Sunday's hands on session content

[Umesh Mohan]

Dear All,

On Sunday's hands-on session, we will as a group try and code a
non-trivial, not very small, biologically relevant program. This
program will make use of most of the concepts covered in Saturday (and
a bit more?).

Please reply to this email thread with your
1) Current area of research
2) The kinds of problems that you need to address computationally in your research

Based on the replies (which are in by Sunday morning), I will choose a
problem and we can all crack it together.

Best,
Umesh Mohan

[Kambadur Ananthamurthy]

Hey Umesh,

I work on Systems Neuroscience, understanding the spatio-temporal pattern of activity in the Hippocampal CA1.

I would require coding primarily for my analysis, which includes,

1. Reading .tiff files,

2. Realigning images (to correct for motion artefacts)

3. Correlation analysis between vectors

4. Clustering, based on correlations

5. Receiver Operating Characteristics (ROC) with my datasets

Sincerely,

Ananth

[Umesh Mohan]

Dear All,

I have not got enough inputs from you all (only two people replied :
1st - protein folding, 2nd - systems neuroscience). So to choose a
problem for today's hands-on session, I will take a poll in the class
itself (2pm today, Malgova).

See you all at 2.

> --
> You received this message because you are subscribed to the Google Groups
> "Programming and Computing Group, NCBS Bangalore" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to pncg+uns...@googlegroups.com.
> To post to this group, send email to pn...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.



--
Umesh Mohan,
Research Scholar, Insect Flight Lab (Lab-6),
National Centre for Biological Sciences,
Tata Institute of Fundamental Research,
GKVK, Bellary Road,
Bangalore-560065, India.
http://www.ncbs.res.in/node/249

உமேஷ் மோகன்
http://bit.ly/umeshmohan

[Dilawar Singh]

Dear Umesh,

I booked the room from 3pm onwards.

   Dilawar

[Umesh Mohan]

The session starts at 3pm.
I am sorry for the confusion.

See you at 3.

[Arunabha Sarkar]

Dear All,

Some suggestions, regarding this course (I feel great and excited about it by the way):

I think all of us serious about this student driven course to come with atleast 2 simple biologically oriented problems (perhaps 2 problems every week) which when we solve via code writing will help our programming + algorithm (the latter is of less priority to us biologist). If we post something that is too deep into our own work, then it may not be worth doing for rest particularly if it is very time taking. Plus, some sort of questions coming from different participants may help us knowing something entirely new and super useful like gnuplot or .csv file that we heard about in the last class.Examples of these kind I am suggesting, the first one is very basic and easy and those who don't recognise it or know about it at first will marvel at the answer.... (This question has some historical significance in the field of bioscience). More on the second problem later.

Problem 1:

Suppose a newly-born pair of rabbits, one male, one female, are put in a field. Rabbits are able to mate at the age of one month so that at the end of its second month a female can produce another pair of rabbits. Suppose that our rabbits never die and that the female always produces one new pair (one male, one female) every month from the second month on. 

Problem 2:

Modelling/simulating a positive feedback loop imbedded inside a negative coherent feedback loop type 3 (http://2009.igem.org/wiki/images/thumb/c/c3/FFd_global.jpg/250px-FFd_global.jpg). Doing this will have many benefits like in order to simulate this, we generate output data files in .csv files. Use this file's data to plot it (and learn a graphical plotter in the process) and better understand what is going on. This is how most genes are regulated, so we can get a deeper understanding of the biology. Also, this the output of this can be transient peak, we can investigate what parameter changes can result in sharpening of this peak to a pulse. Can neuron firing modeled like this for a particular set of parameter values (the physical meaning of those parameters will not be gene activation or silencing, rather they will be some calcium reservoir getting used up or something or I might be completely wrong (most likely :P))? 

Also, I thought of starting Project Euler problem list (https://projecteuler.net/) with python to get a hang of the language. I would suggest those new to this to try the first few problems (later ones will benefit only those interested in maths). Doing the first problem really made me marvel programming. It took me more than 30 mins to do it correct. In the end, code was only 6 lines out which only 2 had any calculation. I have done till problem 3, Those who are brilliant in maths and programming can take up this challenge: Try solving the most difficult ones :).

Project Euler got me thinking, it is of immense benefit to physics and maths student but no so much to biologists to will deal with say strings or data files, image data files, video data files. So, should there be an equivalent of Project Euler in Biology that will help students like us immensely? Few google searches later, I have found one. It is called Project Rosalind I think: http://rosalind.info/problems/locations/. Will update more on this if I get useful stuff from it. Everyone curious about this, please let me know if you find anything usefull/helpful.

Also, we students have another exercise at hand: Taking DNA sequence as input and giving back protein sequence(s) (if they exist)... So 3 problems for the week already to think about.

Suggestions welcome.. and necessary

Cheers,

Arunabha

How many pairs will there be in one year?

[Arunabha Sarkar]

Sorry, problem 1 was incomplete, the final question was missing. Here it is:

Problem 1:

Suppose a newly-born pair of rabbits, one male, one female, are put in a field. Rabbits are able to mate at the age of one month so that at the end of its second month a female can produce another pair of rabbits. Suppose that our rabbits never die and that the female always produces one new pair (one male, one female) every month from the second month on.

How many pairs of rabbits in a year?

[Umesh Mohan]

I disagree with algorithms being less priority to biologists. The whole
point of programming is to first devise an algorithm and only then
type it out in whichever language as a program. I would even go as far
as to say that putting together an algorithm is half the battle in
programming. Once you have the algorithm ready, you only have to
translate each step in the algorithm into code. I agree that this is
also daunting to many especially those new to the programming
language.

I agree that there should be a regular stream of simple problems for
people to try out and get help on. Learning is faster that way.

An equivalent of Project Euler to biology (not specifically
bioinformatics) would be really helpful.

Best,