December newsletter

Ed Griffiths edgrif at sanger.ac.uk
Fri Dec 22 13:15:53 EST 2000


As promised, the December newsletter.

Please note that the December monthly build will not be available until the
first week in January, sorry, there just isn't time to test it before Christmas.

cheers Ed

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| Ed Griffiths, Acedb development, Informatics Group,                    |
|               The Sanger Centre, Wellcome Trust Genome Campus,         |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |
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ACEDB User Group Newsletter - December 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 sees: the announcement of ChickAce, a reminder for Unix users
about environment limits and "out of memory" errors from Acedb, major
reworking of the Acedb website, quite a number of bug fixes, and a proposal
for some new variations of the Rename function.

General News
************

ChickAce
++++++++

Martien Groenen emailed to say that he has been setting up an acedb database
for the chicken:

From: Martien.Groenen at Alg.VF.WAU.NL

During the last 6 months I have set up ChickAce which now contains almost all
the mapping information that is available for chicken including the linked
data such as references (abstracts), sequences, Comparative mapping
information (human and mouse), primers, SNP's etc.
Currently the database is running satisfactory under Windows in our lab, and
someone within my group is using the available CGI script to make the database
available on our website (hopefully running in the beginning of next year).

In one of the latest newsletters I also saw that URL's are now recognized
correctly from within AceDb. Can I use that to link data directly to other
databases that are available through the WWW (e.g. for all genes in ChickAce I
have also added an extra entry for the Locuslink ID for human and mouse. Can I
make a direct link with Locuslink?).

Could you add me to the mailing list for the AceDb newsletter (you could also
mention that an AceDb database for chicken has been set up in wageningen).

Best regards,
Martien

Articles
********

User Environment Limits and Acedb on Unix
+++++++++++++++++++++++++++++++++++++++++

This is a brief reminder about user limits which can cause acedb to crash if
they are set too low ( applies to unix not MS-Windows users).

All users who log on to a unix box (whether directly or via a network
terminal) have a set of user limits which control the amount of memory/files
etc. that they are allowed to use. You can look at these limits using the C
shell command "limit":

> limit
cputime         unlimited
filesize        unlimited
datasize        262144 kbytes
stacksize       2048 kbytes
coredumpsize    0 kbytes
memoryuse       505664 kbytes
descriptors     4096

"datasize" and "stacksize" particularly affect Acedb and can cause it to
crash by running out of memory. In the above example "stacksize" is about
2MB which is too low, whereas "datasize" is fine for most uses at about
260MB.

If Acedb crashes unexpectedly with either of these warnings:

"Memory allocation failure when acedb requested NNNNNN bytes,
 acedb has already allocated NNNNNN bytes...."

or

"ABORT : Fatal program fault, signal NN...."

then you should try increasing your limits using the "unlimit" C shell
command:

> unlimit stacksize
> unlimit datasize

If this does not fix the problem then report it either using the ddts bug
reporting system:

   * http://www.sanger.ac.uk/cgi-bin/webddts/WebDDTS.pl?Project=Acedb

or by sending a description of the problem to the acedb developers at:

   * acedb at sanger.ac.uk

Acedb Web Pages re-organisation
+++++++++++++++++++++++++++++++

John Sturdy has been undertaking a major reorganisation of the acedb web
pages and download site. If you visit the Acedb website you will see that
the front page has changed and will continue to change quite radically until
about mid-January.

Of special interest are:

   * Separate "User", "Administrator/Curator" and "Developer" sections.
   * A Search box which allows you to make keyword searches of acedb
     documents both on the Acedb website and the Acedb document library in
     the States. Please do try this and if you find notable omissions then
     either send mail to the Acedb newsgroup or to acedb at sanger.ac.uk.
   * There is a new "downloads" set of pages under construction to give
     better access to the ftp site (available in January).
   * There is a new "Site map" link which gives a quick overview of the
     document structure of the Acedb site as a whole.

John will be adding a lot of new material to the website over the next
couple of weeks and our intention is to make it a lot more usable. Comments
or suggestions are welcome, please send them to the Acedb newsgroup or
acedb at sanger.ac.uk.

New Features
************

New position readout in fmap
++++++++++++++++++++++++++++

A small change courtesy of Jean Thierry-Mieg, fmap has a friendlier readout
for the position on the sequence which will now be in kilo (kb) and Mega
(Mb) bases, making it a little easier to read than 1238749217498123794 as
used to be displayed for long sequences.

Better diagnotics from Rename/Alias failures
++++++++++++++++++++++++++++++++++++++++++++

Previously Acedb has not reported the reason for these failures, only that
they happened, now parsing will report in detail the reason for any Rename
or Alias failures so that fixing them should be easier.

Bugs Fixed
**********

Colours bug with gifs
+++++++++++++++++++++

GIF images produced by Acedb 4_8c were sometimes in garish/hard to read
colours, this is now fixed in the December monthly build.

