REU Site: ICompBio - Engaging Undergraduates in Interdisciplinary Computing for Biological Research

REU 网站：ICompBio - 让本科生参与生物研究的跨学科计算

• 批准号: 1852042
• 负责人: Hong Qin
• 金额: $ 35.11万
• 依托单位: University of Tennessee Chattanooga
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-01 至 2024-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1852042&HistoricalAwards=false
• 关键词: REU; Site; ICompBio; Engaging; Undergraduates

This REU Site award to the University of Tennessee at Chattanooga, located in Chattanooga, TN, will support the training of 10 students for 10 weeks during the summers of 2019 to 2021. This REU focuses on interdisciplinary computational biology (iCompBio) training for college sophomores and juniors in STEM majors. The student application includes an application form, transcripts, a personal statement, a resume, and 2 letters of recommendations. Applications will be reviewed by a team of faculty research mentors. Students will learn various computational methods and apply them to address biological questions. Each student will be jointly mentored by a computer science mentor and a biology mentor. A one-week computing bootcamp will be provided to teach students essential data science using R, and advanced data processing and deep learning methods using Python. The biological research topics include aging and longevity, ecological networks, biodiversity, microbial pathway evolution, aquatic ecology, environment sustainability, nanoparticle fertilizers, field ecology, herbarium digitization, protein structures, and cell membrane structures. The computing training includes coding, modeling, simulation, deep learning neural networks, computer vision, parallel computing, statistics, data visualization, and mobile App development. Students will also go through training in ethics and responsible conduct for research. It is anticipated that a total of 30 students, primarily from schools with limited research opportunities, will be trained in iCompBio. Students will learn how to conduct reproducible computational research, and will make their coding projects publicly available through GitHub. Students will also be encouraged to present their research results in scientific meetings. A common web-based assessment tool, SALG URSSA, used by all REU Site programs funded by the Division of Biological Infrastructure will be used to determine the effectiveness of the training program. Students will be tracked after the program in order to determine their career paths. Students will be asked to respond to an automatic email sent via the NSF reporting system. More information about the program is available at http://utc.edu/icompbio or by contacting the PI (Dr. Hong Qin at [e-mail] ) or the co-PI (Dr. Soubantika Palchoudhury at [e-mail]).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该REU SITE奖授予田纳西大学查塔努加分校，位于田纳西州查塔努加，将在2019年至2021年夏季支持10名学生进行为期10周的培训。该REU专注于为STEM专业的大学二年级和三年级学生提供跨学科计算生物学(ICompBio)培训。学生申请包括一份申请表、成绩单、一份个人陈述、一份简历和两封推荐信。申请将由一个教师研究导师团队进行审查。学生将学习各种计算方法，并将其应用于解决生物问题。每名学生将由一名计算机科学导师和一名生物导师共同指导。将提供为期一周的计算训练营，向学生传授使用R的基本数据科学，以及使用Python的高级数据处理和深度学习方法。生物学研究课题包括衰老与长寿、生态网络、生物多样性、微生物途径进化、水生生态学、环境可持续性、纳米颗粒肥料、田间生态学、标本馆数字化、蛋白质结构和细胞膜结构。计算培训包括编码、建模、模拟、深度学习神经网络、计算机视觉、并行计算、统计、数据可视化和移动应用程序开发。学生还将接受道德和负责任的研究行为方面的培训。预计总共将有30名学生接受iCompBio培训，这些学生主要来自研究机会有限的学校。学生将学习如何进行可重复的计算研究，并通过GitHub公开他们的编码项目。还将鼓励学生在科学会议上展示他们的研究成果。将使用生物基础设施司资助的所有REU站点方案使用的通用网络评估工具SALG Urssa来确定培训方案的有效性。项目结束后，将对学生进行跟踪，以确定他们的职业道路。学生将被要求回复通过NSF报告系统发送的自动电子邮件。有关该计划的更多信息，请访问http://utc.edu/icompbio，或联系国际和平组织(Hong Qin博士，电子邮件：[e-mail])或联合国际组织([e-mail])。该奖项反映了美国国家科学基金会的法定使命，并已通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

The local topological free energy of proteins

• DOI: 10.1016/j.jtbi.2021.110854
• 发表时间: 2021-08-17
• 期刊: JOURNAL OF THEORETICAL BIOLOGY
• 影响因子: 2
• 作者: Baldwin, Quenisha;Panagiotou, Eleni
• 通讯作者: Panagiotou, Eleni

Advances in Smart Nanomaterials: Environmental Perspective

智能纳米材料的进展：环境视角

• DOI: 10.1155/2020/6715765
• 发表时间: 2020
• 期刊: Journal of Nanomaterials
• 作者: Palchoudhury, Soubantika;Aich, Nirupam;Zhou, Ziyou
• 通讯作者: Zhou, Ziyou

Integrating Quantum Computing into De Novo Metabolite Identification

将量子计算集成到从头代谢物识别中

• DOI: 10.54808/jsci.21.02.83
• 发表时间: 2023
• 期刊: Cybernetics and Informatics
• 作者: Tsai, Li-An;Nuckels, Estelle;Wang, Yingfeng
• 通讯作者: Wang, Yingfeng

Applying for, Operating, and Renewing a Research Experience for Undergraduates Site Program in Computational Biology

申请、运营和更新计算生物学本科生研究经验现场项目

• DOI: 10.54808/imcic2022.01.171
• 发表时间: 2022
• 期刊: Informatics and Cybernetics
• 作者: Qin, Hong

Life history and the evolutionary loss of parental care

生活史和父母照顾的进化丧失

• DOI: 10.1098/rspb.2022.0658
• 发表时间: 2022
• 期刊: Proceedings of the Royal Society B: Biological Sciences
• 作者: Udu, Isimeme N.;Bonsall, Michael B.;Klug, Hope
• 通讯作者: Klug, Hope