Tools and Services
Resources
Communication
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:
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.
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:
Syllabus and Tools (TBC):
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.
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
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
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
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.
The course curriculum will cover the following main themes (subject to slight changes):
**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:
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
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:
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.
Page 2 of 2
Tools and Services
Resources
Communication