Acedb - June Newsletter

Ed Griffiths edgrif at sanger.ac.uk
Thu Jun 29 08:14:30 EST 2000

Below is Junes Acedb Newsletter.

Please note that the newsletter is biased towards Sanger Centre users, I'm happy
to see this emphasis change a but will need articles (of a few paragraphs) from
other people. I can't undertake to do a "world-wide" newsletter on my own !!

cheers Ed

| Ed Griffiths, Informatics Group,                                             |
|               The Sanger Centre, Wellcome Trust Genome Campus,               |
|               Hinxton, Cambridge CB10 1SA, UK                                |
|                                                                              |
| email: edgrif at sanger.ac.uk      URL: http://www.sanger.ac.uk/Users/edgrif    |
|   Tel: +44-1223-494780 (switch  +44 1223 834244) Fax: +44 1223 494919        |


ACEDB User Group Newsletter - June 2000

If you want to have this newsletter mailed to you _or_ you want to make
comments/suggestions about the format/content then send an email to
acedb at sanger.ac.uk.

This month saw the first Acedb Workshop since 1997, which took place in
Vancouver. Thanks go to Richard Bruskiewich and Steve Jones (a former Sanger
person, who now works at the Genome Sequence Centre, Vancouver) for their
efforts in organising the workshop. This issue will be about the conference
and what happened there.

General News


Apologies for no Acedb Users meeting this month, in the end there just was
not time to organise one.

There will be a meeting in July, if you have issues you want to raise before
then, please come and see the acedb developers in our new room (D2-12) which
is just down from reception, near personnel/accounts etc.

The Newsletter

Partly as a result of requests at the conference and partly because of
independent requests from acedb users at other sites, this newsletter is now
being added to the acedb newsgroup each month and is also being sent out to
users at other sites. I hope to solicit some useful articles from contacts
made at the conference.

Acedb2000 at Vancouver

I'm not going to cover everything that happened at Vancouver, the following
sections deal with subjects most relevant to the Sanger Centre. A fuller
description of the conference will appear on the acedb web site in due


Gudmund Thorission from Iceland gave a short presentation on how he hopes to
use the grid models/display for micro-array data. The main points for
discussion were:

   * scale - can acedb hold the amount of data that micro-arrays would
   * colours - is it possible to colour code the squares in the grid
     display so that they look meaningful to the user.
   * intelligent display - can the grid display be made to work to allow
     reasonable scrolling across a micro-array but not need to load in the
     data for the entire array at once (as this may require prohibitive
     amounts of memory).

This conversation mirrors several that have happened in the Sanger Centre
over at least the last year (e.g. with Dan Lawson and Adam Butler). What's
required now is an initial specification which includes:

   * expected size of micro-arrays
   * amount of data per micro-array element
   * some typical colour schemes

Adam Butler is going to take an initial stab at this, but if you are
interested in seeing this done then don't sit back, either start a
discussion on the acedb newsgroup or email the acedb developers direct
(acedb at sanger.ac.uk).


Richard Durbin spent much of his time at Vancouver working on a new storage
layer for acedb. This is the part of acedb that stores/retrieves objects
to/from disk. The idea here would to allow a choice of "backends", perhaps
including free (e.g. mySQL, BerkeleyDB, the original acedb system) or
commercial (e.g. Oracle, Sysbase) systems to be used. The backend would not
"know" about acedb objects, it would only be used to store/retrieve them and
provide other services such as locking.

The rationale for doing this is that the backend system could be used to
allow truly concurrent reading/writing via threading and more reliability
via support for transactions. This would be a great advance for acedb and
would supply features requested by Sanger and external users.

This work is currently only at the "broken prototype" stage, much work needs
to be done on further prototyping, in particular to assess whether
performance would be good enough with a different backend.

The acedb web site

The session on the format/usability of the acedb web site produced one main
conclusion: it's not very user friendly. Fortunately there were also a lot
of suggestions for improvements including:

   * completely revamping the downloads section
   * less developer, more user stuff
   * provide search facilities for acedb keywords
   * sort the documentation out !

and a host of other good suggestions.

We plan to substantially reorganise the web site over the next few weeks.

socket server

There were a number of talks/tutorials on how to use/set up the new
sockets-based version of the acedb server/client (available now in Acedb
4_8c in ~acedb/RELEASE.DEVELOPMENT/bin.XXX directories). If you would like
more information or a tutorial on the new server/client system (how to set
up user passwords etc.) then contact Ed Griffiths (edgrif at sanger.ac.uk).

Other important developments related to the socket server included:

   * AcePerl - Lincoln Stein has produced a new version of AcePerl that
     now talks directly to the socket server, you can get more information
     on this from: http://stein.cshl.org/AcePerl/. Note that because AcePerl
     can now talk directly to the server you will be able to use AcePerl
     from Windows and Apple Macs because AcePerl is now purely in Perl with
     no C code compilation required.
   * AcePython - Sean Powell & Siegfried Schloissnig wrote a python
     interface to the socket server whilst at the conference. If you want
     access to this code send a note to Ed Griffiths (edgrif at sanger.ac.uk).

Note that you can also interface to the socket server from Java:

SMAP - a new way to construct sequences

There has been a lot of discussion at Sanger over how to construct larger
sequences up to whole chromosome level. There was a whole session devoted to
this with an introductory talk by Richard Bruskiewich, followed by a talk by
Richard Durbin which gave an overview of the proposed model for SMAP and a
model for exons.

A fair summary would probably be that the SMAP model should solve a lot of
the problems that were experienced with chromosome 22 and with large
sequence construction in general. The difficult bit of the code still needs
writing but that should happen over the next few weeks.

What to do about building haplotype sequences remains unsolved however.


There was a lot of interest in AQL as a more powerful replacement for the
Query language and TableMaker. We would welcome more reports about how
people find AQL to use, any performance problems etc.

A major requirement for AQL is some kind of query builder and also more
tutorial documentation of the "how to..." type. Anyone fancy writing an
article on how to use AQL ??

Acedb and the Mac

There were a significant number of users who would like to see a more up to
date copy of acedb available on the Mac. Simon Kelley has made some headway
with obtaining a software environment in which to build acedb on the Mac.
The basic problem here is that we do not have the resources to maintain code
that requires a completely different build environment, graphics routines

Things look hopeful but no more than that.

Next User Group Meeting - D213, 2.30pm, Thursday, 13th July

Ed Griffiths <edgrif at sanger.ac.uk>
Last modified: Thu Jun 29 14:03:23 BST 2000

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