GenMAPP-CS, a dynamic resource pathway analysis

GenMAPP-CS，动态资源路径分析

• 批准号: 7470710
• 负责人: Bruce R Conklin
• 金额: $ 40.11万
• 依托单位: J. DAVID GLADSTONE INSTITUTES
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-08-18 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7470710
• 关键词: AIM1 gene; Animal Model; Appendix; Architecture; Bioinformatics; Biological; Biological Models; Biological Process; Biology; Cell model; Cells; Cellular biology; Chromosome Mapping; Client; Communities; Complement; Complex; Computer software; DNA Microarray Chip; DNA Microarray format; Data; Data Set; Databases; Development; Development Plans; Documentation; Engineered Gene; Environment; Exons; Face; Figs - dietary; Floods; Future; Generations; Generic Drugs; Genes; Genetic Polymorphism; Genetic Transcription; Genome; Genomics; Goals; Graph; Hand; Imagery; Internet; Java; Laboratories; Link; Methods; Modeling; Pathway Analysis; Pathway interactions; Principal Investigator; Publications; RNA Interference; RNA Splicing; Research; Research Personnel; Resources; Single Nucleotide Polymorphism; Standards of Weights and Measures; System; Tertiary Protein Structure; Time; Transcript; Update; Variant; Work; base; computer program; data modeling; design; digital; driving force; file format; open source; programs; protein protein interaction; research study; size; tool

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.

描述（由申请人提供）：基因组信息的面向途径的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（基因图注释者和途径profiler）作为一种免费的，开源的，独立的计算机程序，用于在生物途径的背景下组织，分析和共享基因组规模数据。该程序广泛用于DMA微阵列研究（> 12,000个独特的用户注册，> 200个出版物）。现在，我们的用户的持续需求以及数据集的规模和复杂性不断增加，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建立了关键的联盟，他们的努力补充了Genmapp。我们加入了Cytoscape（www.cytoscape.org）联盟作为核心开发人员，因此我们可以使用Cytoscape中已经可用的高级布局和可视化工具来构建GenMapp-CS。为了促进路径交换，我们正在与社区驱动的标准（例如Biopax和SBML）以及几个主要的公共途径数据库（例如Reactome; www.reactome.org）紧密合作，以增强路径内容和交换。为了实施该计划，我们提出了三个具体目标。特定目的1：构建GenMapp-CS（genmapp的客户端版本），为可视化和分析生物途径的基因组数据提供了动态环境。 GenMapp-CS正在开发为基于Java的开源程序，以可视化和分析Genmapp当前功能的数据集，同时保持用户界面和对生物学家直观的特定功能。特定目的2：将GenMapp-C与主要基因和途径数据库动态整合，以适用于20多种主要模型生物。新的GenMAPP-CS结构将使我们能够整合基因外显子，单核苷酸多态性（SNP）和蛋白质结构域信息，并以探针信息的规模与Genmapp 2.0不切实际。特定目标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。分析这些庞大且复杂的数据集的挑战是推动GenMapp-CS发展的主要力量。