How to Organize a Bioinformatics Project for Reproducibility

Date: 10th June 2019 APPLY HERE

Time: 9 am to 5 pm

Venue: Bioinformatics Training Lab, Carol Wilson

Capacity: The training lab has a capacity of 20; therefore, please secure your spot by applying through this link before 21st April 2019.

Website: The resources used in this training are – or will be – available on this GitHub Repo.

Introduction

Genomic research data generated by researchers, including those at icipe, has grown exponentially. This growth has increased the demand for bioinformatics skills for genomic data analysis, and the need to optimize the research output from the data. Besides, to ensure reproducible and collaborative research, there is a need for the adoption of open science practices in data storage and workflows. The bioinformatics team plans to host a one-day workshop to train icipe researchers on how to plan a genomic project to ensure reproducibility. This training will set the foundation for other workshops the team has planned for the year.

Competencies

In this short course, we intend to impart knowledge and skills in the following competencies (See ISCB Competencies):

1. Knowledge and skills: Details of the scientific discovery process and the role of bioinformatics in it.
2. Knowledge: Bioinformatics tools and their usage.
3. Knowledge and Skills: Command line and scripting based computing skills appropriate to the discipline.
4. Knowledge and skills: Data management

Learning Objectives

To attain the above competencies, the workshop participants should be able to:

1. Describe the basic genomics principles
2. Explain the research design approaches in genomics projects
3. Describe the open science principles and explain how they are applicable in Bioinformatics
4. Describe the data management plan in genomics (FAIR data)
5. Know the various open science tools (Git & GitHub, and how they support a reproducible bioinformatics research
6. List the key Bioinformatics resources and capacity available at icipe

Learning Outcomes

From the above objectives, the workshop participant should acquire the following skills;

1. Be able to set up a reproducible genomic project
2. Apply open science principles in a genomic project to ensure reproducibility
3. Develop a data management plan for a genomic project (FAIR Data)
4. Be able to set up version control for their projects using Git and GitHub
5. Be prepared take advantage of the resources and capacity available at icipe for their projects--know who to approach for assistance

Instructors

• Caleb Kibet
• Inusa Jacob
• Gilbert Kibet
• Daniel Ouso
• Careen Naitore
• Kennedy

Who should attend?

This targets students and researchers within icipe who are interested / working with genomic data. There are no pre-requisites for this training.

Training Topics

• Introduction to genomics
• Organizing a genomic project workspace (Genomic Data Management Plan)
• Open science in Bioinformatics
• Introduction to data backup and version control (e.g. Git and GitHub)
• How to ensure reproducible Bioinformatics Research
• An overview of the bioinformatics capacity and resources available at icipe

See Course Content for more details.