Talk:Bioinformatics
From IGGP
Greetings!
I am happy to announce that you can now submit Nimblegen data to PLEXdb :-) For Vitis, we currently support both the "MD" and "Custom" designs for Vitis and our support for "MD" includes both versions (there are two different randomizations of probe positions out there for "MD"). If you have any another Nimblegen gene expression chip design, please contact me about it and I will set it up in PLEXdb as well.
Here are the steps to data submission:
- Login to PLEXdb.org or create an account.
- Click "Submit Experiment Data" on the left hand side. And then "Submit a new experiment"
- Follow the instructions for defining your experiment's design and data upload You will notice we require ".xys" files for Nimblegen submission. I posted a video showing how to produce.xys files from your scan images using the Nimblescan software (it's really just like producing .pair files). If you only have .tif images or .pair files, upload those instead and immediately email me so that I can convert them for you.
Everything remains private on our system until you release it for public view. The same is true for the automatic GEO submission of every experiment. Please feel free to email me if you have any questions or problems. Also, feel free to forward this message to anyone who might be interested in submitting. Lastly, I would also appreciate a list of any other researchers I can contact with this news.
Why submit to PLEXdb?
- It satisfies a growing requirement of journal publications to deposit data in a sustainable public place.
- It exposes your data to all of PLEXdb's mining and visualization tools.
- For new experiments, submission is itself a tool for defining your experiment design. and more!
--Vanhemert 09:07, 22 February 2011 (PST)
