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Visualized the human genome with vvvv - Thesis

question open project/idea GPU particles genome gene data visualization bioinformatics

tekcor 17/01/12 - 11:46

Dear vvvv community,

This is something i wanted to share for some time now.
Over the last year i worked on my bachelor thesis in bioinformatics "Interactive 3D Visualization of High-Dimensional Genome Data" in which i basically created a GPU particle system which builds up an interactive chromosome visualization from genebank files, a standard in gene notation.

It is available here: http://bioinformatics.uni-konstanz.de/student_projects/david_gann/index.php

The data set was a lucky finding due to its innovation and importance for current molecular biologic and genetic research. Although it needed special efforts, vvvv is now the first programming language (as far as i know) with some kind of lib for visualizing the human genome (and of course every other genome) in 3D.

It is still a first step, a proof of concept work and far from being perfect. But further development on the methods could evolve this one to an attractive package for bioinformatics.

The reason why i do not yet create a contribution with it is simply the lack of a good documentation in the modules and a missing line in pin and module naming conventions. I hope to change this as soon as possible.

Thanks to the community who made it possible!
by helping me all the time getting my head around vvvv and providing me with the right input at the right time for almost 2 years now (dottore, kalle, m4d, io, vux, tonfilm, catweasel (thanks for the apple), woei, just to name a few).
Some of your contributions flew into the patch of this thesis as well (properly cited).

So... try it out and tell me what you think.
But be careful, it is a really big patch which takes some minutes at start up and when you load the data.

Thanks,
Dave.

e: slowly began to tear down everything into pieces and making little cotributions out of it.

ratiocurve

16 replies 0 new

link | Flag this reply as a solution. Urbankind 17/01/2012 - 14:21

Congrats on making such interesting project! Will head back home and see this patch in action :)

link | Flag this reply as a solution. h99 (translator) 17/01/2012 - 20:40

Post a screenshot!!!

EDIT: with Ctrl + 3, I mean...

link | Flag this reply as a solution. m4d 18/01/2012 - 10:49

just wow, tekcor.. :o
also congrats on your master thesis! ;)

link | Flag this reply as a solution. ciso 20/01/2012 - 04:18

hii...

scuse me, but how i can dowload the project?

i have click on the link

 http://bioinformatics.uni-konstanz.de/student_projects/david_gann/index.php

but i have found only i file.rar and not for win...

by...

link | Flag this reply as a solution. dannielmach 20/01/2012 - 11:29

this piece is worth money congratulations ....!!!

link | Flag this reply as a solution. antokhio 20/01/2012 - 19:53

vvery cool thx 4 sharing

link | Flag this reply as a solution. tekcor 23/01/2012 - 16:43

Thanks! I hope it will be usefull or inspirational for others.
Did anyone run it? I would be courious about your experience with the performance or any problems you encountered. I'm sure that the 10 minutes loading time (vvvv stuck in calculating one frame) could let people think that it crashed...

@ciso: there is a download link on the page.

screenshots:

link | Flag this reply as a solution. h99 (translator) 23/01/2012 - 20:15

Does it makes any sense to load one module at a time (that DataFormation ones), to reduce loading times?

If yes, there's a order (lightest module>heaviest module, please!), or it doesn't matter?

Cause the patch really gets stuck on my pc!

I found a little workaround that lets me see some more, but when I load RNA module (which, looking down, from left to right, to the bang "Start" IOBox is the fifth, including SystemFolder), well it takes a lot of time.

I'm asking this because TaskManager shows a slowly incrementing memory usage by vvvv (when loading RNA module---the "first four" simply make their 50/75 mb jump and everything then's fine) and experimenting this way is a deep time-comsuming method, since I really never get sure if everything's working properly.

I'll post the automated solution (LFO + Framedelay + etc) if you give me a hint.

Ah! And maybe it's possible to load separate pieces of module, too... no?

Thanks!

link | Flag this reply as a solution. Noir 25/01/2012 - 12:15

thanks for sharing this project!so cooool

link | Flag this reply as a solution. tekcor 25/01/2012 - 17:32

seperating those modules in time sounds like a good idea. would be worth a try. or at least calculating the RNA data after everything else could work, too. i didn't test it yet. but since the RNA data is the heaviest in memory it needs, it could work.

For this purpose connecting all the Ready and Build pins in a chain would be the easyest way.

Or, for instant result, disconnect the mRNA DataFormation module. The intron and exon boundarys won't be shown then, but it should work way better.

Debugging is painfull here, indeed :)I should include a smaller example data set, like for e coli bacteria or something.

link | Flag this reply as a solution. h99 (translator) 26/01/2012 - 02:34

Hi!

So here's my time-switch. It's now set to 16.5 secs, as I found on my pc to be the best time to avoid, uhm, overlapping freezing states of vvvv - it is something less to say the truth, but this gives me a good threshold.
I simply left RMNA module as the last one.
It's still a hard job, but now more affordable. I've added also an automatic bang to build the SlicedParticleMesh.

Renderer was up and running in about ten mins (screensaver told me!) on an Athlon 64X2 Dual, XP 32bit.
It's a skipping and tilting experience, when looking at a particular gene, but who knows, maybe it's possible to get some good results even here.

Let me know you think!

Ciao

time_switch

link | Flag this reply as a solution. tekcor 26/01/2012 - 22:01

Cool thanks for working on this project!
It feels a bit faster and shows that DataFormationMRNA is responsible for most of the loading time. Of course, the LFO thing is not the optimal solution, but good step anyway.

link | Flag this reply as a solution. h99 (translator) 27/01/2012 - 09:36

I agree; but LFO was the fastest and easiest thing I was able to think, and I wanted to see my genes on screen ASAP!

So I think I'll patch something using the other bunch of nodes, to create a readywise start.

Another thing: when I close the patch and then vvvv, Windows pops up a security issue message for Explorer, then kills the process. Have you experienced this?

Ciao

link | Flag this reply as a solution. sapo (translator) 20/02/2012 - 22:06

http://www.nanoporetech.com/news/press-releases/view/39
Can this be used thru a plugin to get the data live?

link | Flag this reply as a solution. tekcor 22/02/2012 - 07:22

i don't know anything about the architecture of this device. but depending on the live data an interface plugin could be possible and then of course live visualization could be possible. This is definately something for a bigger project. Let me know if you start digging in this direction.

Note that there is a difference between DNA sequencing and RNA analysis.
Both using same technology but aiming to different fundamental questions: What is the DNA basepair sequence? and how much RNA is expressed in the cell? One sentence in the article describes that the device is capable of RNA analysis, too, but its main function seems to be DNA sequencing, which would look different when visualized in a sensefull way (dont know how).

link | Flag this reply as a solution. HFS 22/02/2012 - 14:05

Really really amazing work!
Me and my friend (who has a masters in bioinformatics) were talking about doing something like this once. Of course with other work to do we never really got to the point of realizing it

It's amazing what you did here.

Visualized the human genome with vvvv - Thesis

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