Analyzing Next-Generation Sequencing Data
August 10 - August 21st, 2015
Kellogg Biological Station, MSU
Please sign up for the announcements mailing list if you are interested in taking this class now, or in the future.
Course sponsor: NIH.
Instructors: Dr. C. Titus Brown, Dr. Chris Chandler, Dr. Ian Dworkin, Dr. Adina Howe, Dr. Matt MacManes, and Dr. Meg Staton.
Course coordinator. Amanda Charbonneau
Mar 27, 2015 - application form is now open! We will close the application period on April 17th (midnight EST) and notify applicants of decisions on April 27th.
Oct 4th, 2014 - Dates announced for 2015. We will open registration on March 27th, 2015, and announce it on the the announcements mailing list. Please also see the list of other workshops and courses for other courses.
This intensive two week summer course will introduce attendees with a strong biology background to the practice of analyzing short-read sequencing data from Illumina and other next-gen platforms. The first week will introduce students to computational thinking and large-scale data analysis on UNIX platforms. The second week will focus on mapping, assembly, and analysis of short-read data for resequencing, ChIP-seq, and RNAseq.
No prior programming experience is required, although familiarity with some programming concepts is helpful, and bravery in the face of the unknown is necessary. 2 years or more of graduate school in a biological science is strongly suggested. Faculty, postdocs, and research staff are more than welcome!
Students will gain practical experience in:
- Python and bash shell scripting
- cloud computing/Amazon EC2
- basic software installation on UNIX
- installing and running bowtie, Trinity, Velvet, SPAdes and other bioinformatics tools.
- querying mappings and evaluating assemblies
Materials from previous courses are available at http://angus.readthedocs.org/ under a Creative Commons/full use+reuse license.
You can read a blog post about the 2014 course here.
What will students learn?
By the end of the course, students will be able to map short-read data to sequenced genomes and query the mapping for variation, transcript prevalence (from mRNAseq data), and enriched genomic regions (from ChIP-seq data). They will also know how to transfer large data sets between computers, run extended analyses while asleep, execute and modify existing Python scripts, and otherwise effectively make use of basic computational resources.
Location, dates, and course structure.
The course will be held at the W.K. Kellogg Biological Station on Gull Lake in western Michigan from noon on Monday, August 10th through 2pm on Friday, August 21st. Morning and afternoon lectures will be interspersed with practical hands-on labs. Room and board will be provided on-site (see enrolling, below). Sunday, August 16th, will be a day of rest & relaxation. Students should expect to arrive at KBS by Monday, August 10th at noon and stay at KBS through Friday, August 21st at 2pm. KBS is several hours away from the nearest large airports (DTW, GRR, LAN) and students coming from out of state should plan on arriving on Sunday.
Applying for the course
An application is required, and we can accommodate only 24 attendees. We absolutely welcome people unaffiliated with MSU or Davis, and "students" of any career stage, including postdocs and faculty. Applicants are not selected on a first-come-first-serve basis, and we try to create a balanced class of participants.
Applications are not yet open.
Note that some family housing is available, and there may be child care opportunities as well by special arrangement. Please contact Titus _after_ you have been admitted to discuss details!
Tuition, course cost, and enrolling
All students must pay for on-site room and board (see Orchard Dorms) prior to arrival. It should be about $650. We will make arrangements for housing *after* choosing students; please do not contact KBS directly.
We will also charge a course fee of $250/person.
Applicants must commit to spending both weeks on-site! The middle Sunday will be entirely free.
Taking the course for-credit
There is no formal option for taking the course for credit at MSU or elsewhere.
Please plan to bring a laptop (Mac OS X, Windows, or Linux are all OK). We will not have any additional laptops available this year.
Lodging and family
In 2015, we plan to have housing available for family groups. Child care may be available by arrangement.
C. Titus Brown (http://ged.msu.edu/) holds a Ph.D. in Developmental Biology from Caltech, and has worked on digital evolution, physical meteorology, developmental biology, and genomics. He is currently an Associate Professor in Population Health and Reproduction at the University of California, Davis, where his lab works on genomics, transcriptomics, and metagenomics, as well as training. In 2014, he was awarded a Data-Driven Discovery Investigator grant by the Moore Foundation. He tweets under @ctitusbrown and blogs at ivory.idyll.org/blog/.
Chris Chandler holds a Ph.D. in ecology and evolutionary biology from Iowa State University and is currently an assistant professor in the Department of Biological Sciences at SUNY Oswego. His research interests include evolutionary genetics and genomics, primarily involving Drosophila melanogaster, Caenorhabditis elegans, and terrestrial isopods.
Ian Dworkin (https://www.msu.edu/~idworkin/) holds a Ph.D. in Evolutionary Genetics from the University of Toronto, and has worked on Quantitative and statistical genetics, Evolutionary biology, genomics and developmental biology. He is currently a faculty member in the Department of Biology at McMaster University, where his lab works on evolutionary genomics of development, morphology and behavior, in addition to the development of new statistical tools.
Adina Howe (http://germslab.org) studies the impacts of natural and engineered microbial communities in our environments. She is currently an Assistant Professor in Agricultural and Biosystems Engineering at Iowa State University, where her lab works on sequencing-based approaches for identifying, monitoring, and managing microbes in the environment and their impacts on our lives.
Matt MacManes (http://genomebio.org/) holds a Ph.D. in Integrative Biology from UC Berkeley, and has worked in behavioral ecology, population genetics, and more recently transcriptomics and genomics. He is currently an Assistant Professor in Molecular Cellular and Biomedical Sciences at The University of New Hampshire, where his lab works on functional and population genomics in non-model organisms
including desert mice, ladybugs, clams, corals, and doves.
Erich Schwarz (http://emstech.org) is a Senior Research Fellow in the Department of Molecular Biology and Genetics at Cornell University. He works on next-generation genomics and transcriptomics of both model organism (Caenorhabditis) and parasitic nematodes.
Meg Staton (http://agbioinfo.utk.edu/) is an Assistant Professor in the Department of Entomology and Plant Pathology at the University of
Tennessee, Knoxville. She specializes in bioinformatics and genomics of plants and her lab helps build the software Tripal, runs genomic data web portals, and analyzes a wide variety of genomics data.
Board of Advisors
Human genetics and genomics: Kevin White, James and Karen Frank Family Professor at University of Chicago.
Animal genetics and genomics: Paul W. Sternberg, Thomas Hunt Morgan Professor of Biology at the California Institute of Technology; member of the National Academy of Sciences.
Microbial evolution and resequencing: Richard E. Lenski, Hannah Distinguished Professor at Michigan State University; member of the National Academy of Sciences.
Plant genetics and genomics: Robin Buell, Associate Professor at Michigan State University.
Microbial population sequencing and metagenomics: James M. Tiedje,
Professor, Michigan State University; member of the National Academy of Sciences.
Bioinformatics and genomics: Lincoln Stein, Platform Leader, Informatics and Bio-Computing, Ontario Institute for Cancer Research; Professor, Cold Spring Harbor Laboratory.
This course uses materials developed under AFRI Competitive Grant no. 2010-65205-20361 from the USDA NIFA, and is supported by Grant Number R25HG006243 from the National Human Genome Research Institute, both to CTB.