Virtual Gel

URL: http://www.poirrier.be/~jean-etienne/software/vgel/index.php

Last modification: May 2005

Goal

Virtual Gel simply builds a virtual 2D gel from a list of proteins with given pI/MW. The result is a kind of 2D gel obtained here by computation (and not electrophoresis).

To run it, just click here and enjoy!.

I wrote this tool because, for my Ph.D., I accumulate a lot of proteins characteristics in the litterature but I needed to really see where they could be located on a 2D-gel. This tool gives thus a rough idea of the location of proteins of interest.

Other (more advanced) projects like this one : JVirGel (publication), Prime and virtual 2D gels (at the Andrews Research Laboratory), ProtPlot (not sure same goal) and Gelprint.

Usage / Screenshot

After loading the main page, all you need to to is to enter your protein name, pI and molecular weight in the box on the right. It requires a special-but-simple format ... use one line per protein to be drawn. On each line, dispose the information like this :

the protein name without space (Swiss-prot name is a good example but you can use numbers)
a space
the pI (the separation is a point ".", like in UK/US/..., not a comma "," like in France, Belgium, ...)
a space
the molecular weight in Da (you should not separate thousands : 1kDa must be written "1000")
a semicolon

Click on the "submit" button and the virtual gel will be drawn below the form.

If you want, you can customize the appearance of the gel. In the appropriate boxes on the left, you can modify the image width and height, the minimum and maximum pI of the gel, the minimum and maximum MW of the gel and tell the system if you want to see the coordinates and the protein names (near the protein spot). Just click on the "submit" button in order to apply the new values.

When you are satisfied with the result, you can save the virtual gel by right-clicking (Mac : Ctrl + Clic) on the image and choose your brower "save image" function.

How to cite

Since it's a very small project, we didn't published concrete results with this tool. I would greatly appreciate if you cite Virtual Gel in your paper. Just do this like this :

POIRRIER JE., "Virtual Gel", http://www.poirrier.be/~jean-etienne/software/vgel/, 2005.

Since everything is under free licences (GNU FDL for the text, GNU GPL for the script), you can use, modify, distribute, ... Virtual Gel provided you comply with these licences requirements.

Download / Installation / Requirements

Virtual Gel is written in PHP and requires the GD library. It can be run "live" from this website. But if you want to run it locally or on your server, here is the script : virtual-gel-0.3.tar.gz (3 kb).

A browser is the unique requirement for the client side (everyday users).

In order to run it locally (or on any server), you need PHP4 and GD (usually installed with any Apache server in most GNU/Linux distributions). It runs smoothly on my Debian GNU/Linux server in my laboratory. Just put the file in a directory and open them with your browser.

To Do

Although Virtual Gel is already running, here are some planned features ...

Better looking interface
Different shapes of proteins (according to the abundance ?)
DIGE / colors / comparison between gels
Since I did this in a half day, without looking at what others did, I'll see what other did and see if I can improve my script :-)
...

If you see an interesting feature that could be added, feel free to write it to me.

History

v.0.3 (2005/05/19): display as many proteins included in the box on the right
v.0.2 (2005/05/19): display 1 protein (hard-coded in the PHP code)
v.0.1 (2005/05/19): just there to play with GD

Credits / Contacts / Report bugs

Original author and maintainer: Jean-Etienne Poirrier

If you want to contribute, give advice, request features, congratulate, report bugs, ..., feel free to contact me.