Reproducible Computational Environments with Binder

tags: `turing-way` `Workshop` `External`

Event: Boost your research reproducibility with binder
Date: 10 July, 2020 09:00 - 10:00 (UTC)
Instructors: Malvika Sharan, Sarah Gibson
Contact: msharan@turing.ac.uk

Shared notes:

https://hackmd.io/@malvikasharan/BinderJuly2020

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About the event: The East African Network for Bioinformatics training (EANBiT), seeks to upskill students in Bioinformatics using the model: coursework, 5-week residential training and finally research project placement at partner institutions. EANBiT works with universities in Kenya, Uganda and Tanzania, to offer MSc in Bioinformatics. It supports curriculum development, offers MSc fellowships to students, and support placement for research. The residential training (gone online this year), has four tracks: technical, Soft skills, Seminars, and Mini projects. The seminars involve talks from leaders in various areas of genomics, including open science.

About the workshop:

A short workshop was delivered as a hand-on guided training on building a Binder resource using the following agenda:

Agenda

Time	Activity
10:00 - 10:15	Presentation
10:15 - 10:45	Zero to Binder, a guided tutorial for building a Binder resource
10:45 - 11:00	Troubleshooting
11:00 - 11:10	Wrap-up and Open Q&A

This training took place online and a shared HackMD was used for facilitating collaboration and discussion among the participants.

Introductions

Roll call:

Name / Pronouns / Affiliation / GitHub:

Malvika Sharan / she/her / The Alan Turing Institute / malvikasharan
Sarah Gibson / she/her / The Alan Turing Institute / sgibson91
Caleb Kibet / he/him / ICIPE
Kakembo Fredrick E /he/him/ Makerere University
Senamile Fezile Dlamini /she/her / Makerere University/ senamile-dlamini
Olga Nsangi Tendo/ She/ her/ Makerere University
Erica Kariuki / he/him/ Makerere University
Michael Landi /he/him/ ILRI
Jane Njeri / she/her / Pwani University
Peter Muchina/ he/him/ Pwani University
Ivan sserwadda/ he/ him/ Pwani University
Eneza Yoeli /he/ him/ Pwani University
Kester Bevin Bataringaya Tindi /he/ him/ Makerere University
Stella Esther Nabirye /she/her/ EANBiT-Makerere University/StellaNabirye
Shahiid Kiyaga/he/him/EANBiT/Makerere University
Omara Isaac Emmanuel /he/him/ Makerere University
Festus Nyasimi /he/him/ ICIPE
Ruth Nanjala/she/her/Pwani University
Davis Kiberu/she/her/BReCA-Makerere University
Paul Talent /he/him/Makerere University
Edward Lukyamuzi /she/him/ Makerere University
Mthande Mzwakhile S/he/him/Makerere University
Eva Akurut /she/her/BRecA-Makerere University
Winfred Gatua /she/her/EANBiT Fellow/Pwani University
Ibra Lujumba /he/him/ BRecA-Makerere University

What is one of the top 3 things that made you feel the happiest this week? 😅 (learned something new, started a new project, met a friend, baked a cake)

Malvika Sharan - finished a number of half written documents that's been sitting in my computer for months.
Sarah Gibson - I just transferred mybinder.org's CI fron Travis to GitHub Actions and parallelised it across our federation members. This will save us so much time when we have to debug upgrades!
Omara Isaac: New friends, new knowledge
TGIF😅 +1
The Virtual RT is going great. Excited to have managed to move it online
Next flow and snakemake workflows have been the highlights for me!!😅
Mthande Mzwakhile / New knowledge on how to go about in analysis
Senamile F Dlamini/ Added workflow languages to my set of skills
My team won..