Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.

Intended Audience: The course is aimed at individuals from a molecular biology background who have a basic understanding of biochemistry and/or genetics and would like to become bioinformatics users. For an explanation on who 'bioinformatics users' might be, see Figure 2 in http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496. A baseline level of the understanding of the central dogma of biology (DNA -> RNA -> Protein) is a requirement.

Logistics 

Venue of workshop: Local classrooms ( usually ~40 physical/online sites across Africa). Please be aware that the course is likely to make use of a combination of both physical and online sites depending on ongoing Covid-19 restrictions.

Dates for the workshop: 06 July – 12 October 2021; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

Workshop organisers: Paballo Chauke, Verena Ras, Shaun Aron, Sumir Panji and Nicola Mulder

Participation: The course is available to any classroom who meets the requirements and to any participant who is able to attend a physical/online classroom, provided they have been selected via the selection process. Should a classroom decide to host a face-to-face classroom, the participant must be able to attend this classroom in person for the duration of the course.

Workshop Sponsors: H3ABioNet + Local Classrooms

Classroom applications:

Registration for classrooms opens:  26 April 2021

Registration for classrooms closes: 11 May 2021

Link to classroom application form: <Classroom registration is now closed> 

Notification date for successful classrooms: 19 May 2021

Participant applications:

Registration for participants opens:  20 May 2021

Registration for participants closes: 14 June 2021 at 11:59 pm CAT

Application instructions: Participants must select a classroom within their region and that they are able to attend physically should that particular classroom choose to go ahead as a face-to-face classroom. Please be sure to adhere to this as selecting a classroom outside of your region/location may result in your application being rejected. Please also be aware that applying for the course does not guarantee entry - you will undergo a formal selection process.

Click here to apply!

Syllabus and Tools:

The course curriculum will cover the following main themes (subject to slight changes):

• Bioinformatics resources and databases
  • Introduction to bioinformatics, biological databases and resources (NCBI and EBI), data formats, ontologies
• Linux
  • Introduction to Linux, general overview of Linux environment, overview of command line interface, navigating Linux directory structure, manipulating files and directories, basic Linux commands
• Sequence alignment theory and applications
  • Introduction to searching and sequence alignment, BLAST, pairwise sequence alignment
• Multiple sequence alignment (MSA)
  • MSA theory, generating and interpreting MSAs using various tools, visualising and assessing MSA quality
• Genomics
  • Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap, 1000 genomes
• Molecular evolution and phylogenetics
  • Molecular evolution, phylogenetic approaches and methods (Introduction and overview of methods)

 **All modules make use of predominantly web-based tools such as NCBI, Ensembl, etc.

Prerequisites: A basic background/understanding of of biochemistry and/or genetics.

Objectives: After this workshop participants should be able to:

• Explain the use of bioinformatics
• Name the key bioinformatics techniques and tools
• Locate important biological databases and retrieve data
• Use selected tools effectively to run specific bioinformatics analyses
• Understand the strengths and limitations of the various techniques

Workshop limitations: This workshop will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.

For more information on IBT, please visit: https://www.h3abionet.org/training/ibt

Dates for the Course: 28 September to 23 November 2021 (participants will join on 05 October 2021)

Venue of the Course: Successful hosting classrooms

Course Organizers: Verena Ras, Gerrit Botha, Shaun Aron, Sumir Panji, Nicola Mulder

Course Overview:  The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools.

The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics course will use a blended learning approach similar to the popular H3ABioNet Introduction to Bioinformatics Training (IBT) through the use of a combination of theoretical and practical sessions in order for participants to gain knowledge in the use of various tools and resources needed for 16S rRNA microbiome data analysis. There will be 2 contact sessions per week consisting of both theoretical and practical coursework. Participants will generally watch pre-recorded videos (theory) followed by a practical exercise for the remainder of the session. Contact sessions will generally be 4 hours each however the exact format and length of classes will be communicated in due course. 

Course Objectives (TBC): By the end of the course participants should be able to:

• Describe the importance of the microbiome and why it should be studied
• Understand how to design 16S rRNA microbiome studies
• Be able to apply basic syntax and operations in R
• Understand the different NGS data types (e.g. MiSeq reads) produced for a 16S rRNA microbiome study
• Evaluate the quality of NGS sequence reads and samples
• Understand the various bioinformatics tools used for 16S microbiome studies
• Understand the various 16S rRNA bioinformatics pipelines being used to study the microbiome.
• Apply the H3ABioNet’s 16S rRNA pipeline and understand how to execute this
• Understand the use of workflow languages (Nextflow) and containerized images (Singularity) to automate analyses
• Analyze 16S rRNA microbiome data and interpret results

Intended Audience: Anyone who will be working with 16S rRNA microbiome data and would like to learn more about the bioinformatics analyses.

Syllabus and Tools (TBC):

• Introduction to the Linux command line / intro to R
• Introduction to the microbiome and study design – why 16S?
• Sample collection, extraction and library prep for 16S NGS analyses
• 16S rRNA gene amplicon sequencing bioinformatics pipeline: the theory
• 16S analysis pipeline - QC, ASV picking, taxonomic classification and alignment
• Downstream analysis in R - using the packages phyloseq, NMF, vegan, metagenomeSeq (among others)

Prerequisites (for participants): As this is an intermediate course, some familiarity with the Unix command line and R scripting will be assumed. However, should participants wish to gain some background knowledge before the start of the course, the following tutorials will provide a good foundation. 

Linux: http://www.ee.surrey.ac.uk/Teaching/Unix/

R: https://www.statmethods.net/r-tutorial/index.html

R: https://www.datacamp.com/courses/free-introduction-to-r 

Workshop limitations: This workshop provides an overview and guidance on 16S rRNA microbiome analyses and will provide you with the ability to perform a variety of analyses on microbiome data. The course however will not teach any advanced programming or go into depth with R or Unix. Participants are encouraged to explore these tools in greater depth independently.

Click here to access the general course site