Pseudocode to code-suggest the best language to learn

B

baccilus

Skilled
I have a pseudocode from a research paper but I need a real program for it to be of any use to me. I am a researcher and will later be integrating this program in to Cytoscape. Cytoscape is written in Java but it can take input from several languages. With this pseudocode, I should be able to find synergistic microRNAs in protein clusters in a protein network. The pseudocode is in the image:


Pseudocode-Synergy.png


Please note that I have no prior programming experience except a "C" exam I passed in my masters, which I have completely forgotten by now. In my line of work, R can be very useful and also Perl, but for now, I need to pick the best language that can get my work done as soon as possible. I am stuck at a research road block and this will be most useful to me.
Thank you,
Saurabh
 
Fortran or Python for fastest ramp up. If you do a lot of scientific computing on HPC clusters Fortran will be quite useful, else Python. Even though Python is largely used for scripting, it's powerful enough to handle these kinds of programs.
 
If you want to learn a new language then its okay, but if you want a quick solution to your problem then you might want to take a look at some other software packages out there.

Below are “pseudolanguages” that you could use:

1. MATLAB: I’m sure you’ve heard about it. Just a look at your algorithm and it yells out MATLAB (to me at least). But it costs and I don’t know what how long the trial period is for you to hack a solution off it.

2. Scilab: Open-source alternative to Matlab.
https://www.scilab.org/

3. LabVIEW: Graphical programming. Pretty easy to use. Has a lot of math functions. Its about Rs. 28K for the base version. But has a 30 days trial period, which should be enough for you to play around and work something out.

Another thing… What you are looking to do is pretty standard in Bioinformatics I’d imagine. Have you searched for software/apps that already do this? Maybe there’s no need to reinvent the wheel. Say something like this: www.bioconductor.org

Hope this helps,
Mohit.
www.BioZen.co.in
 
biozen said:
If you want to learn a new language then its okay, but if you want a quick solution to your problem then you might want to take a look at some other software packages out there.

Below are “pseudolanguages” that you could use:

1. MATLAB: I’m sure you’ve heard about it. Just a look at your algorithm and it yells out MATLAB (to me at least). But it costs and I don’t know what how long the trial period is for you to hack a solution off it.

2. Scilab: Open-source alternative to Matlab.
https://www.scilab.org/

3. LabVIEW: Graphical programming. Pretty easy to use. Has a lot of math functions. Its about Rs. 28K for the base version. But has a 30 days trial period, which should be enough for you to play around and work something out.

Another thing… What you are looking to do is pretty standard in Bioinformatics I’d imagine. Have you searched for software/apps that already do this? Maybe there’s no need to reinvent the wheel. Say something like this: www.bioconductor.org

Hope this helps,
Mohit.
www.BioZen.co.in
Click to expand...
Thank you for the immensely helpful advice. Although this is a standard thing in bioinformatics, the specific thing (microRNA synergy) I am trying to do is still relatively new. There are a couple publications about it, but all of them from China and are not giving away the source code. One of the authors I contacted did admit that they have a script written in C for this but they can't reveal it.
Thank you again.
Saurabh
 
Where do you work? IMTECH? Quite a few institutes have a Bioinformatics cell these days. Maybe they'd help you with a script in Python.

Could you link to the paper where you've got this algorithm? I'm not saying I can, but I'll give it a shot later this week. Right now am travelling on work not too far from your place... Hamirpur.

Btw, aren't you the same bacillus on Bikeszone? Am just a lurker there although I do cycle. Have a Trek GF Advance MTB... Small world!
 
Hi Biozen. Yes I baccilus on bikezone forum too. I work at PGIMER. I really doubt there is anyone who can help me with this here. Moreover, I want to be able to do this myself too, not just solve this particular problem and forget the skill. It will be useful to me in the long run. The source of the pseudo code is:

http://www.ncbi.nlm.nih.gov/pubmed/20929877
Just take a look at the supplementary sheets.
I am ultimately aiming for the following article, but the authors are not even revealing the pseudocode:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063342

P.S. I ride a Scott S50 :)
 
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