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.

Keywords: 16S, Microbiome, NGS, Genomics, Nucleic acid analysis

Language: English

Skill level: Intermediate

Type of training: face-to-face / in person

Credential awarded: no credential

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

Dates for the workshop: 29^th March to 31^st 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: 8^th February 2017

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

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

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

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):

Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19129943. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

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.

Keywords: Genetics, Genomics, Nucleic acids analysis

Skill level of training: Beginner

Language: English

Credential awarded: Letter of completion

Type of training: Blended/hybrid learning

Logistics 

Venue of workshop: Local classrooms ( usually 30 physical sites across Africa) and online

Dates for the workshop:10 July – 15 October; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

Workshop organisers: Kim Gurwitz, 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 classroom, if one has been set up at a local institution, provided they have been selected via the selection process.

Workshop Sponsors: H3ABioNet

Course Curriculum:

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 ONLY 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.

Training Material Availability:

Training materials for this course are available here: https://zivahub.uct.ac.za/projects/Introduction_to_Bioinformatics_Training_Course_Materials/131552. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

Materials have been made available as a single archive per module containing lecture slides, transcribed videos, practical assignments and any other resources important to complete each module:

Module 1: Databases and Resources

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_1_Databases_and_Resources_Training_Material_Archive/19106741 

Module 2: Linux

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_2_Linux_Training_Material_Archive/19106744 

Module 3: Sequence Alignment

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_3_Sequence_alignment_Training_Material_Archive/19106750 

Module 4: Multiple Sequence Alignment

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_4_Multiple_Sequence_Alignment/19106759 

Module 5: Genomics

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_5_Genomics/19106762 

Module 6: Phylogenetics (2018 - 2021)

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_6_Phylogenetics/19106765 

Module 6: Structural Biology (2016 only)

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_6_2016_Structural_Biology/19129892 

Introduction Week

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_-_Introduction_Week_Training_Material_Archive/19106738 

Wrap Up week

•  https://zivahub.uct.ac.za/articles/educational_resource/Wrap_up_Week/19106768 

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

Workshop Title: H3ABioNet / IBM Research Africa Hackathon on Malaria Drug Resistance for a DREAM challenge

Venue of workshop: Johannesburg, South Africa

Dates for the workshop: 5^th September to 10^th September 2016

Workshop organisers: Amel Ghouila, Jean-Baka Domelevo Entfellner, Geoffrey Siwo, Darlington Mapiye, Pavan Kumar, Waheeda Saaib, Michael Ferdig, Sage Davis, Katie Button, Faisal M. Fadlelmola, Sumir Panji, Nicola Mulder

Registration opens: 23^rd June 2016

Registration closes:  11^th July 2016

Notification date: 21^st July 2016

Application process:

1. Complete the application form available at: https://docs.google.com/forms/d/18bWGjgxc2KIx2cXj9WVkJIfzDxJ78iFQM-scJMeoEBQ/viewform?edit_requested=true
2. After submitting the application form, email a 2 pages CV to  in the format of FIRSTNAME_SURNAME_CV in order to complete your application

Workshop Sponsors: H3ABioNet, IBM Research Africa and University of Notre Dame

Workshop Overview: H3ABioNet, the University of Notre Dame and IBM Research Africa are organizing a joint hackathon on a complex biomedical research question on antimalarial drug resistance to prepare preliminary datasets for a future open collaborative challenge on drug combination prediction.

While malaria, a disease caused most commonly by the protozoan parasite Plasmodium falciparum, remains a major global health challenge, with a global estimate of slightly less than half a million deaths in 2015 [WHO World Malaria Report 2015], the African continent carries a disproportionately high burden of the disease (88% of the world cases and deaths). Nowadays, the World Health Organization (WHO) recommends artemisinin-based combination therapies for the treatment of malaria cases due to P. falciparum. However, emerging resistance of P. falciparum to artemisinins has been observed over recent years in South-East Asia, and the WHO has stated that “The emergence of P. falciparum resistance to artemisinin is an urgent public health concern, threatening the sustainability of the global effort to reduce the malaria burden in all endemic regions.”
In this context, it is the endeavor of consortia like H3ABioNet and IBM Research Africa to foster major breakthroughs in scientific research on diseases having a major impact on the African continent, hence the motivation for this collaboration.

Syllabus and Tools: The Ferdig Laboratory at the University of Notre Dame (Indiana, USA) is generating transcriptional data sets from a range of the malaria parasite isolates exposed to artemisinin in culture. This data needs to be preprocessed and prepared for an open challenge that will be launched under the DREAM Challenges initiative within the next 2 years. The challenge will invite participation of the whole research community in developing computational models for malaria drug combinations. Therefore, H3ABioNet, the University of Notre Dame and IBM Research Africa are organizing a data analysis workshop to prepare data for the launch of part 1 of a two-fold future open challenge on drug resistance prediction from transcriptional response in the context of (1) single drug treatment and (2) multi-drug treatment. In this latter challenge, the scientific problem will involve the prediction of synergistic and/or antagonistic effects of drug combinations from transcriptional responses to individual drugs.

