News and Articles from Bioinformatics.fr

Genes Families hacked by Microsoft Excel

Few months ago I was playing with some data provided by the Sanger Institute. It was Copy Number Variation (CNV) data for 417 genes across a panel of 780 cell lines of interest in oncology. Data was provided in an Excel file where each column represents a gene and each line represents a cell line.

The Bioinformatics Open Space : Get/Give help with Biostar

This article is the kickoff of a sequel of articles called "Bioinformatics Open Space". It will mainly talk about the social web resources that can improve your productivity in bioinformatics. By productivity I mean either it will help you to fix a problem, keep you informed or give you inspiration for you daily tasks related to bioinformatics so that you won't feel alone. Today I will talk about a great resource that will help you to solve your question(s) related to Bioinformatics : "Biostar, Questions and Answers in Bioinformatics".

Cool data visualization using augmented reality animation

Each friday my colleague Steve sends to colleagues his nice "week-end reading" newsletter related to any interesting topics in bioinformatics or biostatistics. Just before christmas vacation it was about an interesting BBC's video of Hans Rosling, a professor of global health at Sweden's Karolinska Institute.

It is very funny because it reminded me that this guy is cited in Garr Reynolds's book "Presentation Zen" on page 207 : "Coventional wisdom say never never stand between the screen and the projector. Generally this is good advice. But as you can see from the photo, Rosling at times defies conventional wisdom and gets involved with the data in an energetic way that engages his audience with tha data and his story".

In this video you have a nice instance showing how Rosling gives life to his presentations. Moreover this time he is using augmented reality animation wich make him one step deeper in the heart of his presentation. In about 4 minutes he shows the evolution of life expectancy against income in 200 countries during the last 200 years.

You can see more cool presentations by Rosling or other good speakers at the TED website. The annual TED (Technology, Entertainment, Design) conference brings together the world's most fascinating thinkers and doers, who are invited to give insanely great talks on stage in only 18 minutes.

My first Bioinformatics Zen Presentation

One year ago I found out two very interesting books related to Power Point/KeyNote presentations "Presentation Zen" and "Presentation Zen Design". Through his books Garr Reynolds gives advices to deliver engaging and appealing oral presentations. I found it very interesting because sometimes it is not so easy to keep the scientists/biologists interested in the bioinformatics application we are presenting. In june 2010 I started to adapt an old excel plug-in dedicated to help scientists of our pharmacology group to analyze their Meso Scale raw data. Meso Scale assay technology provides a rapid and convenient method for measuring one or more protein targets within a single small-volume sample. Their 96-well plates supply a platform for the development of sandwich immunoassays.

When I was preparing my presentation related to the Plug-in I decided to spend some of my spare time to find ideas, pictures and sentences in order to produce a presentation zen that would keep researchers awake even if it take place after lunch time !!!!

So this article shows pictures that helped me to illustrate most of the messages/ideas I wanted to expose to the future users of the application. Hopefully it will give you inspiration for your future bioinformatics presentations. At the end you will find some good book(s) and Iphone application(s) related to the presentation zen philosophy.

The Body Browser By Google

Google is providing a new lab called the Body Browser. This new browser uses the WEBGL technology of 3D representation (instead of Flash). So you are able to explore the human body as you would do with Google Earth. You can show or hide several layers such as skin, bones, muscles etc. Then you can click on objects to get their respective label. If you want to give a try to this new tool you need a recent browser compatible with WEBGL technology such as Chrome 9 or Firefox 4.

New Bioinformatics.fr design

Six years ago, I started Bioinformatics.fr for fun and also in order to improve my HTML, CSS, SQL, PHP and Javascript skills. I also wanted to play with the Google services likes Google Analytics, Adsense, FriendConnect and Search. But during this period of time my experience in ergonomy and the design for websites and web applications was improving. And at beginning of 2010 I was shocked by how ugly the interface of Bioinformatics.fr was.