[Fwd: EMBOSS User Survey & Requirements (post-RFCGR closure)]
Laurent Falquet
Laurent.Falquet at isrec.unil.ch
Wed Jul 14 09:27:38 CEST 2004
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* EMBnet News bulletin of 14-Jul-2004 *
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Dear Users,
The MyHits environment
----------------------
The MyHits web server (http://myhits.isb-sib.ch) is a new integrated
service dedicated to the annotation of protein sequences and to the
analysis of their domains and signatures. Guest users can use the
system anonymously, with full access to (i) standard bioinformatics
programs (e.g. PSI-BLAST, ClustalW, T-Coffee, Jalview); (ii) a large
number of protein sequence databases, including standard (Swiss-Prot,
TrEMBL) and locally developed databases (splice variants); (iii)
databases of protein motifs (Prosite, Interpro); (iv) a precomputed
list of matches ('hits') between the sequence and motif databases.
All databases are updated on a weekly basis and the hit list is kept
up to date incrementally. The MyHits server also includes a new
collection of tools to generate graphical representations of pairwise
and multiple sequence alignments including their annotated features.
Free registration enables users to upload their own sequences and
motifs to private databases. These are then made available through
the same web interface and the same set of analytical tools.
Registered users can manage their own sequences and annotations using
only web tools and freeze their data in their private database for
publication purposes.
Feel free to try it either as anonymous or as registered user!
EMBOSS SURVEY
-----------
The EMBOSS/Jemboss developer team will be drastically reduced in 2005 leading
to the end of the EMBOSS project. This softare package has been used
by many of us,
without even knowing it, as it is the engine behind many web pages.
It has also been used in courses and for daily work in sequence analysis.
So please help the EMBOSS team (and yourself) by filling the survey below
and send it back to the mentionned email address.
Many thanks in advance.
Best greetings,
Laurent Falquet
Swiss EMBnet node manager
---FILL HERE---------EMBOSS SURVEY-----------------------------------
Dear User,
As a registered user, you might already know that the UK Medical
Research Council is to close the Research and Bioinformatics Divisions
of the Rosalind Franklin Centre for Genomics Research (RFCGR) in
mid-2005. RFCGR is the current home of the European Molecular Biology
Open Software Suite, EMBOSS
(<http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/>http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/).
This action will more than halve the current core development team and
will therefore adversely affect the development and support of EMBOSS.
It would help the EMBOSS project tremendously if you complete this
survey. It will help us to both gain support for EMBOSS and to steer the
future development of the project down lines suggested by you. If this
software is not applicable to you then please accept our apologies for
the interruption.
Many thanks for your consideration.
Jon Ison (RFCGR), on behalf of the EMBOSS developers
Alan Bleasby (RFCGR)
Peter Rice (EBI)
THE SURVEY
Please complete the survey below by replacing the underscores between
the asterisks with your own text. Where two or more possible answers
to a question are given please use a single "X" to indicate your choice.
Completed surveys should be returned by email to
<mailto:survey at rfcgr.mrc.ac.uk>survey at rfcgr.mrc.ac.uk.
Please aim to complete at least section 1. Even partially completed
surveys are welcomed.
All replies will be treated in confidence.
