Forum:In search of projects for collaboration.

Question

[cv.napping]

Hi everyone.

I'm a post graduate student of Biotechnology and I'm fond of Bioinformatics. I use the self learning approach and so far I've made myself efficient in various hands on analysis, tools, algorithms and programming (C and python). I'm on a 5 month vacation and I want to utilize it by joining some bioinformatics project . Since there are no such places at my native place to pursue a project from, I thought to search some projects online but I came up with nothing.

I'm planning to pursue my Ph.D. and then research career in Bioinformatics. I've a semester left, after which I'll have to start applying to various scientists for Ph.D.

The motive behind wanting to do a project is not one but two; Apart from brushing up my skills, I really want to have a good CV, something that shows my interest in Bioinformatics. Also I find bioinformatics a really fun subject and I'm totally dedicated to spending next few months with it.

So, any suggestions, any place or site you know where I can pursue my goal, would be really very helpful and appreciated.

Thanks. :)

Answer 1

[Pierre Lindenbaum]

suggestion: fork a bioinformatics project on github.com https://github.com/search?o=desc&q=bioinformatics&s=stars&type=Repositories , modify it, commit and send a pull request.

[cv.napping]

Sorry but I didnt understand how would that work. Can you explain please

[bw.]

which part are you stuck on?

[cv.napping]

basically the finding a project online to collaborate on.

Answer 2

[PoGibas]

As you're going to apply for PhD, my suggestion would be:

1. Find a lab where you want to do your PhD
2. Read their papers and learn techniques
3. Try to replicate their published work
4. Improve results, have questions about methods
5. Present your work/effort while applying for PhD

[cv.napping]

okay and what about doing a project of my own to showcase my skills to them? Any suggestions?

[mikhail.shugay]

A good suggestion. Although I've personally seen cases when certain PIs were not very fond of over-rigorous replication attempts that led to some criticism :)

[cv.napping]

Okay I see. Thanks for the comment. :)

Answer 3

[mikhail.shugay]

My suggestion is to first select a field you're interested in most and then try to understand and master the algorithms and software in this field. There is lots of public data in repositories like SRA and GEO, try to download some data, process it and analyze.

Of course it would be better if you not just straightforwardly apply the software (and simply getting a software to run and yield meaningful results is sometimes very difficult :), but also make some interesting follow-up analysis. Remember that "The formulation of the problem is often more essential than its solution, which may be merely a matter of mathematical or experimental skill". This would develop your skill as a researcher and also provide lots of opportunities for writing your own code (e.g. in python). The examples of simple follow-up analysis are: comparing samples under different conditions or comparing performance of various tools. But remember that you should start with some relatively simple task..

Installing and running most of NGS software available today will teach you with some basic UNIX skills. However you will surely benefit from some additional learning of UNIX systems.

As for having a good CV I believe that the only way nowadays to solve it is to join a really good scientific group, i.e. the one which is actively publishing high-level papers. You cannot improve your CV on your own while being M.Sc..