Some work has already been published on drug sensitivity prediction using genomics data sets, including results from a previous DREAM Challenge [Costello et al, Nat. Biotechnol. 2014] or [Liu et al, Sci. Rep. 2016]. As part of the workshop, we also plan to review the biological foundations and hypotheses for predicting drug combinations.

Objectives:  The main objective of this workshop is to normalize, pre-analyse and curate the microarray data generated in order to prepare for the launch of the two-fold DREAM Challenge that will be open in the near future to the research community.

After the data have been processed, workshop participants will be tasked with developing baseline models for predicting drug sensitivity and assessing the viability of the challenge. The specific aim is to evaluate the predictability of the level of drug resistance of P. falciparum isolates exposed to dihydroartemisinin (DHA), the active form artemisinin, based on their transcriptional response measured at two time-points in red blood cell cultures. The genetic background information on the isolates will be provided to the participants. The genome-wide transcriptional profiles will come in the form of microarray data.

Developing a satisfactory solution to this complex prediction problem will require participants to make use of a mix of skills pertaining to various areas of the broad bioinformatics field: microarray data analysis, drug response (drug mechanism of action and drug resistance), pharmacogenomics, vector-host interactions, discrete modeling, machine learning, biostatistics and computer programming. Therefore, we seek to gather a few motivated participants originating from the H3ABioNet/H3Africa consortium for a five-day workshop.

Intended Audience: Participants should demonstrate confirmed expertise in one or several of the above-mentioned domains and that they will bring an added value in the data analysis process.

This workshop is clearly results-oriented, and training during the workshop will be limited to topic-specific sessions to implement efficient cross-talking between the different subgroups of expertise that will make up the group of workshop participants. It is NOT designed to be a training course. Participants are expected to benefit from learning to integrate skills from statistics, computing and biology to seeking solutions to biological problems in a collaborative manner and within a limited span of time. We anticipate that participants will work openly with each other and will therefore have the chance to learn from each other and develop critical thinking and may develop close collaborations and that the experiences on collaboration and scientific insights obtained will be published at a later date with participants as authors.

Application: All potential applicants must complete the application form (https://docs.google.com/forms/d/18bWGjgxc2KIx2cXj9WVkJIfzDxJ78iFQM-scJMeoEBQ/viewform?edit_requested=true) and email their 2 pages CV to Sumir Panji ( ) before 11th July 2016.  incomplete applications will NOT be reviewed. 
Successful applicants will be brought together to start group discussions prior to the workshop, to ensure that they familiarize themselves with the data at stake and with the collaborative work platform that will be used during the workshop, namely Sage Synapse. Pre-selected applicants might be invited by the organizing committee to take part in a Skype interview between the 25^th and the 28^th of July.

H3ABioNet will provide travel fellowships that cover travel and accommodation costs for selected participants. Once being successfully chosen for the workshop, participants 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.

Course Overview: The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. Our sister project at www.ensemblgenomes.org can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa.

Intended Audience: The workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users.

Keywords: Genetics, Genomics. Nucleic acids analysis

Skill level of training: Introductory

Language: English

Credential awarded:  course attendance certificate

Type of training: face-to-face / in person

Workshop dates: Monday 6^th June 2016

Venue: Health Teaching Labs 1-2, Basement of Anatomy Building, UCT Medical School, Anzio Rd, Observatory, Cape Town, South Africa

Workshop organisers and sponsors: Ben Moore, Nicola Mulder, CBIO@UCT

Workshop trainers and support: Ben Moore, CBIO@UCT

Prerequisites: Participants should complete the application form to attend the workshop. Participants should have a general knowledge of molecular biology / genomics and a familiarity with web browsers. As there is no workshop fees, participants must take care of their own catering needs.

Workshop format: Most modules consist of a presentation and demo, followed by an opportunity to complete exercises and explore Ensembl with assistance. Participants are encouraged to bring problems/questions about their research to try to tackle these during the workshop using Ensembl.

Note: Most examples and exercises in the workshop will be focused on human as this is by far the most richly annotated species. However, most of what is taught in the workshop can be applied to other species in the Ensembl browser (http://www.ensembl.org), as well as to the species in the Ensembl Genomes browser, that contains genomes of invertebrates, protists, plants, fungi and bacteria www.ensemblgenomes.org.

Syllabus: Morning

Objectives:

Training Materials Availability:

Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: http://training.ensembl.org/events/2016/2016-06-07-Cape_Town. Please note, these materials may be governed by different sharing/re-use policies, and you are encouraged to follow the policies of the external providers regarding material re-use and/or sharing.