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    Course
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    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.

    Keywords: Ensembl, Genomes, Genome Browser, Sequencing, Genomics

    Skill level of training: Beginner

    Language: English

    Credential awarded: Certificate of Attendance

    Type of training: Online 

    Venue of workshop: online - Zoom link will be provided to those who are selected. 

    Dates for the workshop: 26 and 28 April 2021 (2 X half days from 9am - 1 pm CAT)

    Workshop organisers: Emily Perry (Trainer), Nicola Mulder, Darren Martin, Verena Ras 

    Registration opens:  15 April 2021 

    Registration closes: 21 April 2021

    Notification date: 23 April  (accepted participants)

    Link to application form: please click here

    Participation: People who will be using or are using the Ensembl genome browser for their research, or would like to learn more about how to use the Ensembl browser. Selection will be done via an application process.

    Workshop Sponsors: H3ABioNet and Ensembl 

    Intended Audience: Wet-lab researchers and bioinformaticians 

    Objectives: After this workshop participants should be able to:

    • view genomic regions and manipulate the view to add features they are interested in.
    • explore information about genes and their sequences, and gene data in bulk using BioMart.
    • analyse genomic variants and associated phenotypes and their own variation data using the VEP.
    • view homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.

    Syllabus and Tools:

    Day 1: Introduction to Ensembl and Ensembl genes. Viewing genes and locations in the browser. Variation and the VEP

    Day 2: Comparative Genomics - gene trees, homologues and whole genome alignments. Features that regulate gene expression. Data export with BioMart.

    Prerequisites: None

    Training material availability: Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: http://training.ensembl.org/events/upcoming/. 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.

    Feedback from previous courses: "There are probably quite few people out there who all assume that Ensembl today is the same as it was years ago. It is not. With many new features and datasets incorporated/interlinked, it offers data exploration like never before. This course was a very useful update on what Ensembl has become" Browser workshop, CRUK, April 2016

    "Very useful workshop, certainly one of the most informative and useful I have attended. Delivered by someone who was extremely familiar with the website and its capabilities, not someone who had used it a couple of times and proclaimed themselves to be an expert." Browser workshop, Cardiff, March 2014

    If you think you'd like to host a similar course at your institute, you can find out more on the Ensembl workshops page.

     

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    Course
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    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. 

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

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

    Language: English

    Skill level: Intermediate

    Type of training: Blended/hybrid learning

    Credential awarded: Letter of completion

    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 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

    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.

    Apply to Host a Classroom Here >

    		 HOST applications have now closed and hosts have been informed of the outcome

    Apply to be a Participant Here >

    Participants applications have closed

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19106780. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

    Click here to access the general course site

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    Course
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    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 ~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.

    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.

     

    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

    Module 2: Linux

    Module 3: Sequence Alignment

    Module 4: Multiple Sequence Alignment

    Module 5: Genomics

    Module 6: Phylogenetics (2018 - 2021)

    Module 6: Structural Biology (2016 only)

    Introduction Week

    Wrap Up week

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

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    Course
    Hits: 11069

    Course overview: EMBO Practical Course on Computational analysis of protein-protein interactions: From sequences to networks.

    Keywords: Systems biology, Protein structure, Protein-protein interactions, Networks

    Skill level of training: Intermediate

    Language: English

    Credential awarded:  No credential awarded

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

    Dates for the workshop: 28th September – 3rd October 2014

    Venue of workshop: UCT, Cape Town, South Africa

    Workshop organisers: H3ABioNet, University of Cape Town

    Trainers and support staff:  

