As part of the Capacity Development, and Bioinformatics and Data Science themes, SynBio Africa will hold a 20-week virtual training of 42 participants in bioinformatics and data science from February to June 2022. On December 22nd, 2021, SynBio Africa requested applications for training in Bioinformatics and Data Science. SynBio Africa received more than 400 applications from Africa and across the world, and SynBio Africa will sponsor 42 participants. We are looking for funds to train those who were not selected. The training will provide a learning forum for researchers in bioinformatics and data science analysis of various “omics” data sets.
Key topics to be covered in the training include;
- Bioinformatics, biological databases, and genomic resources
- Genomics and next-generation sequencing (NGS) technologies
- Linux
- Statistics, and R and RStudio
- RNA and DNA sequence analysis
- Microbial community analysis
The training is sponsored by SynBio Africa. Participants are not required to pay any training fee.
The training will be conducted by a team of facilitators drawn from the SynBio Africa bioinformatics and data science experts who are affiliated with The Ohio State University (USA); Gulu University (Uganda), and Case Western Reserve University (USA)–Makerere University (Uganda).
Program
SynBio Africa Bioinformatics and Data Science Training Program (Cohort 1)
Week 1:
| 8 February 2022 | Training openingOpening Remarks | Geoffrey Otim |
| Welcome and Introduction· Introduce trainers· Introduction of participants· Participants expectations | All Trainers All ParticipantsGeoffrey Otim | |
| Bioinformatics and Data Science· Training mechanics· bioinformatics and data science· Information in Bioinformatics | Stephen OpiyoPeace Aber | |
| 10 February 2022 | Bioinformatics and Data Science· Bioinformatics databases· Searching data in bioinformatics databases· Introduction to Linux | Stephen OpiyoPeace Aber |
Weeks 2 and 3:
| 14 February to25 February 2022 | Introduction to R/RStudio and R syntax· The basic data structure in R: vectors· Data types in R: character, numeric, logical Beyond vectors: matrices, lists, and data frames· Manipulating data: subsetting, replacing, etc.· Basic descriptive statistics and base R graphs· “R 2.0” concepts with the tidyverse environment: the piping operator %>%, tibbles and dplyr, tidyr dataset reshapings (2 sessions)· ggplot2 for beautiful graphs | Stephen OpiyoPeace Aber |
Week 4:
| 1 March and3 March 2022 | Statistical methods for analyzing “Omics” and field data· ANOVA· Non-parametric tests· Regression and Correlations· PCA, PCOA, distance measure, AMOVA, PARMANOVA | Stephen OpiyoPeace Aber |
Weeks 5 and 6
| 8 March to17 March 2022 | RNASeq data analysis | |
| · Quality Control of NGS data | Stephen OpiyoPeace Aber | |
| · Introduction to RNASeq | ||
| · RNASeq Analysis |
Weeks 7 and 8
| 22 March to31 March 2022 | Genomics data analysis | |
| · Genome-Wide Association analysis | Stephen OpiyoPeace Aber | |
| · Genetic diversity analysis |
Weeks 9 and 10
| 5 April to14 April 2022 | Microbial community data analysis | |
| · Species-level identification of bacteria and fungus through common markers (ITS, 16S, 18S)· Databases for species-level identification· Within-sample and across-sample measures of diversity· A pipeline for metagenomics from NGS reads· Further processing with R through packages for microbiome data analysis and visualization | Stephen OpiyoPeace Aber | |
Week 10
| Closing of the training | ||
| 14 April 2022 | · Feedback /evaluation of the trainig· Closing of the training and distribution of Virtual Certificates | Participants Geoffrey Otim |
TRAINERS
is a Bioinformatics Research Scientist at The Ohio State University, USA; a Director of Bioinformatics and Data Science, Research and iGEM, and Innovation Hub at SynBio Africa; an Affiliated Scientist at Biosciences eastern and central Africa-ILRI, Nairobi, Kenya; a Data Scientist and a co-founder of Patira Data Science, USA; a Visiting Scientist at The University of Sacred Heart, Gulu, Uganda; and a Co-Founder and Chief Operating Officer at Umkele an African synthetic biology Innovation startup, registered in Seychelles, and the UK.
