Bioinformatic and Data Analysis

I picked up a personal interest in laveraging bioinformatic tools to do get out more data from less experiments. This is the true spirit for an evolution into Exponential Technology. Here, a collection of all my undertakes, over the years, on Computer Languages and Data

My very first approach to computer programming language: Python

As student at Karolinska Institutet, I started a Python Club with a good friend (he was a computational PhD student, I was a wet-lab minion). We thought ourself how to use the Python language following an incredible book: Python for Biologists, from Martin Jones. I still remember the first time I created a new .txt file on my desktop using the Terminal. The thrill was real

print "Hallo World"

From string manipulation to tables: R

I deepened (seriously) my understanding of the R language during my PostDoc at Genentech. Just like in Sweden, I found an enthusiastic colleague who prompted me to start an R-Club, which became a circle of about 20 scientists, from all over campus, who wanted to get a sense for what that language could do for them

Thank project demystified the R basic to me, but it wasn’t until I discovered Tidyverse, an R Package that excel in table manipulation, that I really understood the power of R. I taught myself Tidyverse following an online course during 2020 Shelter in Place.

Getting Organized and Sharable: GitHub

Until I finally brought myself to understand the Git universe, my code was in bids and pieces all over my hard disk. Now, with a my GitHub account, I can keep track of what I write, I can share it, I can review my code with confidence and I will always know where I kept the “original version”

Go Online: Shiny

November 9th 2020: I just started a course on Shiny. I don’t know yet where it will take me, but I really wanna be able to advertise myself more as a good data scientist, and I would like to be able to make beautiful, interactive data views on my website. It’s pretty incredible what you can do under one hour!

Here, used the Shiny Package to write an app.R file, and uploaded on Shinyapps.io, a server that runs R code provided by RStudio, using the package rconnect.

Go bouncing with Turtle – Python

November 12th 2020, my teacher in elementary schooled used a very ancient program, running on DOS, to teach her puills geometry and redumental computer coding (this was happening in the Italy of 1990s -I am amused). The story she told us was about a little turtle that was walking on the screen to draw shapes.

20 years later, I rediscovered Turtle for Python, a package that let me play with geometry. And with the help of some looping and conditional functions, one can do pretty things with is. If only my teacher could see me today 🙂

Downside: I couldn’t find a freeware server that would let me run my drawing without for free. I found this solution from Trinket. I have a lot more to learn on this.

Simulation with SimPy – Python

November 22th 2020 – followed this tutorial to run my first ever simulation in SimPy. First, I went to this very useful Generator Tutorial