Course Overview: Various data intensive initiatives are taking place in South Africa that will involve in the storing and describing of genomics data in various platforms. The utility of data for research and reuse is how well structured and described the data and meta-data records are as this contributes towards making data FAIR.

Bioschemas (https://bioschemas.org/) aims to improve data findability and interoperability in life sciences. It does this by encouraging people in life science to use schema.org markup, so that their websites and services contain consistently structured information. This structured information then makes it easier to discover, collate and analyse distributed data. The main outcome of Bioschemas is a collection of specifications that provide guidelines to facilitate a more consistent adoption of schema.org markup within the life sciences. 

The course will consist of two parts, an introduction and overview of Bioschemas, current implementation cases and a second part where participants with a technical computing background and access to their repository can work on implementing bioschemas and bioschema type forms on their websites for data deposit.

Intended Audience: People who work with the various data management initiatives and platforms in South Africa and would like to learn more about Bioschemas, and would like to incorporate Bioschemas when provisioning their services.

Keywords: data handling, ontologies, bioschemas, data management

Language: English

Skill level: Intermediate

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

Credential awarded: none

Venue of workshop: Health Teaching Labs 3 – 5, Basement of Anatomy Building, UCT Health Sciences Faculty.

Dates for the workshop: 13^th May 2019 

Workshop organisers: Niall Beard, Paballo Chauke, Sumir Panji, Nicola Mulder

Participation: By invitation only 

Registration opens: 2^nd May 2019 

Registration closes: 6^th of May 2019 (6:00pm) 

Notification date: 7^th of May 2019

Link to application form: https://is.gd/bioschemas_2019

Workshop Sponsors: Bioschemas, Elixir and H3ABioNet

Syllabus and Tools: The workshop will provide an overview of Bioschema.org, its approach and its principles. Focus will be on practical hands-on sessions where developers learn how to annotate their resources using BioSchemas.org specifications. 

Prerequisites: Some basic knowledge of research data management with a focus on genomics data. For the technical part of the workshop having knowledge of the data store one is working with and the ability to edit websites and pages on their data stores. Some background information can be accessed at: https://bioschemas.gitbook.io/training-portal/

Objectives: After this workshop participants should:

• Understand how schema.org works and the motivations for using it
• Know about Bioschemas
• Know what are relevant Bioschemas profiles for their type of resource(s)
• Have annotated (a selection of) their resources with Bioschemas
• Be able to independently continue the work at their institution to annotate all their resources

Workshop limitations: This workshop provides and overview and guidance on using and implementing Bioschemas.

Training Materials Availability:

Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: https://www.slideshare.net/NiallBeard/bioschemas-workshop. 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.

Venue of workshop: Face to face workshop/working meeting at the Tsogo Sun Hotel, in Newlands, Cape Town

Dates for the workshop:  14^th May – 17^th May 2019 *(13^th May 2019 - Bioschemas workshop at UCT) 

Workshop organisers:  Nicola Mulder, Verena Ras, Paballo Chauke, Shaun Aron, Sumir Panji, Kim Gurwitz, Cath Brooksbank, Niall Beard, Sarah Morgan, Celia van Gelder, Michelle Brazas, Teresa Attwood 

Registration opens: 27^th February 2019 

Registration Closes: 31 March 2019

Notification date for the Education Summit workshop: Selections will only be made if the number of registrations exceeds capacity as space is limited. Notification will be by 5^th April 2019.

Link to registration form:   https://is.gd/education_summit

Participation: The summit is open to Bioinformatics trainers and educators, interested in working together on the development of guidelines, materials and resources for trainers.

Workshop Sponsor: H3ABioNet, GOBLET, ELIXIR and ISCB Education Committee

Summit Overview:

The aim of the meeting is for bioinformatics trainers and educators to:

1. Refine bioinformatics competencies and develop guidelines for applying these to the development of a curriculum and vice versa.
2. Define guidelines and processes for curriculum accreditation/endorsement
3. Develop trainer support materials, including:
   1. Develop an online train-the-trainer course
   2. Develop guidelines for bioinformatics trainers
   3. Curation of training materials using bioschemas

Intended Audience: Bioinformatics Trainers and Educators

Tools: We will be using existing guidelines, reports, strategies and documents to assist us in developing new guidelines and resources.

Prerequisites:  Training and Education knowledge in the field of Bioinformatics broadly including competencies, curriculum, assessments and accreditation. 

Workshop limitations: This will be a working meeting where we hope to make substantial progress on the above objectives/ overview and come out with guidelines and materials. Where required there will be a few talks to introduce or provide context around the topics. If time is limited, we might have to continue developing the guidelines online after the workshop.

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: Wet-lab researchers and bioinformaticians

Keywords: Genetics, Genomics. Nucleic acids analysis

Language: English

Skill level: Beginner

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

Credential awarded: letter of participation

Venue of workshop: UCT Med-school, Anatomy Building, Health Teaching Lab 1 

Dates for the workshop: 20 May 2019 

Workshop organisers: Ben Moore, Nicola Mulder, Sumir Panji, Verena Ras 

Registration opens:  15 April 2019 

Registration closes: 12 May 2019 

Notification date: 16 May 2019  (accepted participants)

Link to application form: https://is.gd/ensembl 

Link to EBI page for additional information: https://www.ebi.ac.uk/training/events/2019/ensembl-browser-workshop-university-cape-town-20th-may-2019 

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 

 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:

Morning: Introduction to Ensembl and Ensembl genes. Viewing genes and locations in the browser. Data export with BioMart.

Afternoon: The afternoon sessions depend on the participants' interest. We can cover genetic variation, comparative genomics and gene regulation, depending on what you express an interest in when you register.

Prerequisites: None

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.

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/2019/2019-05-20-CapeTown. 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.

Capillary Electrophoresis (i.e. Sanger Sequencing) Training Workshop, Durban, South Africa, 25-26 March 2019

Venue of workshop: Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa

Dates for the workshop: 25-26 March 2019

Workshop organisers: Thermo Fisher and KRISP

Registration opens:  currently open

Registration closes: 25 February 2019

Link to application form: http://www.krisp.org.za/manuscripts/KRISPThermoSanger2019.doc

Please submit application forms to: 

Mrs Gugulethu Cynthia Mkhize 

Tel: +27 31 260 4198

Email:

Participation: Cost: ZAR 2,500 (Scholarships available to previously disadvantaged South African learners)

Course Overview: This class is designed for users of capillary electrophoresis (CE) technology. Attendees will benefit by having training in a class environment, hands-on lab practicals and interaction with fellow attendees and Life Technologies application scientists during lecture and discussion sessions. The instrument used during the training will be the 3500 series. 

Intended Audience: Training is open to University Post-Graduate Students & Technical Staff of Commercial and Academic laboratories.

Syllabus and Tools: This hands-on course is a 2-day intensive overview of DNA sequencing. Course topics include application workflow setup and optimization; an overview of instrument hardware, operation and maintenance; use of data collection software; preparation and running of samples and standards; analysis software tutorials, and troubleshooting discussions. Students will run, analyze and troubleshoot sequencing samples as well as fragment analysis samples. Applied Biosystems 3500 instruments will be used for lab practicals. 

Tuition includes laboratory reagents, consumables, course materials, breakfast, and lunch. Travel, hotel, and other incidental expenses relating to the training are the responsibility of the attendee.