[Biojava-dev] Parallel Programming

[Daniel Asarnow]

On Sun, Jun 1, 2014 at 9:19 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
> I feel that there are many frameworks for parallelisation. While BioJava
> should provide the core support for thread safety, I would not want to tie
> it to one specific framework, because that would limit the freedom for the
> user.
>

I agree, but I also wonder where the distributed structure alignment
support fits in. Is it a special case due to the nature of large-scale
structure alignment and the lack of alternatives?


> In terms of documentation for local parallelism, I could write a cookbook
>> entry based on the utility I mentioned (i.e. how to do parallel alignments
>> using a thead pool).
>>
>
> That would be great. Besides the cookbook there is now also the beginnings
> of a new tutorial on github. So far it only covers the structure modules.
> However the github-markdown framework is a great way of doing something
> like that and I hope that more content will get added over time.
> https://github.com/biojava/biojava3-tutorial
>

I will do that then! I will send you what I put down in my fork of the
tutorial page before submitting the pull request. I'll also clean up /
comment the utility I mentioned and put it in my Github account.

-da