H3ABioNet

Pan African Bioinformatics Network for H3Africa

Analysing the Microbiome 29th to 31st March 2017

Venue of workshop: University of the Witwatersrand, Johannesburg, South Africa

Dates for the workshop: 29th March to 31st March 2017

Workshop organisers: Professor Scott Hazelhurst, Professor Nicola Mulder, Ami Bhatt, Gerrit Botha, Africa Wits-INDEPTH Partnership for Genomic Research, Sydney Brenner Institute for Molecular Bioscience, H3ABioNet

Workshop trainers: Ami Bhatt (Departments of Medicine and Genetics, Stanford University), Gerrit Botha (Computational Biology Division, University of Cape Town)

Workshop Sponsors: Africa Wits-INDEPTH Partnership for Genomic Research, Sydney Brenner Institute for Molecular Bioscience, H3ABioNet

Workshop application opens: 8th February 2017

Workshop application closes: 22nd February 2017 for H3ABioNet travel fellowships
                                                7th March 2017 for all other applications

Notification date: 27th February 2017 for H3ABioNet travel fellowships
                             17th March 2017 for all other applications

Link to application form: https://goo.gl/forms/0H3DIVZHsQHiOYT43

Workshop Overview: The development of next generation sequence technology has led to rapid advances in microbiome study. The Sydney Brenner Institute for Molecular Bioscience with support from the Pan-African Bioinformatics Network for H3Africa will be offering a short-course on the bioinformatics of analysing the microbiome. The course will give an overview of conducting a microbiome study, present some of the most important techniques, and will include some hands-on use of some the key tools. The course will cover analysis both using both 16S RNA gene sequences and shotgun sequencing

Participation: The workshop is aimed at individuals of research groups within the University of the Witwatersrand and associated Institutions, AWI-Gen and H3Africa members that will be working on analysing microbiome data. There is a small fee associated with the participation of this workshop to help cover costs. This includes the cost of the workshop, but does not include lunches or tea breaks. The fees are:

  • R500: Members of Wits and associated institutions (this is defined as being the ability to pay with a Wits internal requisition; if you can't pay with an I/R you need to pay the external rate).
  • R600: Other research and non-profit institutions.
  • R1200: For profit company.
  • H3ABioNet travel fellowship awardee: No course fee will be levied (please see below for more information on applying for an H3ABioNet travel fellowships)

N.B – Due to the limited number of places, workshop participation selection will be done on a competitive basis through the completed application form.

H3ABioNet travel fellowships: A maximum of five travel fellowships will be awarded by H3ABioNet for H3Africa members to attend this workshop based on the competitiveness of the completed application. In order to be eligible for an H3ABioNet travel fellowship, an applicant must be part of an H3Africa project and provide details of their PI for the selection committee to contact them. The H3ABioNet travel fellowships will cover a return economy flight to Johannesburg, airport transfers within Johannesburg and accommodation for the duration of the workshop. The H3ABioNet travel fellowships will not cover any visa application costs, vaccinations, airport transfers within the applicant’s country and meals as these costs should be borne by the applicant’s Institution.

Workshop Prerequisites: A working knowledge of the Linux command line. An introductory workshop on Linux will be provided on the 27th of March. To apply to attend this, please visit: http://www.bioinf.wits.ac.za/courses/linux17

Participants are also encouraged to go over some of the following resources to enable them to gain the most from the workshop:
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://ryanstutorials.net/linuxtutorial/commandline.php
http://www.h3abionet.org/tools-and-resources/sops/16s-rrna-diversity-analysis
http://qiime.org/tutorials/
https://www.youtube.com/watch?v=pOV_tuZqzso&t=187s
https://joey711.github.io/phyloseq/import-data.html
http://research.computing.yale.edu/support/hpc/user-guide/submitting-jobs-using-torque

Workshop Objectives:

  • Participants will gain an overview of conducting a microbiome study
  • Sample collection and DNA extraction
  • Taxonomic approaches and diversity
  • Analysing 16S rRNA data
  • Assembly of metagenomic data
  • Gene prediction and functional annotation
  • Key microbiome databases and tools

Workshop limitations: This workshop will provide a foundation for continued learning in the bioinformatics handling of microbiome data, approaches to microbiome taxonomic and diversity analyses identification and associated tools and databases. This workshop will not make one an expert on the study design and analyses of microbiome data as it is an introductory workshop.

Registration: All potential applicants must complete the application form by the applications dates provided. Incomplete applications will NOT be reviewed. Once being successfully chosen for the workshop, H3ABioNet travel fellowship awardees will be contacted to complete an airline ticket booking form, a short biosketch with a recent picture and the H3ABioNet workshop policy.

**Please note, if a participant is unable to attend this workshop after acceptance, their place will be passed onto to applicants on the waiting list and not to other recommended members from their H3Africa programme.

Workshop Programme (preliminary draft and subject to change):

Time Topic Trainer
Tuesday 28th March 2017
1:00 pm Introduction to the Linux command line Scott Hazelhurst
4:30 pm Workshop End
Wednesday 29th March 2017
8:00 am Registration TBA
8:45 am Welcome and introductions TBA
9:00 am Microbiome research: where are we now? TBA
10:00 am Overview of a microbiome study TBA
10:45 am Tea Break
11:15 am Sample Collection and DNA/RNA Extraction TBA
12:00 pm What type of study? 16S versus whole-genome versus TBA
1:00 pm Lunch
2:00 pm What are we looking for? The human microbiome – overview of bacteria, fungi, and viruses TBA
3:00 pm Taxonomic approaches: OTUs, alpha, beta diversity, UniFracg TBA
4:30 pm Workshop End
Thursday 30th March 2017
8:45 am 16S Workflow TBA
9:30 am Introduction to QIIME TBA
10:30 am Tea Break
11:00 am Practical exercises with QIIME TBA
1:00 pm Lunch
2:00 pm Uparse and Phyloseq TBA
3:00 pm Overview of shotgun sequence analysis TBA
4:30 pm Workshop End
Friday 31st March 2017
8:45 am Assembly of metagenomic data TBA
9:30 am Practical exercises TBA
10:30 am Tea Break
11:00 am Functional annotation and gene prediction TBA
12:00 am Practical exercises TBA
1:00 pm Lunch
2:00 pm Practical exercises continued TBA
3:00 pm Microbiome tools and databases TBA
4:30 pm Workshop End