SBG Python Meetup #1

Analysing Human Genomes with Python (Goran Rakocevic)

Next Generation Sequencing is a process by which DNA material is taken from an organism and read out in small stretches. Following the biochemical procedure, a computational pipeline is used to reconstruct the original genome that was sequenced, which ultimately results in a set of variant sites, location where the sequenced DNA differs from the established reference genome.

Most common source of the human DNA to be sequenced is from a blood sample, while recent advances in chemistry has led to kits that allow saliva to be used as well. Compared to blood, saliva is both more cost-effective and convenient, but there is an open question whether the final results are of same quality.

This talk will present a one of bioinformatics projects that was carried out in the Seven Bridges Genomics, whose goal was to establish and explain the difference between sequencing done on DNA from the two sources. Whole human genome experiments yield large amounts of data (single genome includes roughly 100GB of reads and 1GB of variant calls; in this project we simultaneously analysed 20 whole genomes), making this project interesting both from biological and engineering standpoints.

Python in Service Oriented Architecture (Viktor Kerkez)

To Django or not to Django? Python2 or Python3? AsyncIO, Tornado or WSGI? Rolling out your own framework or using an existing solution?

Service discovery, configuration, packaging, horizontal and vertical scaling, benchmarking, testing, refactoring in the dynamic (duck typing) language... These are just a few of the questions we faced when we decided to use Python in our service oriented ecosystem.

In this presentation we'll try to give you an overview of the road we took, decisions we made, and the solution we ended up with.