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.

     



     

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

    Dates for the workshop:  14th May – 17th May 2019 *(13th 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: 27th 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 5th 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.

     


    Capillary Electrophoresis (i.e. Sanger Sequencing) Training Workshop, Durban, South Africa, 24-25 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.

     


    H3ABioNet Microbiome & Precision Medicine Portals Design Hackathon

     

    Venue of hackathon: Institut Pasteur de Tunis, Tunis, Tunisia

    Dates for the hackathon: 12th April to 18th April, 2019 

    Hackathon organisers: Kais Ghedira, Faisal Fadlelmola, Souiai Oussama, Samar Kassim, Scott Hazelhurst, Sumir Panji, Nicola Mulder

    Application opens: 18th February, 2019

    Application closes: 25th February 2019

    Notification date: 2nd March, 2019

    Link to application form: https://redcap.h3abionet.org/redcap/surveys/?s=JX9X3MFP3Y

    Participation: Open application for H3ABioNet and H3Africa consortium members who have an element of precision medicine or microbiome in their projects objectives and are able to contribute to the outcomes of the hackathon.

    Hackathon Sponsors: H3ABioNet and Institut Pasteur de Tunis H3ABioNet Node

    Hackathon Overview: This Hackathon aims to develop two H3ABioNet Databases and Resources Work Package Portals:

    1. African Precision Medicine Portal (APMP) - a web based portal to collate and curate pharmacogenomics and other genomic medicine metadata specific to African populations, as well as links to existing precision medicine implementation tools and resources in order to support precision medicine initiatives within Africa.
    2. African Microbiome Portal (AMP) - a web based portal to collate, curate and provide primary references for African specific microbiome metadata and resources for African based microbiome research.

    The hackathon participants will be divided into three streams: Stream A for the African Precision Medicine web portal development, Stream B for the African Microbiome web portal development and Stream C for testing the portals. An additional team for writing and drafting a manuscript about the hackathon will also be formed. Stream A and B will consist of technical programming members as well as portal content experts. Stream C consists local undergraduate students who should be recruited from IPT for testing the two portals.

    The Hackathon will consist of a series of introduction and background talks to the objectives of both portals during the first day and portals design and development breakout group sessions during 2nd- 5th days of the hackathon.

    Intended Audience: This hackathon is aimed at H3ABioNet project members who will be involved in the development of the H3ABioNet portals. 

    Prerequisites: Participants will be are encouraged to work through the following resources to enable them to gain the most from the Hackathon:

    1. SQL querying language
    2. HTML5, PHP, CSS
    3. Bioschemas: http://bioschemas.org/
    4. https://en.wikibooks.org/wiki/Data_Management_in_Bioinformatics

    Please note: Successful applicants will be required to attend a series of online planning meetings before the hackathon commences and post-hackathon meetings.

    Registration: All potential applicants must complete the application form and upload a motivation letter from their supervisor. Incomplete applications will NOT be reviewed. The successful applicants will be contacted to complete an airline ticket booking form (where applicable), a short biosketch with a recent picture and abide by the H3ABioNet workshop policy. 

    Costing: H3ABioNet will cover the costs of a return economy air ticket to Tunisia, accommodation from the night of the 11th of April till the night of the 18th of April, 2019 and lunch meals from the 12th of April till the 18th of April 2019. H3ABioNet will not cover the costs of dinners,  visa fees or airport transfers from your local area. 

    Please note, if a participant is unable to attend this hackathon after acceptance, their place will be passed on to applicants on the waiting list and not to other recommended members from their H3Africa programme.

    A programme will be available shortly.

     


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