GenoCAD: A Computer Assisted Design Environment for Synthetic Biology

该奖项由2009年美国复苏和再投资法案(公法111-5)资助。弗吉尼亚理工大学的弗吉尼亚生物信息学研究所获得了一笔赠款，用于开发基于网络的合成生物学计算机辅助设计环境GenCAD。这一基础设施通过结合蛋白质表达、蛋白质工程、代谢工程和其他应用中使用的基本遗传部分，帮助分子生物学家设计定制的DNA分子。该项目有四个目标。将开发计算机语言来表示在大肠杆菌、酵母、小鼠和拟南芥细胞中使用的合成DNA分子结构。研究小组将开发一种编译器，能够将DNA序列翻译成DNA序列中编码的基因网络的数学模型，以预测设计的DNA序列中编码的表型。协作功能将允许团队在复杂的项目上共同工作。协作工作流环境将允许工作组共享零件、设计、共享制造资源，并定义适合其项目的自定义设计策略。该奖项通过教学、培训和学习来促进发现，从而促进计算机辅助设计用于基因构建。该项目通过与邻近的一所历史悠久的黑人大学联合举办暑期项目，有助于扩大代表不足的群体的参与。最后，该项目将通过外部咨询委员会、一年一度的用户会议和与业界的接触，确保广泛传播成果。这个项目吸引了广泛的用户社区，他们的经验提供了宝贵的反馈。参加合成生物学竞赛iGEM的1,000名本科生可以使用GenCAD。由学术界和工业界领袖组成的外部咨询委员会确保GenCAD的开发满足大量潜在用户的需要。最后，结合研究资助和技术转让的具体计划将确保项目的长期可持续性。欲了解有关GenCAD的更多信息，请访问www.genocad.org。

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).The Virginia Bioinformatics Institute at Virginia Tech is awarded a grant to develop GenoCAD, a web-based computer assisted design environment for synthetic biology. This infrastructure helps molecular biologists design custom DNA molecules by combining basic genetic parts used in protein expression, protein engineering, metabolic engineering, and other applications. The project has four aims. Computer languages will be developed to represent the structure of synthetic DNA molecules used in E.coli, yeast, mice, and Arabidopsis thaliana cells. The research team will develop a compiler capable of translating the DNA sequences into mathematical models of the gene network encoded in the DNA sequence to predict the phenotype encoded in the designed DNA sequences. Collaborative features will allow teams to work together on complex projects. A collaborative workflow environment will allow workgroups to share parts, designs, share fabrication resources, and define custom design strategies suitable for their projects. The award promotes the use of computer assisted design for genetic constructs by advancing discovery through teaching, training, and learning. The project contributes to broadening the participation of underrepresented groups through a joint summer program with a neighboring historically black college. Finally, the project will ensure a broad dissemination of the results by reaching out to the user community through an external advisory board, an annual user conference, and outreach to industry. This project engages a broad community of users whose experience provides valuable feed-back. GenoCAD is made available to 1,000 undergraduate students enrolled in iGEM, a synthetic biology competition. An external advisory board composed of leaders of the academic and industrial community ensures that GenoCAD developments meet the needs of a large community of potential users. Finally, specific plans combining research grants and technology transfer will ensure the project long-term sustainability. Additional information about GenoCAD can be found at www.genocad.org.