- **BioHachathon** (https://github.com/virtual-biohackathons/covid-19-bh20)

Eurasia Call (Dec 18 Thu)
===
:::info
- **Time:**
- 13:30 - 14:00 (CET)
- 21:30 - 22:00 (JST)

Eurasia Call (Oct 08 Thu)
===
:::info
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- **Connection:**
- Zoom
::::
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- [Victoria Dominguez Del Angel](https://github.com/vdda)(FR)
- [Manabu Ishii](https://github.com/manabuishii)(JP)
- [Olivier Sand](https://github.com/olisand)(FR)
- [Makoto Ikeda](https://github.com/percipere)(JP)
- ** Agenda
- [home\-learning](http://www.home-learning.online/)
- DOI for pages
-
- License
- [Creative Commons — Attribution 4\.0 International — CC BY 4\.0](https://creativecommons.org/licenses/by/4.0/)
- [Cette](https://creativecommons.org/licenses/by/4.0/deed.fr)
- [Creative Commons — 表示 4\.0 国際 — CC BY 4\.0](https://creativecommons.org/licenses/by/4.0/deed.ja)
- Meeting Schedule
- Every Thursday Same Time
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- Calendar
- Available Soon.
- BioHackathon Europe
- 350 people join !!
- GOBLET
- [GOBLET \| The Global Organisation for Bioinformatics Learning, Education & Training](https://mygoblet.org/)

Eurasia Call (Sep 10 Thu)
===
:::info
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- **Connection:**
- Zoom
::::
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- [Victoria Dominguez Del Angel](https://github.com/vdda)(FR)
- [Manabu Ishii](https://github.com/manabuishii)(JP)
- [Makoto Ikeda](https://github.com/percipere)(JP)
- Agenda
- Next Two weeks goal (Sep 24th, Thu)
- Getting feedback about each language from people not joining this project.
- About current lessons.
- Duplicate the French page for Spanish lessons
- Next possible projects, Not only COVID-19 but also other stuffs.
- Introduction to Machine Learning
- Galaxy already have.
- [Galaxy Machine Learning Community](https://galaxyproject.org/community/machine-learning/)
- Visualize something about creating graph.
- Totally new stories doing our life.
- Tutorials for CWL.

Eurasia Call (Jul 16 Thu)
===
:::info
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- **Connection:**
- Zoom
::::
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- [Victoria Dominguez Del Angel](https://github.com/vdda)(FR)
- [Olivier Sand](https://github.com/olisand)(FR)
- [Manabu Ishii](https://github.com/manabuishii)(JP)
- [Makoto Ikeda](https://github.com/percipere)(JP)
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- Agenda
- Top Page Contents more rich
- Let's create Issue on GitHub for clear discussion.
- Certificate problem
- [Warning when the URL doesn't include www · Issue \#1 · pitagora\-network/home\-learning](https://github.com/pitagora-network/home-learning/issues/1)
- https://www.home-learning.online/
- This is OKAY.
- https://home-learning.online/
- This is NOT OKAY.
- This site contents are using GitHub Pages.
- Favicon
- [Favicon\! · Issue \#2 · pitagora\-network/home\-learning](https://github.com/pitagora-network/home-learning/issues/2)
- [CollaborationFest • BCC2020](https://bcc2020.github.io/cofest/)

Eurasia Call (Jun 25 Thu)
===
:::info
- **Connection:**
- Zoom
::::
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- Agenda
- CNAME issue
- Current - https://www.home-learning.online
- Expected - https://home-learning.online
- Currently browser complain about certificate if no `www.` .
- Remove `Last update` date from Colab
- Because they have version number.

Eurasia Call (Jun 18 Thu)
===
:::info
- **Participants:**
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- **Connection:**
- Zoom
::::
- Agenda
- CNAME setting for the new domain
- GitHub repository setting
- set home-learning.online as custom domain
- Gandi.net DNS setting
- type: CNAME
- value: pitagora-network.github.io
- How to create a new translated tutorial
- Workflow
- Notify Admin via Slack
- TODO: write pitagora slack and slack channel here.
- If you do not know who is admin, ask Ryota Yamanaka. He will help you.
- Copy the master tutorial as a draft version
- Assign a version number
- Format is`<OriginalTutorialVersion>.<TranslatedVersion(Start from 1)>`
- e.g. You want to start translating Original Tutorial Version = 2.
- Asssigned version is 2.1
- Translate
- Notify Admin via Slack
- Admin makes a copy and publish it
- copy from Draft version Google Colab.
- Draft version is owned by Translater
- So if someone put comments on it translater will be notified!
- Published version is owned by Admin

