Computer science

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 it roam free ! Releasing your code into the wild…

Today, I thought I'd do something a little different and talk about what one might expect from publicly releasing some code. I figured it might be nice to interview someone from our group which has lots of experience doing so, Tariq Daouda, to gain some of his insights. So without further ado, here we go ! JP: Hi Tariq, glad to have you with us. I thought I might ask you a few questions regarding what happens when one decides [...]

By | 2017-10-16T15:59:03+00:00 October 16, 2017|Categories: Computer science|Tags: , |0 Comments

A Week of Deep Learning

From August 21 to 25, IVADO and the MILA held their first edition of the École d'été francophone en apprentissage profond. The aim of this summer school was to "give [the participants] the theoretical and practical basis for understanding [deep learning]". A few members of the platform and myself participated to these five days of training. I must be honest, I was a little afraid of deep learning the first time it was presented to me. I found the concept [...]

By | 2017-09-22T13:46:35+00:00 September 22, 2017|Categories: Computer science|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

Fast network transfers?

Recently, everyone and their mother started using various tools in order to optimize large data transfer to, from and between supercomputers. Historically, we have seen tools like FDT, BBCP that tried to exceed the performance obtained from other transfer methods, like scp, rsync, ftp, etc. One tool in particular is now gaining traction and is being deployed on most supercomputers: GridFTP and its front-end Globus. The Globus frontend interface. Before jumping into the bandwagon, I thought it would [...]

By | 2017-04-29T17:04:17+00:00 October 13, 2016|Categories: Computer science, Performance|Tags: , |0 Comments