[emboss-dev] Fwd: Request For Work

Peter Rice pmr at ebi.ac.uk
Wed Aug 13 14:21:58 UTC 2008

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.


Peter Rice

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