Course Overview: The Research Data Management (RDM) short course introduces the principles and practices of RDM and practical advice for implementing these practices in African research context. Topics covered include data discovery and re-use, data documentation and organization, data standards and Ontology, data storage and security, repositories and policies, FAIR & reproducibility and best practices in developing an effective DMP.

    Intended Audience: The course is aimed at the graduate students and biomedical scientists who are currently working on clinical, genomics and bioinformatics projects in Africa.

    Logistics 

    Venue of course: Online through Zoom.

    Dates for the course: 27-30 June 2022; from 10:00 CAT to 14:00 CAT.

    Course organizers: Faisal Fadlelmola, Katherine Johnston, Verena Ras, Melek Chaouch, Lyndon Zass, Ziyaad Parker, Ayton Meintjes, Sumir Panji and Nicola Mulder

    Participation: The course is available to any participant who is able to attend the Zoom sessions and the interactive hours with the course instructors for the days of the course.

    Course Sponsors: H3ABioNet

    Participant applications

    Registration for participants opens:  4th April 2022

    Registration for participants closes: 24th April 2022

    Notification date for successful Applicants: 6th  June 2022

    Link to participant application form: Click here

     

    Course Curriculum:

    Module 1: Data & research life cycle

    Module 2: Curation, data types and privacy issues

    Module 3: Standards, taxonomy & Ontology

    Module 4: Preservation, repositories, security and policies

    Module 5: FAIR & Reproducibility

    Module 6: Data Management Plan (DMP)

     

    Course Schedule:

    Date

    Session 1

    10:00-11:00am CAT

    Session 2

    11:00-12:00am CAT  

    Session 3  

    12:00-1:00pm CAT

    Interactive hour with Instructor/s 

    (1:00-2:00PM CAT)

    Monday

    27 June 2022

    Module1: Lecture

    Module 2: L1

    Module 2: L2

    Faisal; Katherine & Verena

    Tuesday 28 June 2022

    Module 3: Lecture

    Module 4: L1

    Module 4: L2

    Lyndon & Verena;  Ayton and Ziyaad

    Wednesday  

    29 June 2022

    Module 5: Lecture

    Module 5: FAIR Tutorial

     

    Melek & Ziyaad

    Thursday  

    30 June 2022

    Module 6: Lecture

    Module 6: DMP Tutorial - Group A

    Module 6: DMP Tutorial - Group B

    Faisal; Ayton

     

    Prerequisites: A basic background/understanding of biochemistry, molecular biology and/or genetics. Those with a computer science background with experience in bioinformatics are welcome to apply.

    Objectives: After this RDM short course participants should be able to:

    1. Understand what research data management is;
    2. Recognize why research data management is necessary;
    3. Understand best practices and aspects for research data management; and
    4. Have knowledge of the RDM tools available at your institution and online.

    Course limitations: This course will only provide a foundation for continued learning in research data management and will not teach any advanced RDM aspects.


    Course Overview: he Research Data Management (RDM) short course introduces the principles and practices of RDM and practical advice for implementing these practices in African research context. Topics covered include data discovery and re-use, data documentation and organization, data standards and Ontology, data storage and security, repositories and policies, FAIR & reproducibility and best practices in developing an effective DMP.

    Course Overview/description:

    Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover an introduction to The Shell, Python and R. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

    Keywords: Carpentries, programming, coding, novice, R, Python, linux 

    Skill level of training: Beginner  

    Language: English

    Venue of workshop: Online via Zoom; link will be communicated to those who are accepted.

    Dates for the workshop: 14 - 18 March 2022 from ~10 am – 2:30 pm all days

    Registration opens:  02 March 2022 | Registration closes: 09 March 2022 | Notification date: 10 March 2022

    Link to application form: This is a closed workshop aimed at students and staff at the Faculty of Health Sciences at the University of Cape Town.

