| Time |
S |
Nick |
Message |
| 14:29 |
|
pdurbin |
"A rule-based language for modeling protein interaction networks" http://kappalanguage.org |
| 14:30 |
|
pdurbin |
via http://fontana.med.harvard.edu/www/Documents/Lab/research.signaling.htm |
| 14:58 |
|
dotplus |
I was a Chemistry undergrad and I took various subspecializations in biochem. I remember thinking then (~20years ago) that in order to really predict outcomes, we're going to have to have a *much* better understanding of the rules *and* so much more computing power that I couldn't even imagine it. |
| 15:00 |
|
dotplus |
I haven't kept up (you know my area now:). Are we actually able to predict how a particular protein will behave? inside a cell? generally in vivo? |
| 15:00 |
|
dotplus |
I assume not, not even under rather rarefied circumstances |
| 15:01 |
|
pdurbin |
it's neat to think of two proteins interacting is like code |
| 15:03 |
|
pdurbin |
dotplus: time to brush up on your OCaml and dive into https://github.com/Kappa-Dev/KaSim :) |
| 15:11 |
|
dotplus |
well, yes on a theoretical/elegance basis it's superfun. But remember, proteins are (merely!) big molecules of individual atoms, albeit wrapped up in crazy ways. And there are so many different things going on in a *single* protein (1ary -> 4ary structure, and the various electronic/interatomic forces, the intermolecular forces that acutally act intramolecularly because polypeptide chains aka proteins are so big and convoluted (don't forget ... |
| 15:11 |
|
dotplus |
... chelation to metal ions and the crazy interactions with the "solvent" (cytosol) that that brings), etc.) that you can only predict if you can ignore/account for all this complexity. |
| 15:11 |
|
dotplus |
whew it's all fun & games until you actually want the correct answers! |
| 15:12 |
|
pdurbin |
:) |
| 22:57 |
|
sivoais |
hehe, speaking of... |
| 22:58 |
|
sivoais |
I was reading the case of a chemistry group that needed to retract many papers because of a software bug in their analysis code |
| 22:58 |
|
sivoais |
and you know what that bug was? |
| 22:58 |
|
sivoais |
flipped handedness |
| 23:01 |
|
pdurbin |
sivoais: wrong chirality? |
| 23:01 |
|
sivoais |
yep |
| 23:01 |
|
pdurbin |
bummer |
| 23:03 |
|
sivoais |
here's the reference: <https://en.wikipedia.org/wiki/Geoffrey_Chang#Retracted_papers>, <http://science.sciencemag.org/content/314/5807/1856> |
