[Pipet Devel] Re: The Loci Project

Peter Rice pmr at sanger.ac.uk
Tue Jul 20 10:44:24 EDT 1999

Jeff Bizarro wrote:

>Thomas Junier wrote:
>> One thing I could not find on the Loci page: what kind of
>> collaboration do you have with EMBOSS ?

>Peter Rice, the coordinator of EMBOSS, reads our list and I read
>theirs.  (He's sure to read this :-) And we've corresponded a few
>times, but that's about it.

Yup, I'm here :-)

>If I can take the liberty to speak for them, they are developing a
>command-line based system much in the spirit of the GCG Wisconsin
>Package.  They have chosen not to choose a GUI because there are
>several existing that can interface with the EMBOSS command-line
>(Loci could be on that list but doesn't really "exist").  We would
>like to make translators (here's where you guys come in) to interface
>EMBOSS with Loci, but EMBOSS has taken no official position on Loci.

EMBOSS appears to be command line based, but internally it uses a
simple "AJAX command definition" file (the idea comes from VMS). These
"ACD" files can be converted to other GUI definitions, so that we hope
to automate implementing EMBOSS under most other GUIs in

There are many of these around the EMBnet community and
beyond. Examples are BioNavigator (eBioinformatics and EMBnet
Australia) AppLab (Martin Senger, EBI), W2H (Martin Senger and EMBnet
Germany), www2gcg (EMBnet Belgium), SRS applications (EBI and Lion),
ACEDB utilities (Sanger Centre and Montpelier), Staden (Rodger Staden,
Cambridge), SeqPup (Don Gilbert, Indiana). No doubt there are others
and I would be interested to hear of your favourites. Each has its own
definition format, but all have similar content.

ACD files define everything that an application needs, and have
extensions which EMBOSS ignores to allow HTML forms and other GUIs to
be specified. These are very easy to extend.

Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/

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