Bioinformatics

A multiprocessing example and more

Recently, I had to search a given chemical structure into a list of structures. Using the python chemoinformatics packages pybel and rdkit, I was easily able to do so but the operation took a little too much time for my linking. Wondering how I could search faster, I immediately thought about Jean-Philippe's previous blog post titled Put Those CPUs to Good Use. I've decided to follow his instructions and give it a try. Goal Look for a molecule (a given [...]

By | 2017-12-11T12:55:55+00:00 December 11, 2017|Categories: Bioinformatics, Computer science, Performance|0 Comments

Let Your Data Flow: Streams and Reactive Programming

What's all this about ? ReactiveX is a combination of the best ideas from the Observer pattern, the Iterator pattern, and functional programming. Using Rx, you can easily: - Create event or data emitting streams from sources such as a file or a web service - Compose and transform streams with query-like operators - Subscribe to any observable stream and "react" to its emissions to perform side effects Reactive programming has been gaining traction these past few years. Maybe you've [...]

By | 2017-05-03T09:19:14+00:00 May 2, 2017|Categories: Bioinformatics, Computer science, Data Analysis|Tags: , |2 Comments

SNP Filtering with pyGeno

Looking over the contents of our growing blog (good job guys !), it occured to me that we had not yet posted an article pertaining to the fantastic (and homegrown !) bioinformatics resource that is pyGeno. It turns out I need to use pyGeno to generate data and it's also my turn to write a blog post, how convenient ! I'll focus the article on writing a SNP filter, which can be a bit surprising the first time you try [...]

By | 2017-04-29T17:57:51+00:00 December 9, 2016|Categories: Bioinformatics, Python|Tags: , |0 Comments

Bioinformatic in a container

A recent tendency coming from the world of cloud computing is gaining more and more popularity in the bioinformatic community. This tendency is to develop and deploy application in a container. This container contains not only the application but all the needed libraries and a minimalist version of the applications of the operating system. As soon as it is built, the container is ready for use on a host computer containing the environment required to start the container. For a [...]

By | 2017-04-29T22:52:19+00:00 July 21, 2016|Categories: Bioinformatics|Tags: , |0 Comments

Good resources to learn R

Since it's the summer vacations, why not take some time to learn R. There are numerous free resources online to dive into this powerful language. For whomever wants to learn it, the challenge more related to finding the time rather than finding resources. Videos Coursera is an inevitable for online learning. There are a few good video courses offered for R beginners that are more or less oriented toward genomics : https://www.coursera.org/learn/r-programming https://www.coursera.org/learn/exploratory-data-analysis https://www.coursera.org/learn/bioconductor (Bioconductor is a life science packages [...]

By | 2017-04-29T16:57:17+00:00 July 11, 2016|Categories: Bioinformatics, R|Tags: |0 Comments