Eurasia Call (Jun 4 Thu)
===
:::info
- **Participants:**
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- **Connection:**
- Zoom
::::
- Core working time for Japan Team
1. 18:00 - 19:00 (JST)
2. 21:00 - 22:00 (JST)
- Agenda
- How to create a new translation
- Next week with @Manabu
- Google Form (feedback form) for different languages
- I said I will make separate Google Forms, but in my second thought, maybe it increases maintenance cost because the responses will be saved into different spreadsheets
- [decided] Not to have multiple ones for different languages
- Link to the original language tutorial (published version) from translated version
- [decided] To put a link, let's see where (Should we put "original" link? @Olivier)
- Spanish version on-going :)
- New domain, home-leaning.online !!!!

Eurasia Call (May 28 Thu)
===
:::info
- **Participants:**
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- **Connection:**
- Remo: https://live.remo.co/e/virtual-biohackathon-2
::::
- Core working time for Japan Team
1. 18:00 - 19:00 (JST)
2. 21:00 - 22:00 (JST)

Eurasia Call (May 20 Wed)
===
:::info
- **Participants:**
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- **Connection:**
- Remo: https://live.remo.co/e/virtual-biohackathon-2
::::
- Core working time for Japan Team
1. 18:00 - 19:00 (JST)
2. 21:00 - 22:00 (JST)

Eurasia Call (May 14 Thu)
===
:::info
- **Participants:**
- **Time:**
- 14:30 - 15:00 (CET)
- 21:30 - 22:00 (JST)
- **Connection:**
- Remo: https://live.remo.co/e/virtual-biohackathon-2
::::
- Core working time for Japan Team
1. 18:00 - 19:00 (JST)
2. 21:00 - 22:00 (JST)

Eurasia Call (May 06 Wed)
===
:::info
- **Participants:**
- **Time:**
- 02:30 PM - 03:00 PM (CET)
- 09:30 PM - 10:00 PM (JST)
- **Connection:**
- Remo: https://live.remo.co/e/sparqlthon91
::::

Eurasia Call (Apr 23 Thu)
===
:::info
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- [Haruo Suzuki]()(JP)
- [Tatsuya Hattori](https://github.com/Hattyoriiiiiii)(JP)
- [Olivier Sand](https://github.com/olisand)(FR)
- [Manabu Ishii](https://github.com/manabuishii)(JP)
- **Time:**
- 02:30 PM - 03:00 PM (CET)
- 09:30 PM - 10:00 PM (JST)
- **Connection:**
- [Remo](https://live.remo.co/e/sparqlthon91)
::::

- Put version number of translated document to Wiki page
- Today and Yesterday discuess ideas
- Idea 1
- Original version: 10
- Translate version: 1
- Idea 2
- Version: *Original Version*.*Translate Version*
- ex.
- Version: 10.1
- This means same thing as Idea 1
- Today Conclusion
- We take Idea 2.
- Every number started from 1 (not 01 , not 0)
- Discuss about translator's name credit
- Translated documents should be owned by translators
- Today Conclusion
- Translator Credit is not mandatory.
- Someone want to write own name as translator.
- But someone do not want to write name as translator.

Eurasia Call (Apr 22 Wed)
===
:::info
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- [Victoria Dominguez Del Angel](https://github.com/vdda)(FR)
- [Manabu Ishii](https://github.com/manabuishii)(JP)
- [Tomoya Tanjo]
- **Time:**
- 02:30 PM - 03:00 PM (CET)
- 09:30 PM - 10:00 PM (JST)
- **Connection:**
- [Remo](https://live.remo.co/e/virtual-biohackathon)
::::

Eurasia Call (Apr 16 Thu)
===
:::info
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- [Victoria Dominguez Del Angel](https://github.com/vdda)(FR)
- [Olivier Sand](https://github.com/olisand)(FR)
- [Manabu Ishii](https://github.com/manabuishii)(JP)
- [Tomoya Tanjo]
- [Haruo Suzuki]
- **Time:**
- 02:30 PM - 03:00 PM (CET)
- 09:30 PM - 10:00 PM (JST)
- **Connection:**
- [Remo](https://live.remo.co/e/virtual-biohackathon)
- **Agenda:**
- Rapid update
- How do we can continue with the lessons?
- More actions: Paper, more lessons, translate to other languages..
::::

Some progress

If draft version of document(original document) has version number,
we are ready to translate.

Each original document has `version` number which start from 1.
If someone update original document, increase `version` by 1.
Translate document has also `version` number which formart is `original_document_version_number.translated_version_number`,
if someone update original document, increase `translated_version_number` by 1.
If original version is update, `translated_version_number` becomes 1.

