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VIP Vertically Integrated Project: Undergraduate Research Team   Systems Biology and Metabolomics Systems Biology is big data in biology. It often refers to large “omics” datasets that are modeled and analyzed for biological insight. Increasingly, machine learning and AI are important tools in this analysis. The Edison lab specializes in metabolomics, which is one of the major components of systems biology. These technologies are important in many areas of biological and biomedical sciences and will become more and more critical in human health.   Overall Goal: Our VIP team has between 10-15 undergraduate students. Students tend to stay for 2-3 years, and as they become more advanced, they become mentors for the newer students. Thus, in addition to learning about systems biology, students learn how to work in teams, to teach, and to mentor others. Our former students have gone on to medical school, graduate school, other professional schools, and industry. We strive to have undergraduate students publish with us when their contributions on a project are significant.   Overall Structure of the Team: The team meets weekly as a group. These team meetings allow for research updates as well more general discussions on topics like career goals, ideas for new experiments, and synergy between different research projects. Each VIP student participates in a weekly training module that is taught by graduate students or senior scientists in the Edison lab. The current training modules are NMR and computation, both described below. Finally, VIP students join projects that are often led by graduate students.   Diversity: It is unfortunately that “diversity” has become a divisive term in education. We value diversity on every level of our VIP team. For example, different student majors, can greatly enhance a study. When a math major, biology major, and history major all can work together on a project, interesting and beneficial outcomes can emerge. Students on our team have different career goals, and when premeds work with students planning careers in science or public policy, new perspectives are brought to a problem. Several of our students have been first-generation college students or come from low-income families. These perspectives add an important dimention to our team and are welcome. We also partner with the Peach State LSAMP Program, which is an amazing consortium of six public colleges and universities in Georgia. The Peach State LSMAP has a goal of increasing the number of underrepresented students in science, technology, engineering, and math (STEM). Through the Peach State LSAMP prograam, we have had several outstanding students from UGA as well as Savannah State University and Fort Valley State University. These interactions significantly enrich our VIP team. Finally, we are proud participants in the GRA Student Scholars, which is a great new program in Georgia to further develop our workforce.   NMR training module: Students in the NMR training module will work with real 1D and 2D NMR data from the BMRB. Students use NMR analysis software to analyze the BMRB small molecule data. This provides a foundation to understand the relationship between 1D and various 2D data, and students learn how to assign peaks in an NMR spectrum to atoms in a molecule. Interested students can also get hands on training in our state-of-the-art CCRC NMR facility. Students also will get introducted to metabolomics data analysis using computational tools and NMRbox. Computational training module: Students in the computational training module will learn to use the command line in linux computational environments. They will be introduced to simple scripts and tools like Github. Languages such as python or MATLAB will be introduced to give students an introduction to various techniques in bioinformatics and even AI and machine learning. Projects: Projects are the core of the VIP experience. One or more VIP students work directly with graduate students or postdocs in the Edison lab on significant biological projects. At the start of each semester, graduate students who are seeking VIP team members will present their project to the whole team and indicate the training that is most important for that project (NMR or computation). The research conducted in these projects is organized by the grad students with the VIP team members. Look at our research page for information on current research projects.   For more information, contact Prof. Art Edison.

VIRTUAL JOURNAL CLUB

Virtual Journal Club COVID-19 has shown us that some things, like journal clubs, can be effectively done on-line. This opens up the possibility to include participants from different universities or even companies, as we are constrained only by time-zone differences. Both trainees and PIs are encouraged to join, but the goal is to make this a trainee-based discussion with minimal PI input except to clarify and steer the discussions.   This virtual journal club will take place in the spring semester, 2021. If there is enough interest, we can continue it the following fall. We will meet for 1 hour each Wednesday at 3 pm (eastern time), beginning on January 27 and ending May 5.   Format: In order to accommodate as many presenters as possible, we will have two 30 min presentations each week (15 min presentation/15 min discussion). These can be independent or coordinated (e.g., a technique paper followed by an application paper using that technique). Preference will be given to trainees (students, postdocs), but anyone is welcome to present if slots are available. We will provide a signup sheet with the complete schedule shortly after the New Year. The schedule will show papers that have already been chosen.   Scope and choice of paper: All areas of metabolomics analytical technology (MS, NMR, other), bioinformatics/chemoinformatics/biostatistics, and applications are welcome. While the most recent literature (within ~2 years) is encouraged, highly impactful older papers are also appropriate. The overall goals are to get introduced to interesting papers in metabolomics and to learn something new from them. People should not present work from their own lab, but it is fine to present work from another group that participates in the journal club. We want to use this to build community, so we encourage presenters to reach out to authors of papers to ask questions in preparation and to invite them to join. Papers will be posted in advance for participants to read in preparation for the presentations.   Many papers will be too long to fit into these short timeslots. Therefore, presenters should not feel compelled to cover everything. In fact, just focusing on a key take-away, such as a method, analysis or result and explaining it in detail with a few figures or tables is better than trying to cover the whole paper.   If you are interested in participating in this virtual journal club, send an email with your name and position (student, postdoc, staff, faculty, other) to Karen Howard. She will add you to the list and will send you a schedule, signup list, and zoom link after January 4. This Virtual Journal Club is facilitated by the Metabolomics Association of North America

BINF 4550/6550

Introduction to Bioinformatics This class is offered every fall semester, and taught with Jim Leebens-Mack and Jonathan Arnold. It is for advanced undergraduates or graduate students. The overall class focuses on systems biology, with introductions to omics (metabolomics, genomics, and RNAseq), an overview and introduction to trees for analysis of phylogentic and omics data, and an introduction to programming in MATLAB. The 3 instructors attend and participate in most of the classes, so it is not a traditional team-taught class.

NMR BASICS

Lecture notes in NMR I have compiled a set of 9 lectures that provide an overview of NMR. I hope to update these soon.