Workshop on Microbiome and Transcriptome Analysis in Durban, South Africa

Date: 

Mon - Fri, Oct 8 to Oct 12, 9:00am - 5:00pm

Location: 

Nelson R. Mandela School of Medicine, University of KwaZulu-Natal

Workshop on the Analysis of Biological Data for Studies on the Microbiome and Host-Gene Expression
Registration is closed.  This event is at capacity with the maximum number of people registered. 
If you have registered and have not paid, please make payments before 1 October 2018.  For payment questions, please contact Candace Gregg at cgregg@mgh.harvard.edu or Amanda gorey at amanda_gorey@harvard.edu with questions.

Submit an application letter of interest and letter of support from a supervisor here: https://fs3.formsite.com/divofaids/form273/index.html
Download the workshop flyer

After your letters are received, you will be sent a link to the online registration.  There is a $100 USD registration fee.

This intensive, hands-on course will feature morning and afternoon sessions taught by expert faculty and technical assistants. All participants will acquire fundamental computational skills, appropriate study design, data interpretation, and overall literacy in bioinformatics.

Accommodations: We are not able to offer accommodations in conjunction with the workshop, but some participants have found rooms at the Chelsea Villa GuestHouse http://www.chelseavilla.co.za/index.html

Topics covered include: 

  • Intro to computing
  • Intro to R
  • Computational study design
  • Microbiome data analysis
  • Transcriptional data analysis
  • Differential Gene Expression

When: 08-12 October 2018, Morning Sessions: 9:00-12:00, Afternoon Sessions: 13:00-16:00

Where: AHRI Seminar Rooms 1&2,   Nelson R Mandela School of Medicine,   719 Umbilo Road, Durban, South Africa

Fee: There is $100 USD registration fee for this 5- day workshop. Breakfast, lunch and access to Amazon Web Services cloud infrastructure are included.

Requirements: Students are required to bring their own laptops to participate in the course. All software and data will be provided and managed by the course organizers. No previous experience in bioinformatics is needed.

 

Modern biological research projects regularly employee techniques capable of generating extremely large data sets. Specifically, microbiome investigations utilize amplicon surveys (16S rRNA, ITS, or 18S rRNA gene sequence) or metagenomic approaches to assess microbial ecology and gene expression studies take advantage of RNA-seq technology to identify differential gene regulation. Analysis of data resulting from any of these techniques requires proficiency in computational (UNIX, R) and statistical (exploratory data analysis, hypothesis testing, uni- and multivariant analysis) techniques.

The approach for analysis of both microbiome and gene expression analysis begins with appropriate understanding of the study design and metadata, proceeds through a process of data quality control and filtering, quantifies this filtered data and ultimately results in the production of tabular count data. In the case of microbiome studies, this is a table of each microbial taxa per sample and for gene expression studies a table of transcript counts per sample. Additional data types (e.g. taxonomic assignments, gene functional information) may also be created during this process and ultimately associated with or merged with the count table. These data types can then be explored using various plots and interrogated using statistical techniques. This Workshop provides instruction for how to proceed through each of these stages providing a strong foundation for working with count data and subsequent statistical analysis, plotting and interpretation.

Collaborating Institutions:

Harvard University Center for AIDS Research (CFAR)
Ragon Institute
Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE)
Centre for the AIDS Program of Research in South Africa (CAPRISA)

Organizing Team:

Scott Handley, Washington University
Doug Kwon, Ragon Institute
Matt Hayward, Harvard University
Barry L. Hykes, Washington University
Chandni Desai, Washington University

SCHEDULE
Visit the evomics website for the latest schedule updates as the workshop approaches

DATE

DAY

TIME

PRESENTER

TOPIC

LOCATION

7 Oct

Sunday

6p – 10p

Everyone

Reception

AHRI Seminar Rooms 1&2

8 Oct

Monday

9a – 12p

Sophie Shaw

Introduction to UNIX

AHRI Seminar Rooms 1&2

 

Monday

2p – 5p

Sophie Shaw

Introduction to Sequence Data and Sequence Data Quality Control

AHRI Seminar Rooms 1&2

9 Oct

Tuesday

9a – 12p

Lindsay Droit

Building Successful Sequencing Libraries

AHRI Seminar Rooms 1&2

 

Tuesday

2p – 5p

Scott Handley

Introduction to Data Science with R

AHRI Seminar Rooms 1&2

10 Oct

Wednesday

9a – 12p

Scott Handley

Preprocessing Microbiome Data for Quantitative Microbiome Analysis (lecture)

AHRI Seminar Rooms 1&2

 

Wednesday

2p – 5p

Scott Handley

Preprocessing Microbiome Data for Quantitative Microbiome Analysis (lab)

AHRI Seminar Rooms 1&2

11 Oct

Thursday

9a – 12p

Chandni Desai

Host Differential Gene Expression Analysis (lecture)

Onomo Hotel Durban
56 K.E. Masinga Road, CNR Sylvester Ntuli, Durban 4001

 

 

 

Thursday

2p – 5p

Chandni Desai & Barry Hykes

Host Differential Gene Expression Analysis (lab)

Onomo Hotel Durban
56 K.E. Masinga Road, CNR Sylvester Ntuli, Durban 4001

12 Oct

Friday

9a – 12p

Matt Hayward

Metagenomic Analysis

Onomo Hotel Durban
56 K.E. Masinga Road, CNR Sylvester Ntuli, Durban 4001

 

Friday

2p – 5p

Everyone

Open Lab

Onomo Hotel Durban
56 K.E. Masinga Road, CNR Sylvester Ntuli, Durban 4001

 

See also: Symposia