Tutorials & Workshops

ISCB-Africa ASBCB Conference 2021 is pleased to offer the following five tutorials and workshops. Registration to the tutorials and workshops is complimentary with conference registration; due to limited capacities conference registration is required.

June 7, 2021 Morning Tutorials and Workshops

Infectious Diseases Genomics Workshop (RNA seq data analysis in Linux)

Malaria vector control is currently dependent on a single class of insecticides. Pyrethroids are the most widely used and are the main class recommended by WHO. RNA seq has been rapidly adopted for the profiling of transcriptomes in many areas of biology. In this workshop, we will sketch RNA seq analysis of datasets conferring the metabolic resistance to pyrethroids in the mosquito Anopheles funestus, a major malaria vector in Africa.

Lead Trainer:
Lambert Nzungize, PhD, Center for Research in Infectious Diseases, CRID-Cameroun; Synbio_Rwanda

Workshop maximum capacity: TBD

Requirements:
A fast and reliable laptop with Linux OS (dual boot):
Dell XPS 15 9500 15.6 inch UHD+ Touchscreen Laptop
Intel Core i7-10750H 10th Gen, 16 GB DDR4 RAM, 1 TB SSD,
Nvidia GTX 1650 Ti with 4 GB GDDR6

Learning Adventures on Bioinformatics Data Investigations

There is a continuous need for researchers who can successfully conduct bioinformatics data investigations for innovative solutions to societal challenges in food, health, energy and environment.

 Upon the completion of the workshop, participants will be able to:

  1. Identify bioinformatics research categories.
  2. Explain the stages of bioinformatics data investigation.
  3. Conduct a bioinformatics data investigation.
  4. Identify strategies for designing and delivering learning adventures.

The 2.5 hours workshop is for individuals interested in teaching, learning or conducting bioinformatics data investigations. Participant prizes during the adventures include career development sessions including cover letter and resume reviews for global bioinformatics positions.

Tutorial Presenters:
Raphael D. Isokpehi, Center for Trans-Disciplinary Data Analytics, Bethune-Cookman University, USA; H3ABioNet University of Ibadan Bioinformatics Group Node, University of Ibadan, Nigeria
Angela Makolo, H3ABioNet University of Ibadan Bioinformatics Group Node, University of Ibadan, Nigeria Bukola Smile, H3ABioNet University of Ibadan Bioinformatics Group Node, University of Ibadan, Nigeria
Junell McCall, Center for Trans-Disciplinary Data Analytics, Bethune-Cookman University, USA

Workshop maximum capacity: TBD

June 7, 2021 Afternoon Tutorials and Workshops

An introduction to biomedical text mining in the era of deep learning

This tutorial aims to familiarize the audience with an introduction to text mining the biomedical literature using deep learning methods. The tutorial will address questions such as “What is biomedical text mining?”, “What is deep learning?”, “How can deep learning be applied to address biomedical text mining problems?”, and “What biomedical text mining tools are currently available?”. The tutorial will cover the basics of biomedical text mining and deep learning. The latest deep learning methods in biomedical text mining will also be explained and discussed. Also, the audience will have the opportunity to learn common biomedical datasets and open challenge tasks which have been developed for over a decade by the community. After attending the tutorial, the participants are expected to:

  • Understand the basics of biomedical text mining pipeline
  • Understand the basics of deep learning in biomedical text mining applications
  • Familiar with current biomedical text mining tools and servers
  • Familiar with current biomedical datasets and challenge tasks

Tutorial Presenters:
Qingyu Chen, National Library of Medicine, National Institutes of Health
Robert Leaman, National Library of Medicine, National Institutes of Health
Cecilia Arighi, Delaware Biotechnology Institute, University of Delaware
Zhiyong Lu, National Library of Medicine, National Institutes of Health

Workshop maximum capacity: 60

Tools for reproducible research in Bioinformatics

The reproducibility of bioinformatics analysis is a major challenge in OMICS research. Overlooking this aspect may jeopardize research projects at different levels including the collaboration stream, interpretability of data, reliability, and many others. Operating computational studies within a reproducible framework is a critical ability for bioinformaticians. The proposed workshop aims to increase awareness about the importance of reproducibility within the community of African researchers by providing theoretical knowledge and practical training to the participants. Ultimately, we are seeking to establish the reproducibility mindset as a collection of innate practices, set to be deployed explicitly or implicitly in the research environment.

Tutorial Presenters:
Houcemeddine Othman, Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
Jorge da Rocha, Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
Phelelani Mpangase, Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
Scott Hazelhurst, Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.

Workshop maximum capacity: TBD

June 9, 2021 Tutorials and Workshops

From idea to a brilliant company - ways to build academic commercialization programs, create startups, validate market and bring innovation to society

There is much innovation happening in the academia around the world but very few institutions understand how to build successful companies and help get that innovation into the marketplace. This workshop will analyze best cases for academic innovation program based on the University of Pennsylvania UPstart program. However, it is not enough to just start a company, it is important to validate that the product or services are indeed needed in the market. Pretotyping is a new market validation approach, and this workshop will introduce a concept of Pretotyping to anyone interested in building a successful company.

Lead Trainer:
Karina Sotnik, WorldUpstart

Workshop maximum capacity: TBD

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