[EMBOSS] emboss, a web interface for EMBOSS

[Dr T. Carver]

Hi Mat,

It is possibly worth adding some of the main aspects of the Jemboss GUI:

Jemboss :
========

-launched via the web (Java Web Start) or a script
-works communicates to EMBOSS via SOAP (client-server) or directly
(standalone)
-optional user authentication (unix)
-presents programs as group listings & as a scroll list, parameters
displayed with pop-up help & help links
-local and server file management systems
-stores client-server results on the server, along with the run
information.
-provides direct access to the Jemboss Alignment Editor (though this can
be run independently of the main Jemboss GUI).
-dynamically calculates default parameters based on the users input (as
EMBOSS does from the command line).
-interactive or batch submission of EMBOSS applications to job queues
(NQS, OpenPBS or just the background).
-installation script provided to set up client-server or stadalone. This
install EMBOSS, Jemboss, axis, & tomcat on all EMBOSS supported platforms.
Plus a web-launch installation script

For more information on the design have a look at:
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14512356&dopt=Abstract

Regards

Tim Carver
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494500  Fax: +44 1223 494512
E-mail: tcarver at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk


On Tue, 13 Jan 2004, [ISO-8859-1] Martín Sarachu wrote:

> Hi Mat,
>
> 1) wEMBOSS is written in Perl while jEMBOSS is in Java.
> 2) wEMBOSS works from the browser (tested with IE 6 & Netscape 7) while jEMBOSS
> does not need a browser.
> 3) jEMBOSS needs extra installation (Jakarta & Java WebStart), nearly everything
> wEMBOSS needs comes in a regular Linux (except some Perl modules).
> 4) At this point, wEMBOSS is faster than jEMBOSS, but this is because of actual
> tecnology.
> 5) jEMBOSS has (not sure) batch capabilities, wEMBOSS not yet.
> 6) jEMBOSS has a file browser (for local & server files), wEMBOSS not yet.
> 7) Both jEMBOSS and wEMBOSS have a private workspace for each user.
>
> Hope this helps.
>
>  > Thanks for what looks like a good effort!
> Thanks, we're somewhat tired ;)
>
>
> Regards,
>
> martin
>
>
> Wiepert, Mathieu wrote:
> > Hi,
> >
> > Thanks for posting this.  Do you think it might be useful to post why this is different than JEMBOSS, or perhaps enumerate the differences between the two packages?  We are wanting a web interface here, and most people had pointed me to JEMBOSS, but this seems like a new entry to the field?  I didn't post this to the whole list, but they might be interested in the reply, but I wanted to leave that up to you.
> >
> > Thanks for what looks like a good effort!
> >
> > -mat
> >
> >
> >
> >
> >>-----Original Message-----
> >>From: Martín Sarachu [mailto:mad at biol.unlp.edu.ar]
> >>Sent: Tuesday, January 13, 2004 7:32 AM
> >>To: EMBOSS General
> >>Subject: [EMBOSS] wEMBOSS, a web interface for EMBOSS
> >>
> >>
> >>wEMBOSS, a web interface for EMBOSS
> >>===================================
> >>
> >>Features:
> >>
> >>     * Each user has a separate and private workspace.
> >>     * Organize your work by creating projects and subprojects.
> >>     * Results saved for easy recover & review.
> >>     * Inline help.
> >>     * Keyword search for programs and documentation.
> >>     * Administrator can exclude EMBOSS programs from wEMBOSS.
> >>
> >>You can download wEMBOSS from
> >>http://www.ar.embnet.org/programas/wEMBOSS
> >>
> >>Authors: Marc Colet, Martin Sarachu
> >>
> >>wEMBOSS is a joint effort between BEN & AR.EMBnet
> >>
> >>
> >>--
> >>Martín Sarachu
> >>mad at biol.unlp.edu.ar
> >>EMBNet Argentina
> >>http://www.ar.embnet.org
> >>
> >
> >
>
> --
> Martín Sarachu
> mad at biol.unlp.edu.ar
> EMBNet Argentina
> http://www.ar.embnet.org
>