Computational biologist

[MadScientist !!lOQ5EsK5OzE No.4339156]

Hi /sci/,

I'm quite new here, I noticed that most of the discussion is about maths and math problems with some exception, and was asking myself if any of you come from my specialization, computational Biology.
So if it's the case, what are you working on and why is it interesting.
I'll start, I'm working on protein structure prediction and I'm trying to use some new methods for making moves in the MC search instead of the "naive" sampling. Solving the prediction problem will be a break through in drug design and all..

[Anonymous No.4339165]

>MadScientist
>new here

I don't remember the tripcode, but you might wanna change your name.

[Anonymous No.4339184]

How much of what you do is maths and computers and how much is biology? What languages do you primarily use? What sorts of math?

[MadScientist !!lOQ5EsK5OzE No.4339188]

>>4339165
It's normal that you don't remember the trip code, it's the first time I post. But I don't understand why I should change my name, anyone already using it?

[MadScientist !!lOQ5EsK5OzE No.4339193]

>>4339184
I would say 50/50. Personally I never had a proper studies in Biology, I just took two courses in Bioinformatics and self-learned all about genetics.
But most what I do is theorizing (finding new formula, algorithm or methods), implementing it, but always taking account of the biological background, and always trying to analyze the results from a biological point of view.

The problem is biological but the solution is computational. You need to master the second part and understand the first (you don't need for example to know all Amino Acids and their properties, but have an idea what kind of properties they are and how they influence protein folding)

[Anonymous No.4339200]

>>4339188
>>4339188
>anyone already using it
Precisely.

[MadScientist !!lOQ5EsK5OzE No.4339202]

>>4339184
Languages, I prototype in matlab and python. And I code in C++ (the problem is an NP Problem and take a lot of CPU power, it needs to be clustered)
For math, I would say probabilities, statistics, algebra, geometry, graph theory, and everything that seems useful in the moment

[Anonymous No.4339211]

>>4339193
>>4339202
Thank you this is both very helpful and exactly what I wanted to hear.

[TN5 !/sci/TN5.. No.4339213]

Several friends of mine have worked in thing that maybe you call computational biology, one in his master thesis and another in his PhD thesis. The master thesis was about DNA sequencing: you probably know the domain better than I, so I won't try to explain anything, but it's quite cool.
The PhD thesis was about modeling, simulating and verifying biological regulation networks (just roughly copying the title here), for instance, using stochastic petri nets and temporal automata asa models for protein interactions in cells and validating with statical, dynamical, and quantitative dynamical analysis.
I'm not sure if the biological part is big in these examples though, the two guys are both from a pure math/CS background.

And about "MadScientist", http://archive.installgentoo.net/sci/?task=search2&ghost=&search_text=&search_username=m
adscientist&search_tripcode=!!Q11PG81nz2n&search_media_hash=&search_del=dontcare&sea
rch_int=dontcare&search_ord=new

(sorry about the long link)

[Mad Scientist !!Q11PG81nz2n No.4339219]

Cool, I've always wanted my own doppleganger.

[TN5 !/sci/TN5.. No.4339222]

>>4339219
Now you're going to have to figure out a way to convert this guy to deep sea exploration.

[Mad Scientist !!Q11PG81nz2n No.4339224]

>>4339222

That's the easy part. Pic related.

Probably best for him to choose a new trip, though, so as to avoid confusion.

[Anonymous No.4339263]

Protein NMR here; I give guys like you (who know how to program) comparitive shifts between wild-type and tagged versions so you can whack them into a tensor to determine structure - not quite ab initio prediction like your description leads me to believe..

[Anonymous No.4339330]

What's your opinion on Dwave's quantum computer, and how it could be used to speed up protein structure prediction.
If I understand correctly protein folding could be written up as a discrete optimisation problem, and those are the kinds of problem this machine was designed to solve.

http://www.dwavesys.com/en/dev-tutorials.html

[MadScientist !!lOQ5EsK5OzE No.4339387]

>>4339330
>>4339330
Honestly, I don't know much about Quantum Computing, I've just read the tutorials that you've sent. Interesting stuff, I think it can be interesting, although it seem more appealing for Machine Learning applications, the problem we encounter are more of minimization-search problems in extremely big room (~300 Dimensions).
As a first impression, I would say that QComputers may be really helpful in the future if they became less pricy (1 Million dollars for 128 qubit is a bit much).

[MadScientist !!lOQ5EsK5OzE No.4339391]

>>4339213
Actually my background is also pure CS with a bit of math. My Bachelor Thesis was quite theoretical. But then I got bored, and wanted to try my knowledge in practical problems, so I got interested in computational neuroscience and computational Biology.
I love it here.

[Anonymous No.4339393]

fold extracellular domains, OP !!

[MadScientist !!lOQ5EsK5OzE No.4339395]

>>4339263
Yep you got it right, I do abinitio prediction, although we try to use information in a novel way from the pdb

[TN5 !/sci/TN5.. No.4339397]

>>4339391
I have yet another CS/math friend who works with neural networks, specifically associative memories using neural networks. His former PhD advisor (and potentially future boss again) got a 2M€ grant for this project, so it should be quite awesome. He plans to actually build something in the relatively near future ("near" as in "research-near").

[MadScientist !!lOQ5EsK5OzE No.4339400]

>>4339224
For this post I will stay with this name to avoid confusion, in the future I will find something else or stay anon.
I just choose after watching Stein;Gate yesterday (quite awesome actually)