[EMBOSS] Web Interfaces to Emboss Tools

Ryan Golhar golharam at umdnj.edu
Thu Jul 13 17:11:23 UTC 2006

Hi Andy,

Congratulations on your decisions to migrate from GCG to EMBOSS.  We did
it about a 2 yrs ago because of SeqWeb issues with different web
browsers.  We haven't looked back since.  If you would like to see our
installation, go to 

We were using GCG for at least 5+ years (before I started working here).
I discovered EMBOSS about 3 yrs ago and prefer it over GCG for many
reasons.  We didn't make the transition until we found a suitable web
interface as the majority of our users prefer the web interface.  In the
end, we chose EMBOSS-Explorer - it's a simple, clean interface
compatible with a wide range of browsers (a severely lacking feature
with SeqWeb).

I noticed you require server-side storge, EMBOSS-Explorer requires
nothing on the server side not even user accounts, the users store
everything locally on their machines.  This reduced our maintainence
needs for backups.  We find it to be a better solution than maintaining
central storage for this type of data.

I would recommend you tell your users to get their data out of SeqWeb.
You can hold onto the storage in case anyone doesn't.  There is a hidden
file called .gcgwebprojects in /seqweb/config or something like that,
that associates users with projects, so if you have to, you can go back
at a later date to retrieve data for users.  We've only had to do this a
handful of times.  The files are stored in text format, FASTA format I

Good luck!

Ryan Golhar  -  golharam at umdnj.edu
The Informatics Institute of UMDNJ

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Andy Fant
Sent: Thursday, July 13, 2006 12:18 PM
To: emboss at lists.open-bio.org
Subject: [EMBOSS] Web Interfaces to Emboss Tools

Afternoon all,
    After a particularly bad run of defective data DVDs from Accelrys, I
have decided that I want to make a full-court press to convince the
decision makers that we could spend the money we are spending on that
subscription and license on other priorities and migrate our core
bioinformatics service to Emboss.

     I have two primary questions related to this.  First, much of our
user community is using SeqWeb as their interface to GCG.  I know that
there are a few Emboss web interfaces out there, and I would like to get
feedback from people that have deployed them to wide-ranging production
about their experiences.  The ability to store sequence data and results
on the server side is considered to be an essential feature, which
appears to rule out some of the leading contenders.

    Also, does anyone have any experience/scripts/warnings for pulling
the corpus of data stored in SeqWeb out into a format easily accessible
by Emboss and it's various web interfaces?  I'd rather not go in and
manually try to extract it if there is a better way.

Thanks in advance.  If there is demand, I'll summarize for the list.

(My apologies for the nom de plume.  I don't want to telegraph my plans
to managers or vendors until I have all my ducks in a row)
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