2009 Summer Program at the CBCB
This program is supported in part the NSF under grant 0812111
to Mihai Pop and Carl Kingsford.
Students
Chris Hill - University of Maryland, College Park
Petar Stojanov - Bard College
Govin Vatsan - River Hill Highschool
Joshua Wetzel - Rutgers University, Camden
Faculty mentors
Liliana Florea
Carl Kingsford
Mihai Pop
Program Overview
The goal of the summer program is to get you hands-on research
experience in bioinformatics as part of ongoing research projects
within the CBCB. As such, during the first week of your time at UMD
you will get to choose from among several of the projects selected by
the faculty mentors - this will be your primary project for the
summer. You will also get to meet the graduate students in the Center
that work on related projects. They will help co-mentor you
throughout the duration of your project.
At the end of the summer you will be expected to put together a
report outlining the results of your project. In addition, you will
have to give a 30 minute presentation describing your project and what
you have achieved.
In addition to research, we also planned a series of informational
seminars to introduce you to various aspects of bioinformatics. These
seminars will be held on a bi-weekly basis, Thursdays at 11am,
alternating with group meetings. All students are required to attend
both the seminars and the group meetings.
Throughout the summer there will be other seminars and research
presentations, both at the CBCB, and elsewhere on campus. We will
announce any seminars that might be of interest to you and encourage
you to attend them. In particular, within the CBCB there will be a "Works In
Progress" seminar, Mondays at 2pm - please attend (schedule is available at http://www.cbcb.umd.edu/seminars/summer-works-in-progress.html).
Useful information
Info
on getting started at the CBCB: various logistics issues to help
you get started.
Schedule
Mon, May 25 - Memorial Day
Tue, May 26 - Arrival. Mainly paperwork, computer setup, etc.
Wed, May 27 - 11am BSB 3118. Introduction: Summer program,
Logistics.
Thu, May 28 - 11am BSB 3118. Introduction to sequencing and
assembly. Outline of research projects.
Fri, May 29 - 11am BSB 3118. Introduction to useful bioinformatics
tools & CBCB computer setup. (Dan Sommer)
Mon, Jun 1 - 2pm BSB 3118. Works in progress seminar. (Arthur Brady - metagenomic binning)
Thu, Jun 4 - 11am BSB 3118. Introduction to sequence alignment (Mohammad Ghodsi)
Mon, Jun 8 - 2pm BSB 3118. Works in progress seminar. (Dave Kelley - large genome assembly validation)
Thu, Jun 11 - 11am BSB 3118. All hands meeting
Mon, Jun 15 - 2pm BSB 3118. Works in progress seminar. (Guillaume Marcais)
Thu, Jun 18 - 11am BSB 3118. Introduction to gene/motif finding &
genome annotation (Niranjan Nagarajan)
Mon, Jun 22 - 2pm BSB 3118. Works in progress seminar. (Sergey Koren)
Thu, Jun 25 - 11am BSB 3118. All hands meeting
Mon, Jun 29 - 2pm BSB 3118. Works in progress seminar. (Jonathan Epstein - detecting peptide post-translational modifications)
Thu, Jul 2 - 11am BSB 3118. Introduction to clustering (TBA)
Mon, Jul 6 - Independence Day (observed)
Thu, Jul 9 - 11am BSB 3118. All hands meeting
Mon, Jul 13 - 2pm BSB 3118. Works in progress seminar. (Mohammad Ghodsi)
Thu, Jul 16 - 11am BSB 3118. Introduction to biological networks (Bo Liu)
Mon, Jul 20 - 2pm BSB 3118. Works in progress seminar. (Megan Smedinghoff)
Thu, Jul 23 - 11am BSB 3118. All hands meeting
Mon, Jul 27 - 2pm BSB 3118. Works in progress seminar. (James White)
Thu, Jul 30 - 11am BSB 3118. Introduction to metagenomics (James White)
Mon, Aug 3 - 2pm BSB 3118. Works in progress seminar. (Saket Navlakha)
Thu, Aug 6 - 10am BSB 3118. Student presentations
Mon, Aug 10 - 2pm BSB 3118. Works in progress seminar. (Bo Liu)
Thu, Aug 13 - 11am BSB 3118. Wrap-up
Information about the projects
- Joshua Wetzel - Analysis of mate-pairs in assembly graphs
- Petar Stojanov - Analysis of alternative splicing from short read data
- Chris Hill - Analysis of shared genomic segments in bacterial genomes and impact on assembly
|
