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.

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.

This hands-on course is a 2-day intensive overview of Fragment Analysis (i.e. Microsatellite). 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.

DNA Sequencing Fragment Analysis (i.e Microsatellite) Workshop, Durban, South Africa, 28-29 March 2019

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

Dates for the workshop: 28 - 29 March 2019

Workshop organisers: Thermo Fisher and KRISP

Registration opens:  currently open

Registration closes: 28 February 2019

Link to application form: http://www.krisp.org.za/manuscripts/KRISPThermoFragment2019.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 Fragment Analysis (i.e. Microsatellite). 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.