Reproducible Computational Environments with Binder =================================================== ###### tags: `turing-way` `Workshop` `External` :::info - **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 ### Zoom Non verbal communication using zoom buttons: - Options that you see: ![](https://i.imgur.com/KrNOlEh.png) - Click on "Participants" ![](https://lh3.googleusercontent.com/2D5nI9F2Jf90sLkR5d4rRscVcCf_CKtpdUUfkZNzkj_5weAWzbCeodVdKqhHVyWvVsaLUj0reL_wYJ18y_Z7lnx40G7H5SVvydUM-USmaJ6j91C-rYe2wjtcSLJFPMyS4lJmy5SN) **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: :dart: 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. :desktop_computer: 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! :dancer: - 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.. **Introduction to _The Turing Way_** * The Turing Way GitHub repository: https://github.com/alan-turing-institute/the-turing-way * [Online Collaboration Cafes](https://github.com/alan-turing-institute/the-turing-way/blob/master/project_management/online-collaboration-cafe.md) * Chat on Gitter: https://gitter.im/alan-turing-institute/the-turing-way * Join the mailing list: https://tinyletter.com/TuringWay :ballot_box_with_check: GitHub, MarkDown - HackMD --- * Create a GitHub account if you don't have one: https://github.com/join **Extra** * Tutorials and resources: * Markdown cheatsheet: https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet * GitHub for collaboration: https://malvikasharan.github.io/developing_collaborative_document/ * HackMD: https://hackmd.io/ ([Lessons on using HackMD editor](https://hackmd.io/c/tutorials/%2Fs%2Ftutorials)) * Explore Turing Way GitHub: * Main repository: https://github.com/alan-turing-institute/the-turing-way * [Slides explaining how to open a new issue or pull request](https://zenodo.org/record/3676449#.Xmey7UOnzOQ) (starts at the slide number 45) :hammer_and_wrench: Why we need a reproducible computing environment? --- ## Zero to Binder - Presentation: [https://zenodo.org/record/3974919](https://zenodo.org/record/3974919) - Tutorial: [Zero to Binder (in Python)](https://github.com/alan-turing-institute/the-turing-way/blob/master/workshops/boost-research-reproducibility-binder/workshop-presentations/zero-to-binder-python.md) ### All slides and information on Zenodo: - https://zenodo.org/communities/the-turing-way/ (Slides for this talk is a mixed and matched for you! Yay! CC-BY license) ### Read this post by Sarah: https://www.turing.ac.uk/news/diving-leadership-build-push-button-code ### Take shared notes here: - :busts_in_silhouette: :speech_balloon: Build your own Binder: Make it in your own time and share it with us --- - #### Some examples to look at * https://elifesciences.org/labs/d42fe2b9/integrating-binder-and-stencila-the-building-blocks-to-increased-open-communication-and-transparency * https://github.com/binder-examples #### Connect with us! We love hearing about how you're using _The Turing Way_. Stay in touch through one of the many different pathways below! - [About the project](https://www.turing.ac.uk/research/research-projects/turing-way-handbook-reproducible-data-science) - [_The Turing Way_ book](https://the-turing-way.netlify.com) - [GitHub repository](https://github.com/alan-turing-institute/the-turing-way) - [Gitter chat room](https://gitter.im/alan-turing-institute/the-turing-way) - [YouTube Videos](https://www.youtube.com/channel/UCPDxZv5BMzAw0mPobCbMNuA) - [Twitter account](https://twitter.com/turingway) and [#TuringWay Hashtag](https://twitter.com/hashtag/TuringWay?f=live) - Get in touch with _The Turing Way_ community manager [Malvika Sharan](mailto:msharan@turing.ac.uk) winfred Gatua Pwani University/