1. GENERAL
2. FUNDING AND SUPPORT
3. FUTURE PREFERENCES
4. USING EMBOSS
5. OTHER PACKAGES
SECTION 1. GENERAL
Name:
*___________________________________________________________________*
Email:
*___________________________________________________________________*
Place of work (name of department and institute or company):
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
What best describes your place of work:
*___* Academic / not-for-profit
*___* Government (e.g Research Council Institute)
*___* Commercial
What is your primary role:
*___* Management
*___* Systems administration
*___* Bioinformatics
*___* Biology
*___* Software development
*___* Other (please specify)
*___________________________________________________________________*
Do you use EMBOSS:
*___* Yes
*___* No
Is EMBOSS a valuable package for your bioinformatic analyses:
*___* Yes
*___* No
What do you consider valuable about EMBOSS:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
Have you ever modified or made additions to EMBOSS:
*___* Yes
*___* No
Would you attend an EMBOSS developers training course:
*___* Yes
*___* No
*___* Maybe
Would you attend an EMBOSS users (bioinformatics) training course:
*___* Yes
*___* No
*___* Maybe
What operating system do you use:
*___* Linux
*___* Unix
*___* MS
*___* Other (please specify)
*___________________________________________________________________*
SECTION 2. FUNDING AND SUPPORT
Should EMBOSS remain free-of-charge at source:
*___* Yes
*___* No
*___* Not sure
What is your preferred funding route for EMBOSS:
*___* Public funding (e.g. Research Council)
*___* Commercialisation
*___* Part public funding / part commercialisation
*___* Other (please specify)
*___________________________________________________________________*
How should EMBOSS development be funded:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
How should EMBOSS support be funded:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
SECTION 3. USING EMBOSS
(skip this section if you do not use EMBOSS)
What best describes you (tick one only):
*___* EMBOSS user
*___* EMBOSS developer
*___* EMBOSS administrator
*___* EMBOSS trainer
*___* Other (please specify)
*___________________________________________________________________*
How long have you used EMBOSS:
*___* < 3 months
*___* < 1 year
*___* 1 - 3 years
*___* > 3 years
What do you use EMBOSS for (tick all that apply):
*___* Applications
*___* Software development
*___* Installation & maintenance
*___* Education & training
*___* Other (please specify)
*___________________________________________________________________*
How do you run the EMBOSS applications:
*___* From the command-line
*___* JEMBOSS
*___* Other (please specify)
*___________________________________________________________________*
What do you like most about EMBOSS:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
What do you like least about EMBOSS:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
What would EMBOSS benefit most from:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
SECTION 4. FUTURE PREFERENCES
What are the most important feature requirements (tick all that
apply):
*___* Broad spread of applications
*___* Powerful / flexible applications
*___* Intuitive applications
*___* Incorporation of other popular software, e.g. BLAST
*___* Interoperability with other software
*___* Interoperability with other programming languages
*___* Interoperability with databases
*___* Graphical interfaces
*___* Workflows
*___* Project management
*___* Graphics
*___* Documentation
Please indicate training & support requirements (tick all that apply):
*___* Applications support
*___* Programming support
*___* Installation & administration support
*___* Developer training courses
*___* User training courses
*___* Bespoke training courses / consultancy
Please indicate your preference for delivery of EMBOSS support:
*___* Email helpdesk
*___* Telephone helpdesk
*___* Other (please specify)
*___________________________________________________________________*
Please indicate your preference for future EMBOSS development:
*___* Exclusively molecular sequence analysis.
*___* Diversify into other areas.
*___* Primarily sequence analysis with some diversification.
What areas (if any) should EMBOSS diversify into:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
Please indicate your preference for future EMBOSS applications:
*___* Small, distinct applications that perform a single task.
*___* Bigger applications that integrate a variety of related tasks.
*___* Not bothered so long as I can easily find / use what I want.
How do you like to run applications:
*___* From the command-line
*___* GUI (stand-alone application)
*___* GUI (on the web)
*___* Other (please specify)
*___________________________________________________________________*
SECTION 5. OTHER PACKAGES
What non-commercial packages (other than EMBOSS) do you use:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
What commercial packages do you use:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
What do you like most about these:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
What do you dislike most about these:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
What do these provide that is not in EMBOSS:
*___________________________________________________________________
___________________________________________________________________
___________________________________________________________________*
Letters of Support
We hope that alternative sources of funding can be found. In addition to
completing the survey, if you feel that EMBOSS is valuable, please
send your letters of support to:
EMBOSS User Survey
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
E-mail: <mailto:survey at rfcgr.mrc.ac.uk>survey at rfcgr.mrc.ac.uk
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