[emboss-dev] Fwd: Request For Work

jitesh dundas jbdundas at gmail.com
Tue Oct 14 14:10:32 UTC 2008

Dear Sir,

I apologize for dissappearing from the activity after assuring to work on
this issue of trying to parallelize the EMBOSS project. I was not feeling
well and have not been able to work for 1-2 months. I am fine now and will
start working right now.

By the way, I want to congratulate you for getting the funding from BBSRC( I
saw on one of the science blogs).I hope we can continue to contribute on
this wonderful project.

I wanted to know the algorithm used in making the EMBOSS software. Maybe we
can fine tune the algorithm to getting better and longer patterns...

Any advise is most welcome.

Jitesh Dundas

On Wed, Aug 13, 2008 at 7:51 PM, Peter Rice <pmr at ebi.ac.uk> wrote:

> Dear jitesh,
>  Thank you for your reply. Please excuse me for the delay in replying as I
>> was out of town.
>> I am looking at working on this issue in 2 ways:-
>> 1) I wish to parallelize the phases of different softwares( if they are in
>> develpment stage).
>> 2) Next, if there is a connection or dependency between two or more
>> projects( or applications), then we can try to give the output that is
>> needed based on the current status of the output-supplying application.
> Aha ... so you are looking at running several EMBOSS applications in
> parallel? That is a very interesting issue for us.
>  I will need to know if there is any relationship identified between any of
>> the applications defined in the  EMBOSS project. If there are any
>> relations
>> already present between the applications, it will become easier to get a
>> handle to move the execution from one point to another.
> The inputs and outputs of all EMBOSS applications are marked up in the .acd
> files with a "knowntype" that identifies common outputs that could, for
> example, be combined and visuallised together - and also which ooutput could
> be used as inputs by other applications. For sequences, features, alignments
> and reports this includes whether the type is nucleotide or protein.
>  Also, Running applications in parallel will require a change in the way we
>> make our applications. We need to define a master relationship between all
>> the apllications, so as to relate all the applications with each other.
> We are also looking at adding definitions for the algorithm used by an
> applications, and a standard way to represent the transformations of inputs
> into outputs.
> Any feedback on these issues would be very welcome.
> We are also interested in looking at executing EMBOSS code in parallel is
> anyone is looking at that.
> regards,
> Peter Rice

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