23 May 2016

Last weekend I went to Genehack - annual bioinformatics hackathon held in Moscow. It was great!

This was my second attempt to take part in hackathon or hackathon-like event not remotely. There was almost no one person I know - for me it’s hardest part.

Working hard on our team's task in Genehack-2

This photo shows me and one of my teammates yesterday. Having almost no sleep for 2 days makes me look concentrated and pretty :)

Our team had to write a tool for predicting drug biomarkers in metabolic pathways from gene expression data for different cell lines (a project given by Pepper Biology). We tried to reproduce pipeline given in certain article, use different machine learning methods and then try to adopt it to different metabolic pathway database.

It took almost 2 days to figure out what authors of original study used for preprocessing, to repeat the same algorithm, to apply it to a smaller amount of data %) And anyway we didn’t fit on time to predict something with our results.

It was very stressful, but interesting experience :) I like hackathons because they make me more productive and curious - especially when it turns out that there are many things I don’t know yet. Hope it helps with my Outreachy internship, which officially started today!

We also won some prizes - coupons to internet shop (quite expensive shop, but with a lot different things - and books! - in stock). I want to spend it on biophysics book) Usually I read something freely-available or buy it on Amazon/O’Reilly and read in Kindle app (I realized that paper books are heaviest things in the world when me and my husband moved from Arkhangelsk to St.Petersburg), but recently I saw that book in local book store and fall in love =)

I have ordered one-way ticket to Moscow before hackathon because I didn’t know what to expect - all project themes were kept in secret and were unknown before the event. At Sunday morning my husband found train ticket with quite discounted price and booked it for me - it was my first trip by Grand-express train. I felt myself like nouveau riche there - because of stable working Wi-Fi and electrical socket in my compartment. Free breakfast was also included, but their coffee was not so great as one might expect. I read Debian-Med wiki for several hours there (to refresh things I learnt while applying to Outreachy), then fall asleep. Saint Petersburg woke me up with sunny morning, great coffee at the train station and optimism supercharge!

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