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Survey: Bioinformatics in your organisation


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#1 John Carroll

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Posted 09 February 2010 - 04:33 AM

Hi

I am a computer graduate who recently started a research masters in bioinformatics.
The masters will be focused on the software side of bioinformatics rather than the biology.

Here is a link to a short survey: Bioinformatics Survey It has 10 questions and will take only a few minutes to complete.

The purpose of the survey is to see what tools are being used, area of use and any comments people have.

The survey is based on interviews with post graduate students in the Cork Institute of Technology Biological Sciences department. Feedback from other people would be great.

Any comments good or bad would be greatly appreciated!

Thanks,
John

Edited by John Carroll, 09 February 2010 - 04:33 AM.


#2 DELETEMYACCOUNTPLEASE

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Posted 09 February 2010 - 03:11 PM

5. Please select the best bioinformatics tool that you used.

#!/usr/bin/perl or #!/usr/bin/python ... perhaps linux, maybe matlab, no wait, R.

#3 John Carroll

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Posted 10 February 2010 - 05:20 AM

5. Please select the best bioinformatics tool that you used.

#!/usr/bin/perl or #!/usr/bin/python ... perhaps linux, maybe matlab, no wait, R.


I know there are loads more tools out there and ways to solve a problem.
The postgrads i have talked to or interviewed do not have have any unix/linux or perl experience.

I have 10 replies so far to the survey. Thanks all!

#4 DELETEMYACCOUNTPLEASE

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Posted 10 February 2010 - 05:31 AM

5. Please select the best bioinformatics tool that you used.

#!/usr/bin/perl or #!/usr/bin/python ... perhaps linux, maybe matlab, no wait, R.


I know there are loads more tools out there and ways to solve a problem.
The postgrads i have talked to or interviewed do not have have any unix/linux or perl experience.

I have 10 replies so far to the survey. Thanks all!


I hope they don't claim to be bioinformaticians. I just don't think that the question is very good. If you are a CompSci grad why are you doing an MSc that focuses on CompSci? Believe it or not, learning biology/chemistry/physics is crucial for bioinformatics*.


*includes computational biology/chemistry - bioinformatics is building databases, putting sh*t in and then pulling it back out at a later date (yawn).

#5 John Carroll

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Posted 10 February 2010 - 06:10 AM

Yes... on reflection that question is poor. This is the sort of feedback i want. To hear from people in the industry!

No, they are not bioinformaticians. They are molecular biologists that need to use bioinoformatic tools. I think they had 2-3 hours formal training in bioinformatics, a few labs in the undergraduate degree. The masters i am doing is a software development project but i also have to learn basic biology, chemistry, molecular biology. I wont be doing any "wet work" as i dont have a clue about that side. I am interested in how the databases, algorithms and tools work and how they are applied to biology. The survey is really an attempt to see what tools people are using out there.

I am not doing this masters to become a bioinformatician but become a software developer in the domain.

#6 DELETEMYACCOUNTPLEASE

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Posted 10 February 2010 - 07:06 AM

Yes... on reflection that question is poor. This is the sort of feedback i want. To hear from people in the industry!

No, they are not bioinformaticians. They are molecular biologists that need to use bioinoformatic tools. I think they had 2-3 hours formal training in bioinformatics, a few labs in the undergraduate degree. The masters i am doing is a software development project but i also have to learn basic biology, chemistry, molecular biology. I wont be doing any "wet work" as i dont have a clue about that side. I am interested in how the databases, algorithms and tools work and how they are applied to biology. The survey is really an attempt to see what tools people are using out there.

I am not doing this masters to become a bioinformatician but become a software developer in the domain.


These areas get mentioned occasionally
1. storing and accessing large amounts of data - graph databases or oracle/sql
2. MapReduce - we have lots of data but lack the tools to manipulate it
3. Graphical programming
4. GPU processing / muti-thread - speeding up current tools, speed is an issue for protein structure simulations

#7 John Carroll

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Posted 11 February 2010 - 04:06 PM

These areas get mentioned occasionally
1. storing and accessing large amounts of data - graph databases or oracle/sql
2. MapReduce - we have lots of data but lack the tools to manipulate it
3. Graphical programming
4. GPU processing / muti-thread - speeding up current tools, speed is an issue for protein structure simulations


Thanks alot perlmunky!




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