的服务的调用，从而实现了无需用户学习复杂概念或安装复杂软件即可进行协作的生物信息学门户联邦网络。虽然专注于最终用户，但 Mobyle 系统还满足了生物信息学家对自动化远程服务执行的需求：PlayMOBY 是一个配套工具，它使用 Mobyle 程序定义来自动化 BioMOBY Web 服务的发布。
Mobyle 系统根据 GNU GPLv2 的条款在项目网站（http://bioweb2.pasteur.fr/projects/mobyle/）上分发。它已经部署在三个服务器上：http://mobyle.pasteur.fr、http://mobyle.rpbs.univ-paris-diderot.fr 和 http://lipm-bioinfo.toulouse.inra.fr/Mobyle。PlayMOBY 配套工具根据 CeCILL 许可证分发，并可在 http://lipm-bioinfo.toulouse.inra.fr/biomoby/PlayMOBY/ 获得。
