Log in

    Training
    Hits: 3589

     

    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.

     

    ,

    Training
    Hits: 1453

    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.

     

    ,

    Training
    Hits: 1090

    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.

     

    ,

    Training
    Hits: 737

    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.

    ,

    Training
    Hits: 1681

     Introduction to Bioinformatics Training

    H3ABioNet‘s Introduction to Bioinformatics course (IBT) provides an introduction to the field of bioinformatics, with a focus on important bioinformatic tools and resources.

    Over a period of 3 months of intensive biweekly contact sessions, the course combines theoretical and practical sessions to allow participants to gain practical experience in using various tools and resources. During contact sessions, classrooms meet virtually to discuss the session’s content with each other and the trainer.

     

    In 2018 IBT was hosted in 29 classrooms across 13 African countries. The map below shows the distribution of classrooms.

    IBT map of classrooms in 2018

     

     Interested in hosting an IBT classroom at your institution? contact  

     

    Why?

    A number of H3Africa members expressed an interest in and need for basic Bioinformatics training for individuals entering the discipline, or for those who need a basic foundational understanding of Bioinformatics before moving on to more complex areas. A task force, from the H3ABioNet Education and Training Working Group, has therefore developed an Introduction to Bioinformatics course in order to meet this need.

     

    Who?

     

    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 basic Bioinformatics users. A base line level of the understanding of the central dogma of molecular biology (i.e. DNA to RNA to Protein) is a requirement.

     

    How?

    Course logistics

    A distance-based learning model is used for this course. Classrooms are set up at different sites (which meet certain infrastructure requirements) and link to the trainer via the Adobe conferencing system during biweekly contact sessions. 

    To ensure that internet instability is not a barrier to education, lectures are pre-recorded, downloaded, and watched locally in classrooms.

    There are appropriately trained local teaching assistants at each of the sites to assist with the practical components of the course, which run using online tools as far as possible.

    There is no application or participation fee. Local sites provide the physical resources for the course and the course core team provides logistic and course management support via the Vula platform.

     

    What?

     

    Course objectives

    By the end of the course participants should be able to:
    • Explain the use of Bioinformatics
    • Name 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

     

    Course modules

    Databases and Resources

    • Biological databases and resources (NCBI, EBI)
    • Advanced literature searching – PubMed
    • DNA analysis – e.g. sequence features, start site, restriction sites etc
    • Protein function classification

    Linux

    • Introduction to Linux, UNIX and the command line
    • Manipulating files – useful commands and tips
    • Permissions, groups, and process control

    Sequence Alignment

    • Introduction to searching and sequence alignment
    • Pairwise sequence alignment
    • BLAST algorithm

    Multiple Sequence Alignment

    • Applications of multiple sequence alignment
    • Choosing the right sequences with the right software

    Genomics

    • Genome sequences – sequencing technology and brief NGS overview
    • Genome browsers and annotation
    • Comparative Genomics
    • Human variation

    Molecular Evolution and Phylogenetics

    • Historical perspective, mechanisms of molecular evolution, and speciation.
    • Traits, phylogenies, evolutionary models and divergence times.
    • Tree building with distance matrix methods. Parsimony approaches.
    • Tree building with maximum likelihood approaches. Bayesian viewpoint. Branch support measures.

     

    Additional elements of the course:

    Staff Training

    Introduction Week

    Wrap up Session

    Bonus Module – Gene Expression

    1. African Genomic Medicine Training Initiative (AGMT)
    2. H3ABioNet Cloud computing hackathon
    3. GOBLET Bioinformatics Training Best Practices Workshop
    4. Introduction to Genome-Wide Association Studies (GWAS) for complex diseases

    Subcategories

    Page 1 of 4

    H3ABioNet is funded by NIH Common Fund Award / NHGRI Grant Number U41HG006941
    NHGRI-logo_footer.png
    NIH-logo_footer.png
    h3africa-_partner.png
    Contact Us
    Follow us
    © 2017 H3ABioNet.org
    The H3ABionet website content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Health
    Image
    © University of Cape Town 2017. All rights reserved.