Open Science in Bioinformatics Workshop

August 9-10, 2018

This project seeks to sensitize and promote open and reproducible Bioinformatics research within Nairobi. The target groups are the researchers, graduate students and highly motivated undergraduate students in local universities within Nairobi region. Through the project, we aim to promote open, reproducible and collaborative Bioinformatics research and produce researchers equipped with tools -- Git & GitHub, reproducible research notebooks (Rmarkdown and Jupyter) -- for open and collaborative research. The participants will be ready to tackle local Bioinformatics challenges. In addition, this project is a step towards building a community of Open Scientists in Nairobi.

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Schedule

The schedule can be found in the workshop repository here.

Presentations

The link(s) to the presentation(s) can be found below.

  1. Welcome: Open Science Seminar - In this presentation, we'll give a quick recap of our seminar for the benefit of those who did not attend. It also serves as our introduction

Sessions

    Introduction to Command line

    A quick introduction to the basics of the command line.

    1. Learn Command line: Link to training materials for this session.
    2. command-line bootcamp: Learn command-line at your own pace using this tutorial

    Markdown

    A quick introduction to the basic markdown syntax. This is a pre-requisite to working with GitHub and Literate programming tools (Rstudio, Jupyter)

    1. Introductory Markdown: Link to training materials for this session.
    2. Markdown Markdown-Cheatsheet: A reference guide to basic markdown syntax.

    Git and GitHub

    Learn how to create and use GitHub for collaborative research and coding projects. We will introduce how you can set up local git repositories, and how to push the local changes to GitHub.

    1. Teaching Git: Link to training materials for this session.
    2. Friendly GitHub: Link to slides used in this session.
    3. Friendly Github Workshop Repository: .

    Rstudio

    We introduce the power of Rstudio for collaborative and reproducible research using R.

    1. Reproducible Research with RStudio: Link to training materials for this session.
    2. RMarkdown-Cheatsheet: A reference guide to basic markdown syntax.

    Jupyter

    We introduce how you can harness the power of Jupyter Notebooks for collaborative and reproducible research using Python. Jupyter notebooks can also be used with Julia and R.

    1. Reproducible Research with Jupyter: Link to training materials for this session.

Notes

We have a living etherpad where we will be collecting any questions from participants and answering either on a rolling basis or after the workshop. Hop on the pad if you've got questions, comments, or want to help answer any of the questions.

Help

  1. Getting Help

    Here we'll hopefully answer questions you might have.

    • What is the workshop hashtag?

      • Tweet with #OpenScienceKE

    • Where is it being held?

      • KENET Training Lab, Jomo Kenyatta Memorial Library, University of Nairobi

    • What is the WIFI code?

      • KENET:
        • username
        • password
      • Guests:
        • username
        • password

    • Where can I find the Code of Conduct?

      We subscribe to the Science lab code of conduct, which you can find here. In summary, we subsribe to the golden rule: Do unto others as you would have them do unto you.

    • Who can I approach if I have any problems or issues to report that violate our Code of Conduct?

      • Caleb Kibet - @Cakkibet, kipkuruis[at]hotmail.com
      • Pauline Karega - @karegaP, karegapaul[at]gmail.com

  2. Finding Resources

    Here we'll list some persistent resources that you might use throughout the workshop.

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