Computer science

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

Speed up random disk access

When working with a software that accesses data from disk in a random fashion, it is common knowledge that best performance will be reached using SSD hard drives, with SAS disks being less efficient and SATA disks being the worst. However, high capacity SSD drives are still relatively expensive and thus, when working with large datasets, one typically ends up working with data stored on larger, and more common SATA drives. I recently experimented with the Jellyfish software to analyze [...]

By | 2017-04-29T17:05:04+00:00 August 4, 2016|Categories: Computer science, Performance|0 Comments

Realize your Bash potential

A bioinformatician's best tool is his shell. While some have already mastered the dark arts of the bash shell, I often see beginners (and even catch myself at times!) unknowingly repeating key sequences when they could be getting the same result with a few simple built-in keybindings or programmatic shortcuts. Let's have a look at some of the most useful bash shortcuts that no self-respecting bioinformatician should be without. This is by no means an exhaustive list of what Bash has to offer but will hopefully serve to save [...]

By | 2017-04-29T22:57:32+00:00 May 26, 2016|Categories: Computer science, Shell scripting|0 Comments

Client-side storage on the web

Web applications can provide users with cross platform tools which can easily be maintained and updated. It is therefore little wonder why bioinformatic tools are often published as web applications. However, some legal as well as computer security considerations can arise while operating on certain types of data  (e.g. medical or proprietary). In such cases, it may be preferable to store some of this data locally on the client's browser. Local data storage options are plentiful but can quickly become a little disorientating. Here's a small rundown [...]

By | 2017-04-29T15:47:47+00:00 January 28, 2015|Categories: Computer science|Tags: |0 Comments