Dumping objects with very large tag values
++++++++++++++++++++++++++++++++++++++++++

Some tag values can be very large (e.g. DNA) and this has caused acedb to
overrun one of its internal buffers, this is now fixed with dynamically
growing buffers.

File Chooser irritations
++++++++++++++++++++++++

Several irritating features of the File Chooser window have been fixed:

   * If you want to go directly to a directory, you can do this by typing
     the directory name in the bottom "selection" window and pressing the
     <tab> key. This will point the file chooser to this directory so you
     can then choose files from there. The <tab> key also does filename
     completion like the C shell.
   * The File Chooser window now shows a "busy" cursor when it cannot
     respond to user input e.g. because its waiting to list an NFS mounted
     directory.
   * The default size of the window has been increased to make it easier to
     see long filenames.

Cut/Paste bug fixed
+++++++++++++++++++

Cut and Paste of larger texts (e.g. DNA) was broken, this was a bug in the
underlying Window System software (GTK) and is being fixed by installing
updated versions of the software which include the bug fix.

Main Window reset after "Clean Up"
++++++++++++++++++++++++++++++++++

"Clean up" behaviour has been returned to how it was in 4_7, the
local/global search is left as it was before the "Clean up".

Socket Server Admin users permissions bug
+++++++++++++++++++++++++++++++++++++++++

If you noticed problems with Admin users not having access to some commands
for the socket server, this is now fixed. Admin users should have access to
all possible commands as they have the highest permission levels.

Education
*********

HGMP are hosting an Acedb course in the week of 22nd-26th January 2001.

The next Sanger Centre course is likely to be in June 2001.

If you are interested in either please mail Sylvia Martinelli
(sylvia at sanger.ac.uk)

Future Plans
************

If you wish to make suggestions about any of the below, please mail them to
acedb at sanger.ac.uk

Revised INSTALL script for Acedb
++++++++++++++++++++++++++++++++

The current INSTALL script for acedb is being revised, the section for
installing the worm database will be moved into a separate script (available
from the worm web site in the January). The download site will include for
each acedb release the following archives: compilable source code, binaries
for selected platforms, help pages, docs and a test database.

Enhancements to "Rename"
++++++++++++++++++++++++

Discussions with a number of users have suggested that the "Rename"
operation doesn't always so what they would like or expect. Currently it
works like this:

Let's say we wish to rename Sequence object "A" to "B":

If the database does _not_ contain a Sequence object with the name "B", the
operation is straight forward: object "A" is simply given the new name of
"B" and the name "A" ceases to exist.

If the database _does_ contains a Sequence object with the name "B", things
are more complicated, the two objects are combined to form a new "B" object
following these rules:

                                                    value used for
tag type   tag in "A" ?    tag in "B" ?             tag in new "B"
--------   ------------    ------------             --------------
UNIQ           Y               N                      "A"s value
               N               Y                      "B"s value
               Y               Y                      "A"s value

non-UNIQ       Y               N                      "A"s values
               N               Y                      "B"s values
               Y               Y                   (all of "A"s values
                                                   + all of "B"s values)

In this case the original "A" and "B" objects will be replaced with the
single new "B" object.

The new proposal is:

Given that we want to rename object "A" to "B" and that "B" already points
to an object:

  1. The existing rename operation will combine "A" and "B" as before.
  2. New variants of rename will be provided:
        o safe-rename: will fail because "B" points to an existing object
        o replace-rename: will delete "B" and then rename "A" to "B"
        o overwrite-rename: will combine "A" and "B", where tags exist in
          both "A" will take preference.
        o augment-rename: as for overwrite-rename, but where tags exist in
          both "B" will take preference.
     When implemented, the third and fourth operations will probably be
     called "Merge-nnn".

This would allow users to do renames and choose how this should work. They
could for instance do a "safe-rename" which would avoid any loss of data, or
conversely do a "replace-rename" which would avoid any combining of objects.

A question remains about whether these operations should be inclusive or
exclusive for non-UNIQ tags, i.e. should they be combined as before, or
should one set of tags overwrite another. If you are regularly parsing in
data to an Acedb database and have thoughts about how you would like Rename
to work, then please mail acedb at sanger.ac.uk.

December monthly build available in first week of January 2001
**************************************************************

Sorry, not time to do this before Christmas, build has been done and will be
distributed first week in January.

You can pick up the monthly builds from:

_Sanger users_
     ~acedb/RELEASE.DEVELOPMENT
_External users_
     ftp://ftp.sanger.ac.uk/pub/acedb/Sanger-release.2000_12_22.tar.gz

Next User Group Meeting - D319, 2.30pm, Thursday 18th January 2001
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Ed Griffiths <edgrif at sanger.ac.uk>
Last modified: Fri Dec 22 17:38:09 GMT 2000









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