    • Aidan Budd - Session 1: Introduction to bioinformatics, protein modules and sequence alignment [practicals and presentations]
    • Toby Gibson -  Session 1: Modular protein architecture and construction of cell regulatory systems [Keynote Lecture]
    • Nicola Mulder - Session 2: Web resources describing results of PPI experiments: design of such databases, minimal information to describe PPIs [practicals and presentations]
    • Nicola Mulder - Session 2 (continued): Web resources describing results of PPI experiments: design of such databases, minimal information to describe PPIs [practicals and presentations] 
    • Natasha Wood - Session 2: Modelling interactions of the HIV gp120 protein [presentation] 
    • Scooter Morris and Aidan Budd - Session 2b: Introduction to protein structure with Chimera [practicals and presentations] 
    • Miguel Andrade - Session 3: The freaks of protein sequence (I): Repeats [practicals and presentations] 
    • Lars Juhl Jensen: Medical data mining: linking diseases, drugs, and adverse reactions [Keynote Lecture] 
    • Marco Punta - Session 4: Protein families and domains, including repeats (PFAM, SMART, etc.) [practicals and presentations] 
    • Gustavo Galazar - Session 4: A web-based protein interaction network visualizer [presentation]
    • Zsuzsanna Dosztányi - Session 5: Biology and prediction of intrinsically unstructured peptide regions [practicals and presentations]
    • Holger Dinkel and Toby Gibson - Session 6: Linear motif biology, prediction, and cooperativity in cellular signalling [presentations and practicals]
    • Holger Dinkel and Toby Gibson - Session 6 (continued): Using Jalview & Multiple Sequence Alignments to investigate short linear motif biology [presentations and practicals] 
    • Holger Dinkel and Toby Gibson - Session 6 (continued): Automated access of online tools using REST interfaces [presentations and practicals]
    • John "Scooter" Morris - From networks to structures and back again [Keynote Lecture]: 
    • Lars Juhl Jensen - Session 7: STRING, networking, and PPIs [presentations and practicals]
    • John "Scooter" Morris and Nadezhda T. Doncheva - Session 8: Exploring PPI networks using Cytoscape [presentations and practicals] 

    Prerequisites: List of software installed on the Window’s laptops used by trainees

    Logistics information: A list of the information we provide concerning logistics for the course (access restricted)

    Workshop Program:

    SUNDAY 28TH SEPTEMBER

    		  

    Participant arrival and check in at hotel
     

    20.00-21.00

    Dinner: Little Scotia guest house

    MONDAY 29TH SEPTEMBER

    09.00-09.15

    Introduction to the course: Organisers
     

    09.15-10.00

    1:1 Introduction round: all participants
     

    10.00-10.30

    Session 1: Introduction to bioinformatics, protein modules and sequence alignment [practicals and presentations]: Aidan Budd
     

    10.30-11.00

    Coffee break
     

    11.00-12.00

    Session 1 (continued): Introduction to bioinformatics, protein modules and sequence alignment [practicals and presentations]: Aidan Budd
     

    12.00-13.00

    Lunch
     

    13.00-14.00

    Modular protein architecture and construction of cell regulatory systems [Keynote Lecture]: Toby Gibson
     

    14.00-15.30

    Session 2: Web resources describing results of PPI experiments: design of such databases, minimal information to describe PPIs [practicals and presentations]: Nicola Mulder
     

    15.30-16.00

    Coffee break
     

    16.00-17.00

    Session 2 (continued): Web resources describing results of PPI experiments: design of such databases, minimal information to describe PPIs [practicals and presentations]: Nicola Mulder
     

    17.00-17.30

    Modelling interactions of the HIV gp120 protein [presentation]: Natasha Wood
     

    17.30-18.30

    Free practical session: trainees working with their own data
     

    18.30

    Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia
     

    19.00-21.00

    Dinner: Little Scotia guest house

    TUESDAY 30TH SEPTEMBER

    09.00-10.00

    Session 2b: Introduction to protein structure with Chimera [practicals and presentations]: Scooter Morris and Aidan Budd
         
     

    10.00-10.30

    Session 3: The freaks of protein sequence (I): Repeats [practicals and presentations]: Miguel Andrade
     

    10.30-11.00

    Coffee break
     

    11.00-12.00

    Session 3 (continued): The freaks of protein sequence (II): Biased regions [practicals and presentations]: Miguel Andrade
     

