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Computational Genomics
Course summary: The science of genomics involves the intersection of experimentation and computation. Computers are quite obviously required to handle the massive amount of data produced by genome sequencing projects. More importantly however, genome sequencing efforts yield ‘information’ alone, which can only be converted into ‘knowledge’ through the use of computers. In this class, the students will convert raw genomic information (i.e. sequence reads) into knowledge through the use of computational genomics tools and applications. The class will be provided with unassembled genome sequence data from the Centers for Disease Control and Prevention (CDC) and will proceed through five distinct stages of analysis and interpretation of that data:
- 1 - genome assembly
- 2 - gene prediction
- 3 - functional annotation
- 4 - comparative genomics
- 5 - production of a predictive webserver
This course will be entirely practical in nature. Students will learn to do the actual work of computational genomics. Expert guest lecturers will be brought in to provide information on state-of-the-art computational genomics tools. Based on this information, other class lectures and their own research, students will be solely responsible for choosing which tools (e.g. programs and/or databases) to use, how to implement them and for producing and thoroughly documenting their final results. All results will be integrated into a publicly available predictive webserver.
Class lecture sessions will be held synchronously online on Tuesdays and Thursdays from 9:30am to 10:45am. There is no textbook. Required and recommended readings will be made available on the course Wiki page - http://compgenomics2021.biosci.gatech.edu/ - along with any lecture material. Students are required to use online databases and the scientific literature to inform their choice of computational tools to be used. Since there is no textbook and many of the sessions involve class discussion and lab activities rather than formal lecture, attendance and class participation are absolutely mandatory.
Grading scheme:
| Points | Percent | Evaluation |
|---|---|---|
| 100 | 10% | Class attendance & participation |
| 200 | 20% | Exercise sessions (4 x 50 points each) |
| 200 | 20% | Class presentations (4 x 50 points each) |
| 400 | 40% | Group results (2 x 200 points each) |
| 100 | 10% | Documentation (2 x 50 points each) |
Synchronous lecture attendance and participation are mandatory. Class participation will be judged by the degree to which each student participates in class lectures and discussions (by asking questions, answering questions, offering ideas and opinions), during group presentations (by asking questions during others’ presentations, by engaging the audience during their own presentation, by connecting their presentation to previous class discussions, by working successfully in a small group), and during computer laboratory activities (by performing analyses and working with other students). Students who show up late or miss class will be severely penalized.
Each group will give a series presentations and laboratories/demos. Group presentations and labs/demos will be judged by the depth of analysis presented, the clarity of presentation, the utility of the exercises, the appropriateness and justification of the choices made, the validity and robustness of the results and the thoroughness of the documentation. In addition to presentations, results and documentation should be presented on the class Wiki site. All student code and analysis contributions must be shared and documented on Github – https://github.gatech.edu/comgenomics2021/. Specific requirements for the presentations will be provided during class sessions. Contributions of each individual student to the overall group effort must be meticulously detailed and documented.
Hybrid instructional model
The Spring 2021 class will be offered as a hybrid course. Synchronous online lectures and demonstrations will be held during the regular class times. All course assessments – student presentations, exercises, and projects – will be administered online. Student groups will present lectures and the results of their analyses and projects synchronously online during the regular class times. Students will have online and/or in-person on-campus group meetings as needed. Class office hour/problem-solving sessions will be held online and/or in-person on-campus as needed.
Please see http://www.honor.gatech.edu for Georgia Tech’s Academic Honor Code, which you are required to uphold.
Professor: I. King Jordan king.jordan AT biology.gatech.edu
T.A.: Shashwat Deepali Nagar shashwat AT gatech.edu
Office hours are available on request.
Course Materials
- BIOL7210 Syllabus 2021 (Updated: January 07, 2021)
- Class Github
- Lectures
- Exercises
- Literature/Papers
- Profiles
- Resources
Guest Lecturers
Working Groups
Team I:
- Team I - Genome Assembly Group
- Team I - Gene Prediction Group
- Team I - Functional Annotation Group
- Team I - Comparative Genomics Group
- Team I - Webserver Group