He obtained his Ph.D. in Bioinformatics from The University of Nebraska-Lincoln, USA, and Post-Doctoral training at the same University where he developed interests in Data Science and “omics”. His primary research interests lie in machine learning, multivariate statistics, bioinformatics, and data mining. And his training interest lies in the capacity building of African scientists, researchers, students, etc. in bioinformatics and data science, synthetics biology, artificial intelligence, and biotechnology. In the last seven years, he has been supervising, collaborating, and training students, fellows, post-docs, and scientists from eastern, central, and southern Africa.
He lectures, trains, and gives workshops in statistics, bioinformatics, metabolomics, proteomics, genomics, metagenomics, and data science. Dr. Opiyo has many years of experience in data mining, analytics, big data, and crowdsourcing analysis. He uses robust statistical, mathematical, and machine learning, artificial intelligence methods to assess, understand, and analyze data to discover knowledge from structured and unstructured data. In addition, he works as a consultant in private sectors both in developed and developing countries discovering knowledge from data and developing web-based user-friendly tools to solve problems using machine learning algorithms. He leads a team of data scientists, developers, geospatial analysts, and data analysts working in both developed and developing countries to develop predictive analytics tools using machine learning algorithms. Thus, he has all the necessary skills and experience to work with the SynBio Africa team to lead this training.
Additional information about Dr. Opiyo:
PubMed: https://pubmed.ncbi.nlm.nih.gov/?term=Stephen%20Opiyo&sort=date&ac=yes
Linkedin profile: https://www.linkedin.com/in/stephen-opiyo-9465ab2b
Google Scholar profile: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C36&q=Stephen+Obol+Opiyo&btnG=
Bioinformatic tools: http://bioinfolab.unl.edu/emlab/7tmr/index.php
Peace is a Lecturer at Gulu University and a Biostatistician/Bioinformatician heading the CHAIN data section at the Case Western Reserve University–Makerere University Research Collaboration in Kampala. She is also an instructor at the University of Sacred Heart Gulu where she teaches Business Intelligence at a post-graduate level. Over the last five years, she has been teaching students in statistics and artificial intelligence (machine learning) methods for health data analytics as well as bioinformatics. Her research involves discovering knowledge from biological data using bioinformatics tools and working with bioinformatics databases. Her current interest focuses on the application of biostatistics, bioinformatics, and artificial intelligence methods in synthetic biology. She holds a bachelor’s degree in Statistics and an MSc in Statistics (Biostatistics) from Makerere University and a Certificate in Data Science from the Africa Data School.
She is a dedicated Biostatistician/Bioinformatician/data scientist professional with a history of meeting project goals utilizing consistent and organized practices. Skilled in adapting to new situations and challenges to best enhance the outcome of projects. She has 8 years of experience in teaching, analyzing, and interpreting clinical, lab, and research data. Sound experience in designing research, sampling, and validation, developing statistical analysis processes, managing and manipulating data sets, modeling and machine learning algorithms as well as Artificial intelligence. Proficient in R/Studio, PYTHON, STATA, SPSS programming.
