continuing from last week* when we were rudely interrupted ;-) ...

so we were done with the Intro and where starting to code in the browser, moving towards exploring the browser as a full IDE. Some of you want to advocate your own backend serverless systems, don't be shy!

* Checklist

So, to take full advantage of the global Web Computer, we should now be ready to go over the checklist in the home page:

1. Review mission and approach at cloud4bio.github.io.
2. Make sure to have Chrome browser installed - Chrome's Dev Tools will be our reference IDE for client-side programming.
3. Ask for edit access to this wiki if you plan on attending with some regularity. Note each session is documented in its own page, under the corresponding year in the top right banner of this page.
4. Create a GitHub account if you don't have one already and pick a github client - use github's own if you don't have a favorite already.
5. Get node, Chrome's headless browser, for server-side programming.
6. (Optional) If you're looking for a cool text editor, vscode is a good choice.
7. (Optional) Add bit.ly/cloud4bio to your phone's Home Screen.

Web + Cloud development in the browser

We'll use Chrome devtools in your regular chrome browser, and the headless browser equivalent from #5 above for the server side components. If you don'w have a favorite microservice platform already maybe start with salesforce heroku. Why node (discuss, a) same code clinet amd server side; b) non-blocking event loop server).

Observable Notebooks

Literal Programming using the Jupyter Notebooks of the Web, by the creator of data driven documents (d3js) : https://observablehq.com.

Show and Tell

• [Jonas] Importing functions with dependencies without compromising its purity: https://observablehq.com/@jonasalmeida/importing

...

Tidy Data

Eric (Dawson) wants us to tidy our data. Here's a reference paper on why - https://vita.had.co.nz/papers/tidy-data.pdf - and a web page by the same author - https://r4ds.had.co.nz/tidy-data.html. This manual on data wrangling in JS may also be useful - http://learnjsdata.com.

Eric, we're all ears.

I wrote a brief rant on tidy data and its importance in biology here.

----

remember you can all edit the page at the same time

MIS

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5683428/ <-- Bob Grossman call for Data Commons with GDC as a example.

Martin for the rest of us

R Plummer to expose APIs

https://shirinsplayground.netlify.com/2018/01/plumber/

https://bioconductor.github.io/BiocWorkshops/introduction-to-bioconductor-annotation-resources.html

Ben's links (he's involved in GA4GH)

https://github.com/ga4gh/data-repository-service-schemas

https://github.com/ga4gh/tool-registry-service-schemas

Bonus (from Marcin):

• https://blog.jetbrains.com/pycharm/2019/02/webinar-recording-demystifying-pythons-async-and-await-keywords-with-michael-kennedy/
• https://mybinder.readthedocs.io/en/latest/ - Reproducible computational environments via Binder (JupyterHub and Docker)
• https://plot.ly/products/dash/
• https://www.rplumber.io/docs/
• https://bioconductor.github.io/BiocWorkshops/introduction-to-bioconductor-annotation-resources.html

And others:

• http://mathbiol.github.io

GA4GH and other public resources

• https://github.com/ga4gh/tool-registry-service-schemas
• https://github.com/ga4gh/data-repository-service-schemas

Cross Cloud Computing (and accounting)

NCBI Hackathons

https://github.com/NCBI-Hackathons/PrecisionMedicineToolkit

Martin Skarzynski asked for input on a Data Science event planned for September 6, 2019.

https://docs.google.com/document/d/10IiaiyxuInqekTXHywp0GbrZitUKWLRPpBaEJ8ZoKsw/edit?usp=sharing