Workshops will be presented SUNDAY, November 11 from 9 AM to noon.

Currently the topics are:

1) Exploring the mouse genome in Ensembl
The Ensembl-HAVANA team produce manual gene annotation for the human and mouse genomes as part of the Gencode project. We will present the Gencode geneset and explain how this is produced. This workshop will provide a  brief introduction to the Gencode geneset in the Ensembl genome browser (www.ensembl.org) followed by hands-on demonstrations and exercises that describe and demonstrate an adaptable workflow for exploring and exporting genomic data with a focus on mouse. Workshop materials, including slides, demonstration screenshots, exercises, and solutions will be made available before the workshop and will remain permanently online at our training portal: https://training.ensembl.org.

2) Workshop: Easi-CRISPR: CRISPRing Made Easier presented by C.B. Gurumurthy, University of Nebraska Medical Center, USA
The workshop is based on Easi (Efficient additions with ssDNA inserts)-CRISPR, a recently developed method at the laboratories of Drs. Masato Ohtsuka (Tokai Univeristy, Japan) and C.B. Gurumurthy, which is now becoming a widely used approach for achieving higher knock-in efficiencies via homology directed repair. The workshop will cover: 1) General introduction to animal model generation; 2) Overview of animal model generation methods during pre- and post-CRISPR era; 3) Introduction to Easi-CRISPR and its applications; 4) Examples (case studies) of Easi-CRISPR animal model designs; 5) Hands-on workshop on Easi-CRISPR animal model designs; and 6) Demonstration of animal model designing using participant’s projects (time permitting).
Relevant publications on Easi-CRISPR: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1220-4 https://www.nature.com/articles/nprot.2017.153
Pre-prints of Easi-CRISPR: https://www.biorxiv.org/content/early/2017/05/23/141424 https://www.biorxiv.org/content/early/2016/08/17/069963

3) Next Generation Sequencing presented by Thomas KeaneNext generation sequencing has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to assess and analyse the large volumes of sequencing data produced by next generation sequencers. This introduction to next generation sequencing bioinformatics course aims to equip participants with the essential skills and knowledge required to begin analysing next generation sequencing data and carry out some of the most common types of analysis. This tutorial will cover the algorithmic theory and principles of bioinformatics (data QC, alignment, and variant calling), with a strong focus on practical knowledge to use sequence analysis techniques and tools applicable to any species or genome size."
Modified version from the full course webpage at https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=719 

4) Using International Mouse Phenotyping Consortium (IMPC) data
The IMPC is generating multi-dimensional phenotyping data for each protein-coding gene. With data for over 6,000 mouse knockout lines now available, this resource is valuable for a wide range of researchers, not just those working in mouse. This workshop will provide an introduction to the IMPC, including an overview of the various phenotyping tests (https://www.mousephenotype.org/impress/), followed by an interactive session detailing how to use and understand the freely-available data in the IMPC portal, www.mousephenotype.org. Attendees with come away with a clearer understanding of what the IMPC is, how best to search for information on their genes or phenotypes of interest, and what the data actually means.

5) GeneWeaver presented by Jason Bubier

Systems genetics has been an effective strategy for gene discovery and for finding the relations among traits and their mechanisms in genetic reference populations. Integrative functional genomics combines data from diverse experimental paradigms to find the common and distinct biological mechanisms of biological traits within and across species. As these methods have evolved, so too have the software systems that support interactive user initiated analyses. Flexible tools have made rapid interrogation of integrative genetic and genomic data resources possible.
Participants in this workshop will have an opportunity to use the latest version of GeneWeaver for integrative genetic and genomic analyses. GeneWeaver allows users to integrate heterogeneous functional genomics data in an interactive manner. Participants will be guided through simple tutorial demonstrations to use GeneWeaver. Following the introductory tutorial demonstrations, participants will have an opportunity to pose questions related to their own specific research questions or work on challenge problems provided by the organizers.

If you would like to present a workshop, or have a particular topic you would like to see presented as a workshop, please contact Darla Miller  (millerdr@med.unc.edu)