PARTICIPANTS
1st Cohort participants
| Name | Gender | Area | Degree | Country | Profession |
| Philippe Sessou | M | Food and Industrial Microbiology | PhD | Benin | Professor |
| Sarah Salah | F | Medical Biochemistry and Molecular Biology | BS | Egypt | Medical Doctor |
| Chr istian Keambou Tiambo | M | Animal Breeding and Genetics | PhD | Kenya | Scientist |
| Ferrera Laila | F | Microbiology and Molecular Genetics | MS | Morocco | Student |
| Igbokwe Joseph Odunayo | M | Molecular Ecology | MS | Nigeria | Researcher |
| Usama Aliyu | M | Biochenist | BS | Qatar | Student |
| Omer Salih Dawood Omer | M | Computer Science | PhD | Saudi Arabia | Lecturer |
| Duaa Ahmed Idries | M | Biochemistry | MS | Sudan | Laboratory Technologist |
| Damiano Raphael Kwaslema | M | Agronomy | BS | Tanzania | Student |
| Velma Okaron | F | Plant Bredding and Biotechnology | MS | Uganda | Student |
| Lucky Osemu EBALUEGBEIFOH | M | Animal Physiology | MS | Cameroon | Student |
| John Oluwafemi Teibo | M | Biomedical Biology and Genetics | PhD | Finland | Ambassador, Germany |
| MBU’U MBANWI Cyrille | F | Microbiology | MS | India | Student |
| MVOGO NYEBE | M | Microbiology | BS | USA | Student |
| Girma Beakal Tadesse | M | Plant Bredding and Biotechnology | MS | Ethiopia | Student |
| Caroline Chepngeno Tigoi | F | Medical Virology | MS | Kenya | Researcher Officer |
| Willard Kamowa Mbewe | M | Biological Sciences | MS | Malawi | Lecturer |
| Doreen Ditshwanelo | F | Biotechnology | BS | Botswana | Student |
| Diana Kasake | F | Genomic Science | MS | Uganda | Medical Doctor |
| Fanele Mnguni | F | Microbiology | MS | South Africa | Student |
| Otobong Donald Akan | M | Microbiology | MS | China | Student |
| Dennis Mujuni | M | Biomedical Laboratory Sciences & Management | MS | Uganda | Founder |
2nd Cohort Participants.
| Name | Gender | Area | Degree | Country | Profession |
| Rachida NAMOUNE | F | Microbiology | MS | Algeria | Student |
| Nametso Kelentse | F | Medical Laboratory Science | MS | Botswana | Student |
| Otobong Donald Akan | M | Microbiology | MS | China | Student |
| Kevin KARUME LUBULA | M | Molecular Biology | PhD | Democratic Repblic of Congo | Lecturer |
| Molly Kukua Abban | F | Molecular Cellullar of infectious diseases | Mphil | Ghana | Technician |
| Waliyullahi Ajibola | M | Microbiology | MS | Hungary | Student |
| ALAM SURYA WIJAYA | M | Livestock inspector | MS | Indonesia | Scientist |
| Moses Okello | M | Agriculture | MS | Ivory Coast | Student |
| Primrose Muthoni Ndungu | F | Molecular Pharmacology | MS | Kenya | Technical Application Specialist |
| Hasnaa MALLOUK | F | Neuroscience | MS | Morocco | Student |
| IPADEOLA OLADIPUPO BANJI | M | Statistics | PhD/MPH | Nigeria | Senior Public Health Specialist |
| Mabel K. Aworh | F | Veterinary Public Health and Preventive Medicine | PhD | Nigeria | Lecturer |
| Mutangana Dieudonné | M | Biotechnology | PhD | Rwanda | Lecturer |
| Oluwatobi Andrew Adeosun | M | Immunology | MS | Saudi Arabia | Medical Laboratory Scientist |
| Mary Aza-Gnandji | F | Bionformatics | MS | Senegal | Student |
| Khethiwe Mtshali | F | Zoolgy | MS | South Africa | Lecturer |
| Ayman Ahmed Mohamed Elamin Ahmed | M | Public Health | MS | Switzerland | Student |
| Houria DAIM | M | Molecular Biology | PhD | Tunisia | Post-doctoral |
| Anjellina Rukundo | F | Medical Laboratory Technology | BS | Uganda | Technician |
| Sabah Ibrahim | F | Molecular Biology | MS | United Kingdom | Lecturer |
| Olga Kamanga | F | Laboratory Technology | MS | Zambia | Laboratory Technician |