    Workshop trainers: Lyndon Zass, Ruth Nanjala, Verena Ras, Ichrak Benamri, Nihad Alsayed, Melek Chaouch, Ziyaad Parker, Mamana Mbiyavanga 

    Workshop organisers: H3ABioNet, Verena Ras, Lyndon Zass, Nicola Martin, Darren Martin

    Workshop Sponsors: H3ABioNet

    Intended Audience: UCT Computational Biology Honour’s cohort + anyone else from within UCT Health Sciences who may be interested

    Syllabus and Tools: please see workshop website: https://verena90.github.io/2022-03-14-online-UCT_Med/

    Prerequisites: As this is presented at a novice level, no prerequisites are required but you will need to have access to a laptop where you are able to install the required software (R, Python, shell terminal). You will also need good internet access to ensure you are able to be online for the full course.

    Workshop limitations: This workshop will only provide a foundation in Linux, R and Python but will not teach any advanced coding or programming. Should this be what you require, this may not be the appropriate course for you.

     

    Training Materials Availability:

    Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: https://verena90.github.io/2022-03-14-online-UCT_Med/. 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.


     

    Course Overview/Description: There will be two courses offered by the BioConductor community:

     

    Introduction to Bioconductor Annotation Resources (Thursday, 29th April 2021 @ 8am EDT/12noon GMT/1pm WAT/ 2pm CAT/3pm EAT to 11am EDT/3pm GMT/ 4pm WAT/5pm CAT/6pm EAT) (https://jmacdon.github.io/Bioc2020Anno/#introduction-to-bioconductor-annotation-resources)

     

    There are various annotation packages provided by the Bioconductor project that can be used to incorporate additional information to results from high-throughput experiments. This can be as simple as mapping Ensembl IDs to corresponding HUGO gene symbols, to much more complex queries involving multiple data sources. In this workshop, we will cover the various classes of annotation packages, what they contain, and how to use them efficiently.

     

    Epidemiology for Bioinformaticians (Friday, 30th April 2021 – 8am EDT/12noon GMT/1pm WAT/ 2pm CAT/3pm EAT to 11am EDT/3pm GMT/ 4pm WAT/5pm CAT/6pm EAT ) (https://chloemirzayi.com/EpiForBioWorkshop2020/#epidemiology-for-bioinformaticians) Concepts of causal inference in epidemiology have important ramifications for studies across bioinformatics and other fields of health research. In this workshop, we introduce basic concepts of epidemiology, study design, and causal inference for bioinformaticians. Emphasis is placed on addressing bias and confounding as common threats to assessing a causal pathway in a variety of study design types and when using common forms of analyses such as GWAS and survival analysis. Workshop participants will have the opportunity to create their structural causal models (DAGs) and use this model to determine how to assess an estimated causal effect. Examples using DESeq2, edgeR, and limma will be used to show how multivariable models can be fitted depending on the hypothesized causal relationship.

     

    Presented successfully at BioC2019 to 30 people, updates that material by adding a brief demonstration of ggdag, revised conceptual emphasis based on participant feedback, and applied examples using data from curated metagenomic data.

     

    The introduction to hands-on Bioconductor workshop is a virtual two-half-day training to provide an overview of leveraging open-source Bioconductor resources for research studies. The course tools and packages relevant for this course will be hosted on Orchestra, an online platform for teaching and learning hands-on computational skills in self-contained and launchable workshop environments.

     

    The proposed courses will lay a foundation on how to efficiently use open-source Bioconductor resources for bioinformatics analysis. The course will be in two main forms which include;

    • lectures to introduce basic concepts
    • demonstrations and hands-on computer practicals on analysis pipeline/workflows for mapping identifiers, querying multiple data sources, performing epidemiological causal inference, and visualizing results in high-resolution publication format.

     

    The hands-on sessions may provide an opportunity for participants to work with their data. Instructors for the course have experience in developing and applying methods for research analysis and also involved in developing statistical methods/algorithms and Bioconductor packages

    You may now register for the upcoming virtual introduction to hands-on Bioconductor Workshop organized in collaboration with H3Africa, H3ABioNet, and the Bioconductor Community happening from 29-30 April  2021.

    This workshop/course is FREE to register and attend and promises to be interesting and beneficial.

    Refer to the attached document for more details and additional information on the workshop.

    Follow link to registerhttps://htraindb.h3abionet.org/node/2935

    Registration closes: 22nd April 2021

     

     

     


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