[BioRuby] Workflows and Parallelization

MISHIMA, Hiroyuki missy at be.to
Thu Dec 23 01:11:42 UTC 2010

Hi Raoul and all,

Unfortunately I have not had experience in analyzing transcriptome using
NGS. Recently I am working on exome mutation analysis and micro RNA
analysis using NGS. I will let you know if I find good material for NGS
+ transcriptome analysis.

Thank you for information about the Parallel library. It can be
foundations for the workflow management.

And I would like to add Raoul's comment about merits of workflow
automation. I think it has three merits.

First and second are as Rauol mentioned. It is good for wet-side
researchers to simplify the complex tasks, and it is good for dry-side
researchers to simplify the repetitive tasks.

Third is that it is good for workflow sharing. My ideas are like the
followings: Rspec (Ruby's test workframe) is the executable
specification. It is better than paper specification. Rakefile (or some
scripts) can be executable experiment note. It must be better than paper
experiment note. And it is good to share protocols in "experiment notes".

By the way, I afraid that talking about Rake/Pwrake and workflow
automation in the BioRuby mailing list may be kind of out-of-focus. Is 
it OK?


Raoul Bonnal wrote (2010/12/22 2:50):
> My original request was on analysis approach on NGS and transcriptome.
> btw
> Very interesting Hiro,
> searching on github there is also this project:
> https://github.com/grosser/parallel

MISHIMA, Hiroyuki, DDS, Ph.D.
COE Research Fellow
Department of Human Genetics
Nagasaki University Graduate School of Biomedical Sciences

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