[EMBOSS] Accessing Applications

[Peter Rice]

Marc Logghe wrote:

> I have noticed some changes at the EMBOSS web site as well. The docs for
> the individual applications can be found at this url:
> http://emboss.sourceforge.net/apps/cvs/index.html
> A direct link to the docs of diffseq is
> http://emboss.sourceforge.net/apps/cvs/diffseq.html.

These URLs will change as we update the website (we will change the apps/cvs 
part). A new path will appear for the docs for release 3.0.0. Thsi wil be the 
first time we have documented the latest release on the website - although few 
users noticed we were always documenting the latest CVS developers release :-)

EMBOSS does include full documentation for all programs which is installed 
into the share/EMBOSS/doc/programs/html/ directory. This will change in 
release 4.0.0 (July 2006). In release 3.0.0 the EMBASSY packages are still 
documented in the same directory as the EMBOSS main programs.

> I wanted to point you to some wEMBOSS implementations at various EMBL
> nodes but ... in order to use that you need to register, unfortunately.
> I don't know their policies  (http://bigben.vub.ac.be:6080/wEMBOSS,
> https://emb1.bcc.univie.ac.at/component/option,com_wrapper/Itemid,104/).
> Anyhow, the EMBL policies seem to differ from those used by the NCBI or
> EBI for instance, cos there everybody can make use of the tools. Even if
> you don't pay taxes ;-) 

I think you mean "EMBnet" ... I have to be picky as EBI is part of EMBL 
(European Molecular Biology Laboratory in Heidelberg, Germany) ... and also a 
member of EMBnet :-) National EMBnet servers provide access to their 
registered scientists, - that is what they are funded for - and may also allow 
access to those outside. If you are in the UK, you no longer have a national 
EMBnet server as that was the HGMP/RFCGR where EMBOSS was developed until it 
closed in July 2005. The Austrian server machine (univie.ac.at) is about to 
move so may be down for a while.

EBI does provide access to EMBOSS, but not a simple web interface to all the 
programs by name. You can also use many of EMBOSS programs through the EBI 
"Toolbox", but not diffseq which was the that started this thread. EBI also 
provides simple web service access through WSEmboss frok our External Services 
Group http://www.ebi.ac.uk/Tools/webservices/WSEmboss.html and fully featured 
web wervice access through SoapLab http://www.ebi.ac.uk/soaplab/ developed by 
Martin Senger in my group as part of the myGrid project (and now part of the 
EMBRACE project).

I still plan to survey all the EMBOSS interfaces in the near future ... once 
funding is sorted out ...

Hope that helps,

Peter