March

Introduction to Icipe HPC resources at icipe (HPC, RStudio, Galaxy, Jupyter) (30th March)

One day workshop giving an introduction and overview of the icipe's high-performance computing systems, available tools, and responsible use of the HPC.

Audience: Those using or intending to use the HPC

Prerequisite: None

Content:

• Responsible use of icipe Bioinformatics resources and services responsibly (HPC usage)
• Transfer files onto the icipe cluster.
• Data Storage

The schedule and the training materials are attached herein: Schedule

April-May

Genome Assembly and Annotation Hackathon (3rd April - 31st May)

Audience: Two month Hackathon for life science doctoral candidates, MSc students, Undergraduate students and research fellows interested in handling genome reads data. We intend to generate a pipeline for assemblying (ONT/Illumina/PacBio) reads. The emphasis will also be on selection of tools needed for assembly and annotation. We look forward to also automate the workflow in Nextflow. (There is a possibility of writing a manuscript and review paper on genome assembly).

Prerequisite: Basic Knowledge on Bash, Python, and R

Content:

• TBD

May-July

Introduction to Bioinformatics (Three Months)

The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources. The course content and outline is prepared by H3ABioNet and will be facilitated by instructors from icipe MBBU unit. The application for applicants are expected to begin in April and Workshop to begin in May. Exact dates will be communicated.

Audience:

Prerequisite: Basic Knowledge on Bash and R

Content:

• Explain the use of bioinformatics
• Name the key bioinformatics techniques and tools
• Locate important biological databases and retrieve data
• Use selected tools effectively to run specific bioinformatics analyses
• Understand the strengths and limitations of the various techniques

AUG

Data Management for Open and Reproducible Genomics Research (2 Days)

The workshop aims to introduce participants to considerations in planning an -omics project to ensure reproducibility and openness as vital principles for modern research.

Audience: Life science researchers involved or interested in -omics research, people involved with -omic data management

Prerequisite: no prerequisite Content:

• 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)
• Introduction to the iRODS system for data management

SEPT

Using Galaxy for Transcriptomics and Gene Expression Analysis.

Audience:

Prerequisite:

Content:

OCT

The Carpentries Training Workshop (Self-Organised)

Audience:

Prerequisite:

Content:

NOV

Phylogenetics and Evolutionary Analysis

Audience:

Prerequisite:

Content:

DEC

Data Visualization and Communication in Bioinformatics

Audience:

Prerequisite:

Content: