Summer courses for informatics and genomics

Cornwall School House Nº 4 (1892)Here’s a few courses to consider for the summer that cover informatics, genomics, and metagenomics analysis focusing on next generation sequencing. The deadlines are fast approaching so apply soon. (There are undoubtably more, and I’m happy to post here if you have suggestions)

Workshop on Comparative Genomics

Course dates: 10 – 23 July 2011
The Workshop on Comparative Genomics consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of comparative genomics. Faculty are chosen exclusively for their effectiveness in teaching theory and practice in comparative genomics. Included among the faculty are developers and other experts in the use of computer programs and packages such as Ensembl and Galaxy who provide demonstrations and consultations. The course is designed for established investigators, postdoctoral scholars, and advanced graduate students. Scientists with strong interests in the uses of short-read sequence data, analytical methods, comparative structure of genomes, SNP detection and analysis, CNV, genome visualization tools and related areas are encouraged to apply for admission. Lectures and computer laboratories total ~90 hours of scheduled instruction. Admission is limited and highly competitive, with admissions decisions determined by an international committee. No programming experience is required.

Topics to be covered include:

  • Sequencing technologies: short-read sequencing technologies of various types
  • Assembly and alignment: basic analyses in de novo and resequencing studies
  • Gene finding and annotation: functional description of genomic data
  • Genome characterization: gene content; genome structure; synteny; SNPs; copy number variation (CNV)
  • Assigning sequences to taxonomic groups in metagenomic studies: moving from sequences of unknown taxa to known taxa

— The schedule for this year’s class includes my lectures on BioPerl.


Analyzing Next-Generation Sequencing Data

June 6th – June 17th, 2011
Kellogg Biological Station, Michigan State University

Instructors: Dr. C. Titus Brown, Dr. Ian Dworkin, and Dr. Istvan Albert.

Applications must be received by March 25th for full consideration.

More information and application link here:

http://bioinformatics.msu.edu/ngs-summer-course-2011

Course Description:

This intensive two week summer course will introduce students with a strong
biology background to the practice of analyzing short-read sequencing data from
Roche 454, Illumina GA2, ABI SOLiD, Pacific Biosciences, 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.

Students will gain practical experience in:

* Python and bash shell scripting
* cloud computing/Amazon EC2
* basic software installation on UNIX
* installing and running maq, bowtie, and velvet
* querying mappings and evaluating assemblies

Materials from last year’s course are available at http://ged.msu.edu/angus/
under a Creative Commons/use+reuse license.

Ian Dworkin <idworkin@msu.edu>


Next-gen sequencing: data acquisition, comparative genomics, design and analysis for population genetics, systematics and development

Instructors: William Cresko, Brian O’Connor, Mónica Cecilia Muñoz-Torres, Alexie Papanicolaou, Konrad Paszkiewicz, Jennifer Taylor, Francesc López, Jeffrey Townsend
Dates: August 15 – 29, 2011
Application deadline: May 15, 2011
Website: academy.nescent.org
Where: National Evolutionary Synthesis Center (NESCent), Durham, NC

As part of the new NESCent Academy initiative, NESCent is pleased to
open applications for ‘Next-gen sequencing: data acquisition,
comparative genomics, design and analysis for population genetics,
systematics and development’. This course will provide computational
training required for those working with Next-generation sequencing
data and is aimed in particular at graduate students, research fellows
and faculty crossing the field into genomics. The course will be
embedded within an array of biological questions but it will be
focused around specific technical questions such as:

  • sequencing strategies, including libraries and RAD-TAG
  • generation of gene-models from related reference genomes or from NGS transcriptomes
  • variant calling and alternative splicing detection
  • analyzing differential expression
  • generation and use of genome-wide SNP markers
  • analysis of metagenomic data
  • phylogeny reconstruction from NGS

An added advantage of attending will be networking and the creation of a
community of researchers familiar with an inter-operable set of tools,
providing continued support and the potential for collaboration into
the future.


Course on Molecular Evolution

Course dates: July 24 – August 3, 2011
The Workshop on Molecular Evolution at Woods Hole presents a series of lectures, discussions, and bioinformatic exercises that span contemporary topics in molecular evolution. Since its inception in 1988, the workshop has encouraged the exchange of ideas between leading theoreticians, software developers and workshop participants. The workshop serves graduate students, postdoctoral students and established faculty from around the world. The 2011 Workshop will use computer packages including AWTY, BEAST, Clustal W/X, FASTA, FigTree, GARLI, MIGRATE, LAMARC, MAFFT, MrBayes, PAML, PAUP*, PHYLIP, and SeaView to address the topics:

  • Phylogenetic analysis: theoretical, mathematical and statistical bases; sampling properties of sequence data; Maximum likelihood theory and practice; Bayesian analysis; hypothesis testing
  • Population genetics analysis using coalescence theory; maximum likelihood and Bayesian estimation of population genetic parameters
  • Databases and sequence matching: database searching: protein sequence versus protein structure; homology; mathematical, statistical, and theoretical aspects of sequence database searches; multiple alignment
  • Molecular evolution integrated at organism and higher levels: population biology; biogeography; ecology; systematics and conservation
  • Molecular evolution and development: gene duplication and divergence; gene family organization; coordinated expression in evolution
  • Comparative genomics: genome content; genome structure; genome evolution
  • Molecular evolution integrated at lower levels: biochemistry; cell biology; physiology; relationship of genotype to phenotype

STAMPS: Strategies and Techniques for Analyzing Microbial Population Structures

Directors: Mitchell L. Sogin and David B. Mark Welch

Course Dates: August 3 – August 13, 2011.

Deep DNA sequencing using massively-parallel, next-generation technology has enabled nearly comprehensive environmental surveys that can describe the different kinds of microbes in a community and their relative abundance. These descriptions of richness and evenness make possible estimates of microbial diversity, but the size of the required data sets pose enormous computational challenges. The rapidly expanding flow of information from next generation DNA sequencing platforms has fueled healthy debate about best practices for data analysis while at the same time building a user demand for tools that can address important ecological questions. The STAMPS course will promote dialogue and the exchange of ideas between experts in analysis of metagenomic data and offer interdisciplinary bioinformatic and statistical training to practitioners of molecular microbial ecology and genomics.

Topics to be covered include but are not limited to next-generation strategies for analysis of microbial communities; acquisition and organization of next generation sequence data; principles of quality control of sequence data; the theory of cluster and rarefaction analyses; taxonomic assignments for high-throughput data; statistical models for estimating microbial diversity; microbial community comparison methodology and metrics; and analysis of shotgun metagenomic data. The lectures will be augmented by a computer laboratory where students will have the opportunity to use state of the art facilities to test theoretical concepts described in the lectures series. Guided by authors of ARB, CatchAll, Esprit, Mothur, Pyronoise, RDP, Silva, UClust, and Pyronoise for cluster analyses; mother, QIIME, Unifrac, and VAMPS for community analysis; and METAREP and MG-RAST for shotgun metagenomics analysis, participants in the workshop will have the opportunity to compare different analysis techniques for molecular data.

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