    12.00-13.00

    Lunch
     

    13.00-14.00

    Medical data mining: linking diseases, drugs, and adverse reactions [Keynote Lecture]: Lars Juhl Jensen
     

    14.00-15.30

    Session 4: Protein families and domains, including repeats (PFAM, SMART, etc.) [practicals and presentations]: Marco Punta
     

    15.30-16.00

    Coffee break
     

    16.00-17.00

    Session 4 (continued): Protein families and domains, including repeats (PFAM, SMART, etc.) [practicals and presentations]: Marco Punta
     

    17.00-17.30

    A web-based protein interaction network visualizer [presentation]: Gustavo Galazar
     

    17.30-19.00

    DAS Game: all participants lead by Gustavo Salazar and Natasha Wood
     

    19.00

    Shuttle pickup from UCT/Bernard Fuller Building to Down South Restaurant, Rondebosch
     

    19.30-21.00

    Dinner: Down South Restaurant, Rondebosch (including one glass of wine each)

    WEDNESDAY 1ST OCTOBER

    09.00-10.30

    Session 5: Biology and prediction of intrinsically unstructured peptide regions [practicals and presentations]: Zsuzsanna Dosztányi
     

    10.30-11.00

    Coffee break
     

    11.00-12.30

    Session 5 (continued): Biology and prediction of intrinsically unstructured peptide regions [practicals and presentations]: Zsuzsanna Dosztányi
     

    12.30-15.00

    Lunch AND poster session
     

    15.00-16.00

    Session 6: Linear motif biology, prediction, and cooperativity in cellular signalling [presentations and practicals]: Holger Dinkel and Toby Gibson
     

    16.00-16.30

    Coffee break
     

    16.30-17.30

    Session 6 (continued): Linear motif biology, prediction, and cooperativity in cellular signalling [presentations and practicals]: Holger Dinkel and Toby Gibson
     

    17.30-18.30

    Dinner: Pizzas ordered into the venue i.e. UCT Health Science Campus (including wine)
     

    18.30-21.00

    Networking event (Cape Unseminar in Bioinformatics): all course participants and local bioinformaticians
     

    21.15

    Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia

    THURSDAY 2ND OCTOBER

    09.00-10.30

    Session 6 (continued): Using Jalview & Multiple Sequence Alignments to investigate short linear motif biology [presentations and practicals]: Holger Dinkel and Toby Gibson
     

    10.30-11.00

    Coffee break
     

    11.00-12.00

    Session 6 (continued): Automated access of online tools using REST interfaces [presentations and practicals]: Holger Dinkel and Toby Gibson
     

    12.00-13.00

    Lunch
     

    13.00-14.00

    From networks to structures and back again [Keynote Lecture]: John "Scooter" Morris
     

    14.00-15.30

    Session 7: STRING, networking, and PPIs [presentations and practicals]: Lars Juhl Jensen
     

    15.30-16.00

    Coffee break
     

    16.00-17.30

    Session 7 (continued): STRING, networking, and PPIs [presentations and practicals]: Lars Juhl Jensen
     

    17.45

    Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia
     

    18.45

    Shuttle pickup from Little Scotia to Bihari Restaurant, Newlands
     

    19.00-21.00

    Gala Dinner: Bihari Restaurant, Newlands (including a glass of wine)
     

    21.15

    Shuttle pickup from Bihari Restaurant to Little Scotia

    FRIDAY 3RD OCTOBER

    09.00-10.30

    Session 8: Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva
     

    10.30-11.00

    Coffee break
     

    11.00-12.30

    Session 8 (continued): Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva
     

    12.30-14.00

    Lunch
     

    14.00-15.30

    Session 8 (continued):Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva
     

    15.30-16.00

    Coffee break
     

    16.00-17.00

    Session 8 (continued): Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva
     

    17.00-17.30

    Wrap up and final Q and A session: all participants
     

    17.45

    Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia
     

    18.15-20.00

    Dinner: Little Scotia guest house

    SATURDAY 4TH OCTOBER

    		  

    Participant departure and check out of hotel

     

    Training Materials Availability:

    Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19106720. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

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