Part II - Lost in translation
In this section I will try to translate, or at least give enough clues on how to read a job ad from an company. The approach I prefer is to pick one or two real job postings and take them apart line-by-line (sort of). I will anonymize the postings as much as possible because I want to keep the analysis fairly generalizable. A lot of this post is guesswork because I didn’t write any of these nor are these from my employer, so take it all with a pinch of salt.
Part I - Should I stay or should I go
I will start this series answering what I feel is a relevant question: Is it possible to stay in academia without being a professor?
Help. I am a bioinformatician looking for a job
Usually a Data Science job, and I am here to help you. In the past year or so I have been doing a lot of mentoring with bioinformaticians / data scientists who are looking to exit the professorship career path. It seems like I have been doing a decent job because people keep approaching me for help on a regular basis. So I am making a series of posts with thoughts, notes, and advice, collected through several mentoring conversations in the hope of reaching and helping a larger audience.
Convert multiple mercurial repos to git
For historical reasons many of my I have dozens of version-controlled projects using mercurial (hg) hosted on Bitbucket. Since Bitbucket not only discontinued support for mercurial but also decided to delete those repositories, I have been planning to convert those to git - it only took me two years. Since I was getting my hands dirty with this, I took the opportunity to convert hg to git and upload to gitlab in one fell swoop. Here is how.
Improving database performance
I am a bit of a DB n00b but for a project I had to setup and query an rather larger sqlite database from an existing dump and schema. Here are a couple if things I leaned after asking for help.
My visual CV
TLDR; I made a visual timeline of my career (CV) completely in R.
Here I will show how it was done, and in the process how to hack
ggplot objects, add images to plots, and use pretty much any font in
your ggplots.
This is the final result, and if you are interested on how it was generated, read on.
Clone all repositories from a user (bitbucket) - API2.0
My post about cloning all bitbucket, originally posted on my old wordpress blog, got some attention over the internet. Well, three or four mentions. Sadly the information in there has been outdated due to Bitbucket’s API changes. That added to the shocking decision by Bitbucket to stop supporting mercurial repos and delete them (!) pushed me to finally download all my repos (again) and eventually move to gitlab. Maybe in a follow up post I will detail how I converted all hg repos to git.
How style your R code from sublime text
Let’s face it: we all write ugly R code. Either because we are in a hurry, or we copy pasted from stackoverflow, or our coding style just changed over the course of time, it doesn’t really matter: my code is not well formatted and barely adheres to any formatting convention no matter how much I tell myself otherwise. I could do it from an R console or in Rstudio. However the command-line option is too much of an hassle and I use Sublime Text.
My first R package - some notes
I have been toying with the idea of making an R package for sometime. To me this is the natural step after been an R user for some years now. Though I had some ideas they all sounded either a bit too over-complicated for a starting package, or not useful enough. In ideal world, and for me personally, I would write a package with a single function, that I could use, to learn the ropes.