Interested in hearing about any of your quantitative or computational lab research

[neofight]

A previous thread mentioned computer modeling used in lab research. I thought that was an interesting type of research and therefore I am interested in hearing more about any quantitative or computational lab research that you have done considering that most people who apply to Md/Phd programs do "wet lab" research

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[Sonya]

I planned to post the same question a few weeks ago... I am very interested.

Another question is how do you think these are fundamentally different from wetlab research. (besides that you spend your days in front of a computer, or soldering wires). I'll add engineering design into the list: quantitative/computational/design.


I'll share my experiences.
In undergrad, my project was to quantify forces exerted by neurons, so in particular i was designing methods to measure elasticity of biomaterials (on a cellular level).

So, basically it was like making a new technique. Only, it required a lot more thinking/reasoning about the science then most bio lab work. You need to also be able to take absence of data for a long time with design.

But, this was an undergrad project, and my senior year I was just starting this phase of the project. Thus, i believe i don't have a very realistic picture. Besides, i've never been able to find research like that anywhere else.

Hope this helped some.

Sonya

 

[Primate]

Only MSTPs I know for sure (so there are likely many others) that have a computational option for the PhD are Penn and Pitt. Sorry I can't give a better list. I know one person at Penn who did a combination of wet-lab and simulation - pretty cool (and what I proposed for a prelim. exam grant application, but not my actual research area). I also only know about the neuro options available at these schools, so I can't speak to other areas.

Don't know how widely available these types of PhDs are, but I'm interested. Biology is too complex to stick with single gene approaches, so simulation will become increasingly important in deciphering and connecting data into meaningful relationships (IMHO).

P

 

[Taty]

I will add NYU, Cornell, and Columbia

 

[Nuel]

I am currently working in two labs, in an experimental analytical chemistry lab, as well as a computational chemistry lab. To interprete or understand why some things happen (the difficult part), particularly in relation to molecular energy in the experimental set up, I need to return to the computational chemistry/biochem lab to investigate these processes. There is a girl in the analytical biochem lab who also has to return to the computer to look at stuff concerning genes, QM calculations of binding energies, appropriate receptors, etc. These are things that you just can't do without the computer and this avoids all the trial and error crap. So yes, genetics will never be enough, we need the computer. And of course I am in Pitt, one of the major hubs of bio-computation. I would really love to go to UPitt if they decide to accept international students. Well, still hoping.
I got rejected from a neurobiology lab, and I am glad it worked for good. I like what I am doing this summer and would choose it over neuro ten times. As a bio major, this gives me a new and more analytical experience. Actually, a lot of profs in the other labs, from chemistry to genetics, come to the computational lab to speak with the PI to see if he can simulate some of the processes they are investigating, particularly when it involves molecular interaction, and see if he can explain the reasons for certain observed phenomena.

 

[jberg4]

Having done 2 and a half year of wet lab I decided to seek out other kinds or research that didn't confine me to a work bench. I did a summer research project analyzing neuronal responses recorded from monkeys via an intercortical electrode during a reation time task. The purpose was to see if I could detect a systematic relationship between sensory input and motor output. I only did the the computational analysis because of the short time I had with the program, but the whole project was very intriguing. I also work at my university and I am about to start a project where I will try to interpret human EEG waves into commands that can control a motor controlled wheel chair. I really like this project because its non-invasive and I don't have to feel bad for the poor implanted monkeys or rats. I don't have a problem with using animals for research because I understand its neccesary in a way (hopefully this won't open up a debate on this thread-this is just one girl's opinion) but actually working with the animals was a little disturbing. I'm a lot happier now that I am not pipeting!

 

[IrishOarsman]

hey, i'm an undergrad and finishing a project on post-SAH aneurysmal vasospasm and starting one on atrio-ventricular malformations (AVM). in other words, i'm working in a neurosurgery lab. my value added to the lab is my ability with digital images and general programming stuff.

my advice for you is to cast your net wide when looking for a lab if all you want to do is work with computers. you could enter any school and find somewhere that would love to have you. i'm not too sure about getting the right title on your degree, but i am not the expert on that.

 

[strangeattractor]

for my ugrad and current grad work i'm doing computer simulations of molecular behavior using control systems & pk/pd software...computer simulation is getting to be pretty big in pharmacokinetics/dynamics because, as someone else said, it diminishes the amount of trial and error in the experiments and clinical trials to follow. for example: there is an optimal dosing regimen subject to the constraints of when the patient is sleeping, or how many times a day is feasible for a patient to take medication that will maximize the drug's effect (this is essentially an optimization problem for any engineers out there).

basically my idea is this: computers NEED to be integrated into medical science, not only for imaging. if a computer model can predict how your patient will respond, it makes the time and effort designing experimental protocol or patient procedures better spent for the wet labbers.

 

[smd0001]

I have the 'wet-lab' background as does everyone else in this thread...has anyone here made the dive to bioinformatics endeavors. As an undergrad biochem major who is contemplating adding the computer science (minor/major) --has anyone moved on to anMSTP where they are doing bioinformatics?

 

[Nuel]

my computational experience so far is not something I will call great. Even the related experimental work did not really come out well. now i am stuck on the computer to see certain dynamics and hypothesize on the undone experimental portion of the work. actually I have struggling to put things thru, it ain't easy moreso that a life science person is left alone to figure out how a molecular mechanics program works, but it is fun and we've (me, myself and I) been glad at even the slightest progress.

 

[GraC_undr_PrsR]

Hey,

I'm applying MSTP and I have completed three years of computational chemistry research on the HIV protease/protease inhibitor complex and interactions. I finally got some "wet lab" experience as an intern at Merck this summer, but most of my work has been theoretical. I can't wait to explore other areas of research!

'GraC