Tag Archives: workshops

Free workshop at #UCDavis: “Microbial genomics and transcriptomics hands-on”, Sep 24-25

Was informed of this by Titus Brown, one of the instructors.  Info copied from here.

Microbial genomics and transcriptomics hands-on, Sep 24-25

Who: Ben Johnson (Michigan State University); Tracy Teal (Data Carpentry); C. Titus Brown (UC Davis).

Host: C. Titus Brown

When: Sep 24 and 25, 2015

Times: 9am-3pm on both days

Where: TBD (UC Davis campus).

Cost: there is no fee.

This workshop is open to everyone, including graduate students, postdocs, staff, faculty, and community members. We have extra space for UC Davis VetMed affiliates; contact the host if you are an SVM affiliate.

> Register here <


This two-day hands-on workshop will introduce biologists to microbial genomics and transcriptomics. The primary focus will be on genome assembly and annotation, and subsequent transcriptome analysis, of bacteria.

We will be analyzing a stock data set, and we will be using the Amazon cloud.

Topics overview

  • Logging into the Amazon Cloud
  • Short read quality and trimming
  • Genome assembly (with SPAdes or MEGAHIT)
  • Genome annotation (with Prokka)
  • RNAseq analysis
  • Differential expression analysis

Computer requirements

Attendees will need to bring a computer with a Web browser, an Internet connection, and an ssh client; Windows users should install MobaXterm before the workshop.

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons – 0 License (CC0)fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

Announcement: Intntl. BioInformatics Workshop on Virus Evolution & Molecular Epidemiology

This looks pretty good:

18th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
University of Florida, Emerging Pathogens Institute
Gainesville, Florida, USA.
August 25th – August 30th, 2013

Bioinformatics Methods Applied to Virology and Epidemiology

We are announcing the organization of the international workshop on Virus Evolution and Molecular Epidemiology (VEME) in 2013, hosted by the Emerging Pathogens Institute in the warm city of Gainsville and sponsored by several local partners.
We plan to organize a ‘Phylogenetic Inference’ module that offers the theoretical background and hands-on experience in phylogenetic analysis for those who have little or no prior expertise in sequence analysis. An ‘Evolutionary Hypothesis Testing’ is targeted to participants who are well familiar with alignments and phylogenetic trees, and would like to extend their expertise to likelihood and Bayesian inference in phylogenetics, coalescent and phylogeographic analyses (‘phylodynamics’) and molecular adaptation. A ‘Large Dataset Analysis’ module will cover the more complex analysis of full genomes, huge datasets of pathogens including Next Generation Sequencing data, and combined analyses of pathogen and host. Practical sessions in these modules will involve software like, PHYLIP, PAUP*, PHYML, MEGA, PAML or HYPHY, TREE-PUZZLE, SplitsTree, BEAST, MrBayes Simplot and RDP3.
We recommend participants to buy The Phylogenetic Handbook as a guide during the workshop, and to bring their own data set.
For further information and applications we refer to a dedicated website that will be announced here soon.
Abstract and application deadline is April 30th.
Selections will be made by end of May 2013.
The registration fee of 1000 USD covers attendance, lunches and coffee breaks.
Participation is limited to 25 scientists in each module and is dependent on a selection procedure based on the submitted abstract and statement of motivation. A limited number of grants are available for scientists who experience difficulties to attend because of financial reasons.
For further information and applications we refer this website: http://conferences.dce.ufl.edu/vemei/http://conferences.dce.ufl.edu/veme/