IRIC's Bioinformatics Platform

Best practices in data visualization

Sébastien's last post presented a hard-to-understand graph. The Venn diagram with four sets is a good example of visualization gone wrong. Good practices in data visualization is a hot topic right now. Not just in science, but in multiple areas such as journalism and business intelligence. Indeed, the crowd was quite heterogeneous at the first Visualisation Montréal meeting in August where more than 100 persons showed up! And the free ebook that was launched at the meeting targets beginners from all fields. [...]

By Geneviève|2017-04-29T15:40:51+00:00October 31, 2014|Categories: Data Visualization|0 Comments

Venn diagrams: a visualization nightmare!

I was recently reading a paper (a very inspiring read mapper for RNA-Seq!). At some point the authors wanted to present the overlap between splice junctions detected by 4 RNA-Seq read mappers and choose to do so using the ubiquitous Venn diagram (see Fig. 1). I spent a few minutes staring at this colorful mosaic... without gaining much insight. Fig. 1: Example of a four-way Venn diagram. Reproduced from figure 4b of Genome Biology, 14(3):R30, 2013. Which mappers overlapped most in [...]

By Sébastien|2017-04-29T17:20:46+00:00October 20, 2014|Categories: Data Visualization, Statistics|1 Comment

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 Jean-Philippe|2017-05-01T10:27:33+00:00October 5, 2014|Categories: Computer science, Database, Python|Tags: LIMS, ORM, SQLAlchemy, web development|2 Comments

Gene symbols : the challenge

Almost certainly, one day, you'll have between your hands a list of outdated gene symbols. And you'll probably think that updating them is a straightforward task, but it's not that simple! Because there's the word 'bio' in bioinformatician, updating the gene symbols reminds me of the futile cycle. According to Wikipedia's definition, a futile cycle occurs when two metabolic pathways run simultaneously in opposite directions and have no overall effect other than to dissipate energy in the form of heat**. Updating the [...]

By Geneviève|2016-11-08T09:30:17+00:00September 29, 2014|Categories: Bioinformatics, Biology|0 Comments

Teach me how to box-plot!

Boxplots are everywhere! Publishers like boxplots. But ask some people and most don't even know what a boxplot represents! Recently I wanted to examine gene expression data between two samples for a certain gene. The gold standard to look at it would be *drum roll*... A boxplot! Interesting fact #1: Did you know a boxplot is called a “box and whiskers plot” as well? Let's take a look! A boxplot is easily generated in the analysis software R and its interpretation [...]

By Assya|2017-04-29T15:41:25+00:00September 21, 2014|Categories: Data Visualization, R, Statistics|0 Comments