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.

     



    Dates and location:  22nd August to 26th August 2016, University of Pretoria, South Africa

    Workshop organisers: Scott Hazelhurst, Fourie Joubert, Sumir Panji and Nicola Mulder Workshop sponsors: H3ABioNet

    Workshop overview: One of H3ABioNet’s deliverables is to investigate the use of Cloud computing for H3Africa data analysis. It was recently agreed that important pipelines should be made available as Docker containers that can be deployed on public or private clouds. The Wits’ Node has made a start by “containerizing” the Wits GWAS pipeline, and a Cloud Computing Task Force has recently been established in H3ABioNet to examine and implement the use of cloud based technologies for bioinformatics pipelines relevant to H3Africa researchers. In order to further the work of this task force we will be holding a Cloud computing hackathon.

    Workshop objectives:

    • To bring together H3ABioNet staff and students who have some working knowledge of Cloud computing and enable them to interact with international partners with experience in  Docker pipelines
    • To assess existing Docker containers for relevant pipelines
    • To develop Docker containers for specific pipelines of relevance to H3Africa
    • To work on interoperability between containers and portability
    • To document the pipelines and make them available from the H3ABioNet website and/or GitHub
    • To document the available public and private clouds with the appropriate infrastructure for these pipelines to be run on

    Target audience/participants:   

    • H3ABioNet staff and students with working knowledge of Cloud computing and developing containers
    • International collaborators with expertise in developing Docker containers

    Prerequisites and selection:

    The selection will be partly through an open call for applications and part invitation. As this will be a working meeting, participants are expected to have good programming ability (Python is likely to be the working language) and some knowledge of some of the following areas bioinformatics, cloud computing, Docker, pipeline construction (we don’t expect everyone to know everything and will have multi-skilled teams).

    Once applicants have been selected, they will be required to assist with the technical preparatory phase of the hackathon that will include but is not limited to:

    • Analysis of existing cloud based containers/pipelines of relevance to H3ABioNet, e.g.DNAnexus, Clovr, GVL (Genomics Virtual Laboratory), NGS-logistics, UCSC microbiome pipeline, Global Alliance
    • Documentation of existing public and private clouds and their operating systems and costs
    • Attend scheduled online meetings prior to the hackathon for preliminary work
    • Continue working on outstanding Cloud tasks once they return to their home Institutions

    The application form is available at: http://goo.gl/forms/Q5Om2HB4dxY1F3zA3

    Application deadline: 30th June 2016.

    Workshop draft outline:

    Participants will choose (or be assigned to) various streams depending on their skills, interests and to ensure each stream has sufficient participants.

    Proposed streams for the H3ABioNet cloud hackathon
    Stream A Stream B Stream C Stream D

    Illumina genotype chip QC, genotype and SNP calling

    Imputation and phasing

    Population structure, association testing and visualization

    Metagenomics

     

    Time Topic Trainer
    22nd August 2016
    9:00 am Registration, introductions by participants and discussion on the objectives and desired outcomes for the week All participants
    9:30 am

    Report and overview from task force on existing clouds available

    TBD
    10:00 am

    Report back on overview of technologies to be used for Stream A – what is out there and what should be created

    TBD
    10:30 am Tea break  
    11:00 am Report back on overview of technologies to be used for Stream B – what is out there and what should be created TBD
    11:30 am Report back on overview of technologies to be used for Stream C – what is out there and what should be created TBD
    12:00 pm Report back on overview of technologies to be used for Stream D – what is out there and what should be created TBD
    12:30 pm Lunch  
    1:30 pm Discussion of resources and working practices to be used e.g Git, server access, tools, pipeline All participants
    2:00 pm Breakout into Streams and formulate work plan with priorities for each group All participants
    3:30 pm Tea Break  
    4:00 pm Invited talk TBD
    5:00 pm Workshop End  
    23rd August 2016
    9:00 am Report back on work plan and objectives for the day – Stream A TBD
    9:20 am

    Report back on work plan and objectives for the day – Stream B

    TBD
    9:40 am

    Report back on work plan and objectives for the day – Stream C

    TBD
    10:00 am

    Report back on work plan and objectives for the day – Stream D

    TBD
    10:30 am Tea break  
    11:00 am Streams break out to implement work plan All participants
    1:00 pm Lunch  
    2:00 pm Streams break out to implement work plan All participants
    3:30 pm Tea Break  
    4:00 pm Invited talk TBD
    5:30 pm Workshop End  
    24th August 2016
    9:00 am Report back on previous day’s accomplishments and work plan for the day – Stream A TBD
    9:20 am

    Report back on previous day’s accomplishments and work plan for the day – Stream B

    TBD
    9:40 am

    Report back on previous day’s accomplishments and work plan for the day – Stream C

    TBD
    10:00 am

    Report back on previous day’s accomplishments and work plan for the day – Stream D

    TBD
    10:30 am Tea break  
    11:00 am Streams break out to implement day work plan All participants
    1:00 pm Lunch  
    2:00 pm Streams break out to implement day work plan All participants
    3:30 pm Tea break TBD
    4:00 pm Invited talk TBD
    5:30 pm Workshop End  
    25th August 2016
    9:00 am Report back on previous day’s accomplishments and work plan for the day – Stream A TBD
    9:20 am Report back on previous day’s accomplishments and work plan for the day – Stream B TBD
    9:40 am

    Report back on previous day’s accomplishments and work plan for the day – Stream C

    TBD
    10:00 am

    Report back on previous day’s accomplishments and work plan for the day – Stream D

    TBD
    10:30 am Tea break  
    11:00 am Streams break out to implement day work plan All participants
    1:00 pm Lunch  
    2:00 pm Streams break out to implement day work plan All participants
    3:30 pm Tea break  
    4:00 pm Invited talk TBD
    5:30 pm Workshop End  
    26th August 2016
    9:00 am Streams break out to implement day work plan All participants
    10:30 am Tea break  
    11:00 am Streams break out to implement day work plan All participants
    1:00 pm Lunch  
    2:00 pm Streams start wrapping up on tasks and creating plan for continued work on unfinished tasks All participants
    3:30 pm Tea break  
    4:00 pm Report on progress and plan for continued work – Stream A TBD
    4:20 pm Report on progress and plan for continued work – Stream B TBD
    4:40 pm Report on progress and plan for continued work – Stream C TBD
    5:00 pm Report on progress and plan for continued work – Stream D TBD
    5:30 pm Workshop End  

    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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