terdon convo number 2

Conversation started Oct 18, 2015 at 21:35.

TanMath

Oct 18, 2015 21:35

@terdon you available?

terdon

Oct 18, 2015 21:50

@TanMath Kinda. What's up?

TanMath

@terdon want to discuss?

terdon

Sure. What about?

TanMath

@terdon shortest path problem...

and system biology..

What is system biology and are there any applications of shortest path problem to system biology?

terdon

Well, systems science, in general, is the approach of studying entire systems. For most of its history, science would follow what is known as the Aristotelian method. The idea was that if we cut a complex system into little pieces and then understand how each piece works, we will be able to infer how the system itself works.

This is a great tool and has been very useful. However, there are certain characteristics of any complex system that only become aparent when you study the system as a whole. These emergent qualities cannot be inferred by studing the system's constituent parts.

That's where systems science comes in.

Systems biology is one type of systems science.

TanMath

@terdon oh, ok, what is studied in systems biology?

terdon

Oct 18, 2015 21:59

A classic example of systems biology, and one where the shortest path analysis is often useful, is studying networks.

These could be the network of interactions between all proteins in a cell or gene regulatory networks (gene A codes for a protein that suppresses gene B which codes for one which activates gene C and so on).

Wikipedia has a nice little summary:

Systems biology

Systems biology is the computational and mathematical modeling of complex biological systems. An emerging engineering approach applied to biomedical and biological scientific research, systems biology is a biology-based inter-disciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionism) to biological and biomedical research. Particularly from year 2000 onwards, the concept has been used widely in the biosciences in a variety of contexts. For example, the Human Genome Project is an example...

TanMath

@terdon I am interested in biological networks that are more, possibly macroscopic, like spread of diseases.. But biochemical networks are cool as well...

terdon

@TanMath I don't know much about those but for one thing, as I said the other day, they are not really biological as such. They are fully as much anthropological or sociological.

If I happen to be the carrier of a disease and fly from London to Tokyo, then Paris and then New York, then that's the path the disease will have spread by. The shortest path would be Paris -> London -> New York -> Tokyo or whatever but there's no reason to assume the disease will have spread along the shortest path.

TanMath

@terdon then how do they model it?

terdon

@TanMath Don't know the details. Presumably, they have variables describing the possible movement of the carriers.

Really not my field though. You'll want to read up on epidemiology for that sort of thing.

TanMath

Oct 18, 2015 22:14

@terdon check this out - popularmechanics.com/science/health/a9842/…

Effective distance matters...

terdon

@TanMath Of course.

That's basically my point.

TanMath

@terdon But it therefore is the shortest path between, for example, airports put n terms of their effective distance

Correct?

terdon

That would be one way to look at it, yes.

TanMath

@terdon Ah! so it still is a shortest path problem! Correct?

terdon

I guess so, yes.

As I said though, I don't really know much about that sort of thing.

But yes, you could probably twist the SP approach into fitting that.

TanMath

Oct 18, 2015 22:20

@terdon so, I want to look into research for that.. should I search 'shortest path effective distance disease spread' ?

terdon

@TanMath Just read up on epidemiology analyses, probably.

Do you know PubMed?

TanMath

@terdon Yes..

terdon

This looks promising:

ncbi.nlm.nih.gov/pubmed/22877141

And this one:

ncbi.nlm.nih.gov/pubmed/22615729

I really don't know though. I just ran a search on pubmed.

I work on completely different things.

TanMath

@terdon what terms did u use?

@terdon what do you do?

terdon

@TanMath My last project was on protein-protein interaction networks. The paper I linked to in my answer to your question actually.

@TanMath ncbi.nlm.nih.gov/pubmed/?term=shortest+path+epidemiology

TanMath

Oct 18, 2015 22:27

@terdon oh, nice article BTW.. you live in france?

terdon

I used to. I'm now in Greece.

You?

TanMath

@terdon America...

terdon

Yeah, I saw that in your profile but that's a pretty big place. Well, it's actually a continent but I assume you meant the US.

So, where in the States?

TanMath

@terdon yeah... pacific area...

BTW, have you checked out my latest answer?

terdon

Ah, never been to that side. I've visited the East coast a bit and my Dad's from Philly but I've never seen the Pacific.

@TanMath Yeah, well done!

TanMath

Oct 18, 2015 22:30

@terdon thanks, I am very proud.. the most detailed answer I have ever done.. u upvoted?

terdon

yup

TanMath

@terdon thanks man!

terdon

I'd read it before and had forgotten to upvote.

TanMath

@terdon yeah, almost up to a thousand!

terdon

Nice!

I haven't been very active here lately. I spend most of my SE time on Unix & Linux since I'm a mod there.

So I still haven't reached 10k here. It's kind of annoying since I was used to having access to the 10k tools. The threshold was lower when the site was still in beta.

TanMath

Oct 18, 2015 22:34

@terdon yeah, i remember being able to close questions...

anyway, I gota go.. nice talking with you @terdon

terdon

@TanMath Yeah, I'm going to head off to bed as well. See you around :)

Conversation ended Oct 18, 2015 at 22:36.

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