We'll prepare some automatic notification system.
But before finish setup , we notify to slack by hand.

Please also see Wiki for this workflow.
- https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Home-Learning-%28admin%29

Eurasia Call (Apr 15 Wed)
===
:::info
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- **Time:**
- 02:30 PM - 03:00 PM (CET)
- 09:30 PM - 10:00 PM (JST)
- **Connection:**
- [Remo](https://live.remo.co/e/virtual-biohackathon)
::::

English is recommended but it is better to write own language compare to forget to write,
after that translate own language comment into English

Materials: https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Home-Learning

- Ryota Yamanaka
- Sort out the editing workflow [here](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Home-Learning-%28admin%29#for-editing-draft-version)
1. English draft
1. English publised
1. Translated draft
1. Translated published
- **"Four viruses story"** [here](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Home-Learning#what-is-rna-sequence)
（以下の順番にします）
1. SARS-Cov-2 (COVID 19) [MN908947]
1. SARS-related-coronavirus [AY27411.9]
1. MERS-related-coronavirus [JX869059.2]
1. Guandong chinese water stink coronavirus [MG600026.1]
- Manabu Ishii
- Add some comments to existing tutorials
- Tomoya Tanjo
- Add some comments to existing tutorials
- Tatsuya Hattori
- サボってた翻訳の作業を始めたTutorial-HowToDownload-ja
- Translate into Japanese([Tutorial-HowToDownload-ja](https://colab.research.google.com/drive/1SsEARPWrNQrp_I_2su6-R-gyKliLObid#scrollTo=GIaukbarLdBP))
- Makoto Ikeda
- Thinking aboug length comparison for poly-A tail of viruses
- Issues:
- How do we retrieve variety of RNA virus?
- Can't find good repository for the RNA virus sequence.
-

Eurasia Call (Apr 10)
===
:::info
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- **Date:**
- APR 9, 2020 02:30 PM - 03:00 PM (CET)
- APR 9, 2020 09:30 PM - 10:00 PM (JST)
- **Connection:**
- [Remo](https://live.remo.co/e/virtual-biohackathon)
- **Agenda:**
- Schedule from next week
- Every Wed and Thu, 7-10 pm (4 weeks)
- By the expected end of lock-down in Japan (May 6)
- Plan for [Virtual Super Liqueurthon](https://hackmd.io/pMMK_rJSSyOIr-PFJsw29g)
::::

Eurasia Call (Apr 9)
===

- **Location:**
- Eurasia call: Japan, France, UK, Thailand, etc
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- **Date:**
- APR 9, 2020 02:30 PM - 03:00 PM (CET)
- APR 9, 2020 09:30 PM - 10:00 PM (Japan)
- **Connection:**
- [Zoom](https://oracle.zoom.us/j/327034829?pwd=S2tiS3gwQXVIZE9DTEswdXBqK1A4Zz09)
- **Agenda:**
1. Review advances per participants (See lessons)
2. See the possibilite to include the link in the "training material catalogue [Tess](https://tess.elixir-europe.org/)"
3. Ask to other participants if they have any training material for our repository about covid-19 BH topics (?)
4. TODO list
::::

Meeting Minute APR 8
===

- **Location:**
- Eurasia call: Japan, France, Thailand, etc
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- **Date:**
- APR 8, 2020 01:30 PM - 01:45 PM (CET)
- APR 8, 2020 08:30 PM - 08:45 PM (Japan)
- **Connection:**
- [Zoom](https://oracle.zoom.us/j/327034829?pwd=S2tiS3gwQXVIZE9DTEswdXBqK1A4Zz09)
- **Agenda:**
1. Review advances per participants (See lessons)
::::

Meeting Minute APR 7
===

- **Location:**
- Eurasia call: Japan, France, Thailand, etc
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- [Victoria Dominguez Del Angel](https://github.com/vdda)(FR)
- [Hirotaka Suetake](https://github.com/suecharo)(JP)
- [Makoto Ikeda](https://github.com/percipere)(JP)
- [Tomoya Tanjo](https://github.com/tom-tan)(JP)
- [Manabu Ishii](https://github.com/manabuishii)(JP)
- [Jun Hattori]()(JP)
- **Date:**
- APR 7, 2020 02:00 PM - 02:30 PM (CET)
- APR 7, 2020 09:00 PM - 09:30 PM (Japan)
- **Agenda:** (30 minutes)
1. Review advances per participants (See lessons)
2. Overview: how to write and share the tutorials).
3. Look the Memo
- Présentation of Visual Studio [Visual Studio Code \- Code Editing\. Redefined](https://code.visualstudio.com/)
::::

