The unit aims to develop rolling training schedules in bioinformatics to target internal and external participants capacity building. We will put together materials to facilitate the trainings.
This is a foundational training, which aims to introduce participants to considerations in planning a genomics project to ensure reproducibility and openness as vital principles for modern research.
Audience: Life science researchers involved or interested in genomics research, people involved with genomic data management, no prerequisite
• Introduction to bioinformatics (Data, Central dogma of Mol Bio, Online resources, NGS tech)
• Organising a genomic project workspace (Data Management Plan)
• Open and reproducible Bioinformatics research (Data tidiness, Frictionless Data tools)
• Introduction to data backup and version control (Git and GitHub, Pipeline tools)
We have the H3Africa meeting, where icipe will host the fellows training. We are planning for REDCap training at the end of March. This will cover:
- Why REDCap?
- How to use REDCap for surveys
- Setting up robust surveys (We need to find a trainer on this)
- Research data management
This can be a one-week training that targets data analysis using R studio, where we will also emphasise on project management.We'll host this in collaboration with statistics. We could also make use of Carpentries Resources, design.
Since this is running at the same time we have the EANBiT RT, we mayhave to skip, or find a partner to host
H3ABioNet‘s Introduction to Bioinformatics course (IBT) provides an introduction to the field of bioinformatics, with a focus on important bioinformatics tools and resources. It is delivered over a period of 3 months, through a combination of distance, face to face and onlne learning. During face to face contact sessions, classrooms meet virtually to discuss the session’s content with each other facilitated by a trainer and teaching assistants. The course combines theoretical and practical sessions to allow participants to gain practical experience in using various tools and resources. Date: 04 May – 31 July 2020; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT. Content
- Bioinformatics resources and databases
Introduction to bioinformatics, biological databases and resources (NCBI and EBI), data formats, ontologies
- Linux
Introduction to Linux, general overview of Linux environment, overview of command line interface, navigating Linux directory structure, manipulating files and directories, basic Linux commands
- Sequence alignment theory and applications
Introduction to searching and sequence alignment, BLAST, pairwise sequence alignment
- Multiple sequence alignment (MSA)
MSA theory, generating and interpreting MSAs using various tools, visualising and assessing MSA quality
- Genomics
Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap, 1000 genomes
- Molecular evolution and phylogenetics
Prerequisites / Audience: A basic background/understanding of of biochemistry and/or genetics.
This is designed to cater for ICIPE partners who are not part of the 5-week Residential Training.
Audience: Postgraduates students from partner instituitions.
- Version control and collaborative development (Git & Github & Slack etc.)
- Metagenomics (16S and Whole-genome shotgun sequencing)
- Specialised databases (VectorBase, EupathDB) and APIs
- Data Management for Open and Reproducible Genomics Research
This training aims at strengthening bioinformatics technical capacity and skills among the participants; preparing them to work as bioinformaticians and to become project ready so that they have the necessary skills to offer bioinformatics support in projects they are attached to.
Audience: Postgraduates ++ with familiarity to computing/programming and/or life science background
• Version control and collaborative development (Git & Github & Slack etc.)
• Advanced Scripting
• Biological databases and API
• Gene models and annotation
• Reproducibility and package management: workflow languages (CWL, Snakemake, Conda)
• Specialised databases (VectorBase, EupathDB) and APIs
• Phylogenomics (Visualization and Annotation)
• Metagenomics (16S and Whole-genome shotgun sequencing)
• Machine Learning and modelling for big data (fuzzy strings, HMM)
The course aims to provide training to enable participants to gain the knowledge and skills to perform 16S rRNA microbiome data analyses using a variety of bioinformatics methods and tools.
Audience: Life science researchers involved or interested in genomics data analysis, no prerequisite
• Introduction to the Linux command line/intro to R
• Introduction to the microbiome and study design – why 16S?
• Sample collection, extraction and library prep for 16S NGS analyses
• 16S rRNA gene amplicon sequencing bioinformatics pipeline: the theory
• 16S analysis pipeline - QC, ASV picking, taxonomic classification and alignment metagenomeSeq (among others)
• Downstream analysis in R - using the packages phyloseq, NMF, vegan,
This two-day training will target anyone that handles data in any form in the institution.
Audience: All students, researchers and scientists who work with research data in any form.
- How to FAIRrify your data
- Metadata management principles
- Tools and standard for metadata management
This workshop aims to teach data management and analysis for genomics research including best practices for the organisation of bioinformatics projects and data, use of command-line utilities, use of command-line tools to analyse sequence quality and perform variant calling, and connecting to and using cloud computing.
Audience: Life science researchers involved or interested in genomics data analysis, no prerequisite
• Project organisation and management
• Introduction to the command line interface
• Data wrangling and processing
• Introduction to cloud computing
• Introduction to R and RStudio for genomics