Tag: Proteomics

A new home for IPGphor2reader

IPGphor2reader is a software meant to parse log (text) files resulting from an experiment with the IPGPhor and to plot graphs. I previously hosted it on my personal website and just moved it to Sourceforge, here. Amongst the various reasons for this move, I wanted the possibility for anyone to participate in the project and no hassle to manage this.

Slowly, slowly, most software on my website will be hosted on Sourceforge or Bioinformatics.net.

P.S. Obviously I chose the time where they are in the middle of a large scale site changes and upgrades so nothing is available for now (except the screenshot).

The hardware side of Picklist Editor 0.1

This morning, I released Picklist Editor 0.1 with a text introduction … Hmmm … on my photos on Flickr you can see the hardware side of the picking process … (click on pictures to see details).

2D gel after spot picking On the photo on the left, you can see a gel on a low-fluorescent glass plate. This plate is in part in a tray that firmly holds it when the robot is doing its job. The holes everywhere result from the picking process but there are proteins everywhere and you can’t see them in visible light since they are labelled with fluorescent Cy dyes. You can see two white round stickers on each side of the gel: these are the picking references.

Spot picker head on gel

Here, the picker head is in the process of taking a part of the gel with some proteins inside. Exact positions were computed according to the fluorescent images, revealing the proteins. As you can see again: the gel is perfectly transparent for our non-bionic eyes.

Amersham spot picker in action Finally, you can see the spot picking robot in action. The picking head is moving following two axis thanks to the horizontal bar at the back and the perpendicular arm holding the picking head and camera. On the left, you have a pumping station: in addition to some jazz when the picking head is on the gel, the station is aspiring water through the head in order to help getting a plug out of the gel. After that the arm moves to the right of the photo where you have two 96-wells plates to collect samples. When the head is above a well, the pumping station is “blowing” water into the head in order to eject the plug into the well. Everything is under control of a computer and software that is on the right, outside of the camera angle.

GE Typhoon scanner This is the GE Healthcare “Typhoon 9400” scanner used to scan fluorescent gels. It’s a huge beast but it doesn’t make a lot of noise (well, I don’t want to stay the whole day next to it!). And this unit only has the red and green lasers inside. There is a second (smaller) unit below with only a blue laser source in it! You can see two gels ready to be scanned (the upper door has to be closed before!).

Sunday at work Next is the analysis “workstation” where images of the gels are analyzed (after scanning and before spot picking). The software (DeCyder) helps to create pick lists.

Other photos from my labs can be seen in my laboratory photostream.

Picklist Editor 0.1

When you work with 2D gel electrophoresis in proteomics, you end dealing with "pick lists". For this purpose, I wrote Picklist Editor, a tool to help visualize and modify this pick list.

Picklist Editor 0.1 screenshot

As usual, software and source code are available here. Feel free to use it and report any bug or your wish list 🙂

(and if you didn’t understand everything above because you are not in the proteomics field, just go to the page too because I also wrote a small introduction)

I should change this blog title to “Version 0.1” since I recently released version 0.1 of many software tools 😉

Receiving broken vials …

Antibodies vials inside the broken cool-packI was eager to receive some new antibodies for western blotting (I was waiting for them since December 2006!). They finally arrived on Wednesday but everything was broken inside! 😦 A plastic shell was supposed to protect the precious vials (about 300US$ each) but even that was broken. I immediately phoned the company and they promised me new vials for next Wednesday. Suddenly, it’s possible to get them in one week … Well, let’s see what I’ll get on that day …