GenMAPP-CS, a dynamic resource pathway analysis

描述（由申请人提供）：基因组信息的通路导向可视化使生物学家能够在生物过程和系统的背景下解释数据。我们开发了GenMAPP（基因图谱注释器和途径分析器）作为一个免费的，开源的，独立的计算机程序，用于组织，分析和共享生物途径背景下的基因组规模数据。该程序广泛用于DMA微阵列研究（> 12，000个唯一用户注册，>200篇出版物）。用户的持续需求以及数据集不断增加的规模和复杂性现在需要对GenMAPP进行重大修订。我们已经与其他开源生物信息学途径项目形成了关键联盟，这些项目的努力补充了GenMAPP。我们作为核心开发人员加入了Cytoscape（www.cytoscape.org）联盟，以便使用Cytoscape中已有的高级布局和可视化工具构建GenMAPP-CS。为了促进途径交换，我们正在与社区驱动的标准（例如BioPAX和SBML）和几个主要的公共途径数据库（例如，Reactome; www.reactome.org），以加强途径内容和交流。为了实施这一计划，我们提出了三个具体目标。具体目标1：构建GenMAPP的客户端-服务器版本GenMAPP-CS，为可视化和分析生物途径的基因组数据提供动态环境。GenMAPP-CS是一个基于Java的开源程序，用于可视化和分析超过GenMAPP当前能力10-100倍的数据集，同时保持用户界面和生物学家直观的特定功能。具体目标2：将GenMAPP-CS与20多种主要模式生物的主要基因和途径数据库动态整合。新的GenMAPP-CS架构将允许我们整合基因外显子，单核苷酸多态性（SNP）和蛋白质结构域信息与探针信息，其规模在GenMAPP 2.0中是不切实际的。具体目标3：使GenMAPP-CS能够可视化和分析全基因组剪接、多态性和相互作用数据集。分析这些庞大而复杂的数据集的挑战是推动GenMAPP-CS发展的主要力量。

DESCRIPTION (provided by applicant): Pathway-oriented visualization of genomic information enables biologists to interpret data in the context of biological processes and systems. We developed GenMAPP (Gene Map Annotator and Pathway Profiler) as a free, open-source, stand-alone computer program for organizing, analyzing, and sharing genome-scale data in the context of biological pathways. This program is widely used for DMA microarray studies (>12,000 unique user registrations, >200 publications). Continuing demands of our users and the ever-increasing size and complexity of datasets now require a major revision of GenMAPP. We have formed key alliances with other open-source bioinformatics pathway projects whose efforts complement GenMAPP. We joined the Cytoscape (www.cytoscape.org) consortium as core developers so that we can build GenMAPP-CS using the advanced layout and visualization tools already available in Cytoscape. To facilitate pathway exchange, we are working closely with community-driven standards, (e.g. BioPAX and SBML) and several major public pathway databases (e.g., Reactome; www.reactome.org) to enhance pathway content and exchange. To implement this plan, we propose three specific aims. Specific Aim 1: To build GenMAPP-CS, a client-server version of GenMAPP, to provide a dynamic environment for visualizing and analyzing genomic data on biological pathways. GenMAPP-CS is being developed as an open-source, Java-based program to visualize and analyze datasets that exceed GenMAPP's current capabilities by 10-100-fold, while maintaining user interfaces and specific functions intuitive to biologists. Specific Aim 2: To dynamically integrate GenMAPP-CS with major gene and pathway databases for over 20 major model organisms. The new GenMAPP-CS architecture will allow us to integrate gene exon, single nucleotide polymorphism (SNP), and protein domain information with probe information at a scale that is impractical in GenMAPP 2.0. Specific Aim 3: To enable GenMAPP-CS to visualize and analyze genome-wide splicing, polymorphism, and interaction datasets. The challenge of analyzing these massive and complex datasets is a major force driving the development of GenMAPP-CS.