Meeting Minute APR 6
===
###### tags: `Templates` `Meeting`

- **Location:**
- Eurasia call: Japan, France, Thailand, etc
- (Atrantic call: France, USA ..?)
- **Date:**
- APR 6, 2020 02:00 PM - 03:00 PM (CET)
- APR 6, 2020 09:00 PM - 10:00 PM (Japan)
- **Connection:**
- [Zoom](https://oracle.zoom.us/j/913307356?pwd=VFlTNjN3MFI0RGRiOExlbW5yWmZRQT09)
- [Remo](https://live.remo.co/e/virtual-biohackathon)
- **Agenda:**
1. Presentation and objectives `15min`
- [name=Ryota]
- [name=Victoria]
- [name=Hirotaka]
- [name=Makoto]
- [name=Tomoya]
- [name=Manabu]
- [name=Tatsuya]
- [name=Tazro]
- [name=Manabu]
2. Sprint planning `35min`
3. Revisit onboarding v1 `15min`
- **Participants:**
- [Ryota Yamanaka](https://github.com/ryotayamanaka)(TH)
- [Tazro Ohta](https://github.com/inutano)(JP)
- [Victoria Dominguez Del Angel](https://github.com/vdda)(FR)
- [Hirotaka Suetake](https://github.com/suecharo)(JP)
- [Makoto Ikeda](https://github.com/percipere)(JP)
- [Tomoya Tanjo](https://github.com/tom-tan)(JP)
- [Manabu Ishii](https://github.com/manabuishii)(JP)
- [Tatsuya Hattori](https://github.com/Hattyoriiiiiii)(JP)
:::

## Notes

- Format
- Objectives
- Which questions we want to answer for each lesson?
- Duration of the tutorials
- max 10 min
- Prerequisites
- No background
- Beginner
- Software needs
- Google Colab (Jupyter)
- Exercise (Question)
- Survery
- Language
- For users
- Prerequistites
- Browser Only !! - Run notebook on Google colaboratory
- Jupyter notebook on github is easy to run on Google Colaboratory
- just change the URL
- For learning material developers
- Prerequistites
- Tutorial Developer
- VSCode
- Live Share extension
- If the host provides an ivnitation link, it will be automatically done.
- Tutorial Development Host
- Docker
- Remote Container extension
- ~~Jupyter notebook extension~~
- https://code.visualstudio.com/docs/python/jupyter-support
- It is automatically installed when using [Remote container template for Jupyter notebook](https://github.com/tom-tan/jupyter-for-remote-container-template)

- Use VSCode with Jupyter notebook and Live Share extension
- Because Google Colaboratory may cause conflicts when several people edit the same document.
- Where and how do we write ?
- VSCode with Live Share.
- Create template project for creating further tutorial
- Jupyter notebook diff (after pulishing a repository in Github)
- nbdime
- for someone want to colaborate
- Test
- [papermill](https://github.com/nteract/papermill)

# memo

- XCode install
- Upper Right
- VSCode Install
- If you are already using brew, conda or other package mananger, please use that.
- If you do not use any package manager, download from below.
- [Visual Studio Code \- Code Editing\. Redefined](https://code.visualstudio.com/)
- Click Download.
- VSCode Live Share Install
- Open Extension
- Click Sidebar 4blocks icon like TETRIS.
- Search Live share
- "Live Share" requires space between 'Live' and 'Share'

# Overview: how to write and share the tutorials
## In development phase
- Write tutorials using VSCode with Live share extension
- It enables us to write the same document simultaneously
- Push the tutorials to Github repository
- Check that the tutorials work with Google colaboratory correctly
- Google colaboratory provides a way to open notebooks that are already pulished in Github
## For users
There are two options
1. Open the tutorial published in Github with Google colaboratory
- Users only require google account
- (almost) no setup needed
1. Setup Jupyter notebook environment by themselves and open the tutorial with it
- It can prevent vendor lock-in but it might be a hard task for beginners

# Links
- Google Colaboratory
- Used by users
- https://colab.research.google.com/notebooks/intro.ipynb
- Jupyter notebook
- Used by users (OSS alternative)
- https://jupyter.org/
- [jupyter-for-remote-container-template](https://github.com/tom-tan/jupyter-for-remote-container-template)
- Developed during the hackathon
- ~~Used during writing the lessons~~
- Unfortunately Live share extension does not work with Jupyter extension :-(
- See: [vscode-python#10516](https://github.com/microsoft/vscode-python/issues/10516)