Computer science

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+00:00August 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+00:00May 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+00:00January 28, 2015|Categories: Computer science|Tags: |0 Comments

Database Content Versioning Using SQLAlchemy

One of the important functionality required of a LIMS is keeping a history of the changes applied to the data stored within the underlying database. This can be a tricky aspect to develop and/or put in place and there are certainly a number of ways one can go about implementing such a solution. Fortunately for all you SQLAlchemy fans out there, a fully implemented versioning solution is provided in the ORM's examples page. While the examples page provides a few [...]

By |2017-05-01T10:27:33+00:00October 5, 2014|Categories: Computer science, Database, Python|Tags: , , , |0 Comments