Question: Masters Ideas in Computer Science that tackles Bioinformatics Problem
gravatar for amr.ali2021
6.1 years ago by
amr.ali20210 wrote:

Dear Sir,

I would like to ask you to recommend/suggest to me some Bioinformatics area that has problem that needs to be solved and computer science can help in it.

I have a bachelor in computer science, Experience in R , SAS Analytics Software and good Programming skills.

I'm also heading to Big Data field with my work.

I don't have any prior experience regarding Bioinformatics, that's why I need your help to just direct me to the right direction.

I know that this needs a lot of research from my side to find some topic to work on it, but I thought that you might help by just recommending any topic/research area that might be rich for me to tackle and to solve using my R, Analytics, Programming skills.

Thanks a lot for any reply.


R • 1.9k views
ADD COMMENTlink modified 6.1 years ago by Renesh1.9k • written 6.1 years ago by amr.ali20210
gravatar for Renesh
6.1 years ago by
United States
Renesh1.9k wrote:

Consider following topic if you find interesting;

Development of genome assembly tool which should not be memory intensive considering large volume of data and should employ parallel computing approach. The several of genome assembly tool i have tried are very memory intensive and need high performance computers to run (eg. SOAP denovo, AbySS)

ADD COMMENTlink written 6.1 years ago by Renesh1.9k

What about Minia assembler? ( ...performed a complete de novo assembly of human genome short reads using 5.7 Gb of memory in 23 hours.) Also, by the time author of the question develops his assembler, whole field can move to the long reads. I would rather invest into something prospective than something needed right now.

ADD REPLYlink written 6.1 years ago by Biomonika (Noolean)3.1k

Agreed, it's probably better to find a local group that needs something specific (and complicated enough to require a CS master's student) and make that. Things like de novo assemblers (minia is quite impressive) and aligners have too much competition from established groups to be worthwhile for a master's project.

ADD REPLYlink written 6.1 years ago by Devon Ryan97k

@Noolean, thanks for information. But if he still interested in this topic, he can cover the drawback of available tools and aim for assembly tool for longer reads.

ADD REPLYlink written 6.1 years ago by Renesh1.9k

Thanks so much for the suggestion, sure I will consider it.

ADD REPLYlink written 6.1 years ago by amr.ali20210
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