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[edit] 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 (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 and 5-production of a genome browser. 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 computation 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 genome browser.

This class meets on Mondays and Wednesdays from 10:35 to 11:55 pm in the Bioinformatics computer lab in Cherry Emerson room 306. The lab has dual boot Linux/Windows PCs and the students have will also have access to a dedicated Linux server. There is no textbook. Required and recommended readings will be made available on the course Wiki page - 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 required.

Professor: I. King Jordan Cherry Emerson 215 404-385-2224
T.A.: Andrew Conley Cherry Emerson 212 301-526-4515
Office hours are available on request.

[edit] Course Materials

[edit] Guest Lecturers

[edit] Working Groups

[edit] Linux Help

You will need to log into the server using an ssh client, eg:

[note: see Lee's lecture for ssh client use instructions]

You will need a secure ftp client to transfer files to the server, eg:

There are many online resources for Unix/Linux commands, eg:

There are several Unix/Linux text editors that you can use, eg:

[note: or you can work locally and transfer text files to the server]

[edit] Wiki Help

Consult the User's Guide for information on using the wiki software.

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