2018 WGC Fungal Pathogen Workshop

May 13-18, 2018
Wellcome Genome Campus in Hinxton, UK

Overall workshop goals:  The Fungal Pathogen Genomics workshop is intended to bring together fungal researchers interested in learning how to take advantage of various database platforms for data-mining.

This intensive week-long course is a collaborative teaching effort between the web-based fungal data mining resources: FungiDB, Ensembl/PhytoPathDB/PHI-Base, PomBase, SGD/CGD, and MycoCosm/JGI. The course aims to provide hands-on experience in genomic-scale data analysis; including genome browsers and comparison tools, data mining, analysis of genome annotation, developing testable hypotheses, and next generation sequence analysis and visualisation (including RNA sequence analysis and variant calling).



 

 

Download all course materials by clicking here

Sunday - May 13, 2018

  13:00  - 14:00

Registration and Lunch

 

  14:00  -   15:30

Instructor Introductions and Participant Presentations

 

  16:00  - 16:30

Break

 

  16:30  -   18:30

Introduction to Fungal Informatics Databases

 

  18:30  - 20:00

Welcome Drinks and Dinner

 

  20:00  -   21:00

Seminar

Dr. Regina Kanmann

 

Monday - May 14, 2018

  7:30  -   9:00

Breakfast

 

  9:00  -   10:30

Database Resources: EnsemblFungi/PhytoPath

Erin Haskell, Emily Perry

  10:30  -   11:00

Break

 

  11:00  -   13:00

Hands on Exercises: Gene Pages and Genome Browsers

All Instructors

  13:00  -   14:00

Lunch

 

  14:00  -   16:00

Database resources: FungiDB

Evelina Basenko, Jane Pulman, Omar Harb

  16:00  -   16:30

Break

 

  16:30  -   18:00

Hands on Exercises: Database queries and EuPathDB Galaxy: RNA-Seq

Evelina Basenko, Jane Pulman, Omar Harb

  19:00  -   20:00

Dinner

 

  20:00  -   21:30

Seminar

Dr. Tammi Vesth

 

Tuesday - May 15, 2018

  7:30  -   9:00

Breakfast

 

  9:00  -   10:30

Database Resources: JGI/Mycocosm

Alan Kuo

  10:30  -   11:00

Break

 

  11:00  -   13:00

Hands on Exercises: Genome Annotation; WebApollo, MycoCosm

All Instructors

  13:00  -   14:00

Lunch

 

  14:00  -   16:00

Hands-on Exercises: Transcriptomics

Evelina Basenko, Omar Harb, Jane Pulman

  16:00  -   16:30

Break

 

  16:30  -   18:00

EuPathDB Galaxy: RNA-Seq Analysis and Variant Calling Part I

Omar Harb, Jane Pulman, Evelina Basenko

  19:00  -   20:00

Dinner

 

  20:00  -   21:00

Seminar

Dr. Elaine Bignell


 

Wednesday, 16 May 2018

  7:30  -   9:00 am

Breakfast

 

  9:00  -   10:30

Database Resources: SGD/CGD

Kevin MacPherson

  10:30  -   11:00

Break

 

  11:00  -   13:00

Hands on Exercises: Comparative Genomics, Compara, GBrowse, MycoCosm

All Instructors

  13:00  -   14:00

Lunch

 

  14:00  -   16:00

Hands-on Exercises: Functional Analysis: ontologies; enrichment

David Roos, Evelina Basenko, Jane Pulman, Omar Harb

  16:00  -   16:30

Break

 

  16:30  -   18:00

Hands-on Exercises: Genome Analysis, EuPathDB Galaxy: Variant calling Part II

Jane Pulman

  19:00  -   20:00

Dinner

 

  20:00  -   21:30

Seminar

Dr. David Roos


 

Thursday, 17 May 2018

  7:30  -   9:00

Breakfast

 

  9:00  -   10:30

Database Resources: PomBase

Antonia Lock

  10:30  - 11:00

Break

 

  11:00  -   13:00

Hands on Exercises: Functional Analysis, pathways, proteomics, metabolomics

All Instructors

  13:00  - 14:00

Lunch

 

  14:00  -   16:00

Hands-on Exercises: Pattern Recognition, InterPro, Motifs, Regular expressions

Evelina Basenko, Jane Pulman, Omar Harb

  16:00  -   16:30

Break

 

  16:30  -   18:00

Hands-on Exercises: Evolutionaly Analysis, Synteny, Orthology, Cross-species inference

Jane Pulman

  18:00  -   19:00

Introductions to Group Projects

Instructors and Students

  19:00  -   20:00

Dinner

 

  20:00  -   21:30

Group projects, continued

Instructors and Students


 

Friday, 18 May 2018

  7:30  -   9:00

Breakfast

 

  9:00  -   10:30

Group Projects

Students

  10:30  -   11:00

Break

 

  11:00  -   13:00

Group projects, wrap up and presentations

Students

  13:00  -   14:00

Lunch and Adjourn

 

Download all course materials by clicking here
Note: The workshop materials are free to use by anyone, under the Creative Commons BY licence http://creativecommons.org/licenses/by/4.0/. If you wish to re-use these materials, please credit corresponding databases for their creation. If you use any databases for your work, please cite individual databases or corresponding publications.