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<TITLE>ACEDB User Group Newsletter - December 2000</TITLE>
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<H1>ACEDB User Group Newsletter - December 2000</H1>
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<P>If you want to have this newsletter mailed to you <B>or</B> you want to
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make comments/suggestions about the format/content then
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send an email to <A HREF="mailto:acedb@sanger.ac.uk">acedb@sanger.ac.uk</A>.
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<P>This month sees: the announcement of ChickAce, a reminder for Unix users about
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environment limits and "out of memory" errors from Acedb, major reworking of the
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Acedb website, quite a number of bug fixes, and a proposal for some new variations
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of the Rename function.
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<a name="General"></a><H2>General News</H2>
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<a name="ChickAce"></a><H3>ChickAce</H3>
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<P>Martien Groenen emailed to say that he has been setting up an
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acedb database for the chicken:
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From: Martien.Groenen@Alg.VF.WAU.NL
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During the last 6 months I have set up ChickAce which now contains almost all
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the mapping information that is available for chicken including the linked
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data such as references (abstracts), sequences, Comparative mapping
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information (human and mouse), primers, SNP's etc.
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Currently the database is running satisfactory under Windows in our lab, and
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someone within my group is using the available CGI script to make the database
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available on our website (hopefully running in the beginning of next year).
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In one of the latest newsletters I also saw that URL's are now recognized
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correctly from within AceDb. Can I use that to link data directly to other
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databases that are available through the WWW (e.g. for all genes in ChickAce I
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have also added an extra entry for the Locuslink ID for human and mouse. Can I
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make a direct link with Locuslink?).
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Could you add me to the mailing list for the AceDb newsletter (you could also
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mention that an AceDb database for chicken has been set up in wageningen).
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<!-------------------------------------------------------------------------->
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<a name="Articles"></a><H2>Articles</H2>
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<a name="User"></a><H3>User Environment Limits and Acedb on Unix</H3>
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<P>This is a brief reminder about user limits
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which can cause acedb to crash if they are set too low ( applies to unix not MS-Windows users).
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<P>All users who log on to a unix box (whether directly or via a network terminal)
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have a set of user limits which control the amount of memory/files etc. that they
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are allowed to use. You can look at these limits using the C shell command "<code>limit</code>":
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datasize 262144 kbytes
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memoryuse 505664 kbytes
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<P>"<code>datasize</code>" and "<code>stacksize</code>" particularly affect Acedb
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and can cause it to crash
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by running out of memory. In the above example "<code>stacksize</code>" is about 2MB which is too
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low, whereas "<code>datasize</code>" is fine for most uses at about 260MB.
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<P>If Acedb crashes unexpectedly with either of these warnings:
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"Memory allocation failure when acedb requested NNNNNN bytes,
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acedb has already allocated NNNNNN bytes...."
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"ABORT : Fatal program fault, signal NN...."
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<P>then you should try increasing your limits using the "<code>unlimit</code>" C shell command:
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> unlimit stacksize
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> unlimit datasize
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If this does not fix the problem then report it either using the ddts bug reporting
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<li>http://www.sanger.ac.uk/cgi-bin/webddts/WebDDTS.pl?Project=Acedb
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or by sending a description of the problem to the acedb developers at:
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<li><A HREF="mailto:acedb@sanger.ac.uk">acedb@sanger.ac.uk</A>
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<a name="Acedb"></a><H3>Acedb Web Pages re-organisation</H3>
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<P>John Sturdy has been undertaking a major reorganisation of the acedb web pages
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and download site. If you visit the <A HREF="http://www.acedb.org"/>Acedb website</A>
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you will see that the front page has changed and will continue to change quite
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radically until about mid-January.
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<P>Of special interest are:
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<li>Separate "User", "Administrator/Curator" and "Developer" sections.
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<li>A Search box which allows you to make keyword searches of acedb
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documents both on the <A HREF="http://www.acedb.org/">Acedb website</A> and the
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<A HREF="http://genome.cornell.edu/acedoc/">Acedb document library</A> in the States.
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Please do try this and if you find notable omissions then either send mail
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to the <A HREF="mailto:bionet-software-acedb@net.bio.net">Acedb newsgroup</A>
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or to <A HREF="mailto:acedb@sanger.ac.uk">acedb@sanger.ac.uk</A>.
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<li>There is a new "downloads" set of pages under construction to give better access
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to the ftp site (available in January).
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<li>There is a new "Site map" link which gives a quick overview of the document structure
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of the Acedb site as a whole.
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<P>John will be adding a lot of new material to the website over the next couple of weeks and
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our intention is to make it a lot more usable. Comments or suggestions are welcome, please
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send them to the <A HREF="mailto:bionet-software-acedb@net.bio.net">Acedb newsgroup</A>
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or <A HREF="mailto:acedb@sanger.ac.uk">acedb@sanger.ac.uk</A>.
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<a name="New"></a><H2>New Features</H2>
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<a name="position"></a><H3>New position readout in fmap</H3>
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<p>A small change courtesy of Jean Thierry-Mieg, fmap has a friendlier readout for the position on
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the sequence which will now be in kilo (kb) and Mega (Mb) bases,
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making it a little easier to read than
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1238749217498123794 as used to be displayed for long sequences.
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<a name="diagnostics"></a><H3>Better diagnotics from Rename/Alias failures</H3>
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<p>Previously Acedb has not reported the reason for these failures, only that they
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happened, now parsing will report in detail the reason for any Rename or Alias failures
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so that fixing them should be easier.
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<a name="Bugs"></a><H2>Bugs Fixed</H2>
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<a name="Colours"></a><H3>Colours bug with gifs</H3>
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<p>GIF images produced by Acedb 4_8c were sometimes in garish/hard to read colours,
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this is now fixed in the December monthly build.
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<a name="Dumping"></a><H3>Dumping objects with very large tag values</H3>
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<p>Some tag values can be very large (e.g. DNA) and this has caused acedb to overrun
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one of its internal buffers, this is now fixed with dynamically growing buffers.
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<a name="Filechooser"></a><H3>File Chooser irritations</H3>
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<p>Several irritating features of the File Chooser window have been fixed:
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<li>If you want to go directly to a directory, you can do this by
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typing the directory name in the bottom "selection" window
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and pressing the <tab> key. This will point the file chooser
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to this directory so you can then choose files from there. The
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<tab> key also does filename completion like the C shell.
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<li>The File Chooser window now shows a "busy" cursor when it cannot
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respond to user input e.g. because its waiting to list an NFS
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<li>The default size of the window has been increased to make it
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easier to see long filenames.
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<a name="Cut"></a><H3>Cut/Paste bug fixed</H3>
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<P>Cut and Paste of larger texts (e.g. DNA) was broken, this was a bug
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in the underlying Window System software (GTK) and is being fixed by
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installing updated versions of the software which include the bug fix.
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<a name="Main"></a><H3>Main Window reset after "Clean Up"</H3>
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<P>"Clean up" behaviour has been returned to how it was in 4_7, the local/global
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search is left as it was before the "Clean up".
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<a name="Socket"></a><H3>Socket Server Admin users permissions bug</H3>
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<P>If you noticed problems with Admin users not having access to some commands
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for the socket server, this is now fixed. Admin users should have access to
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all possible commands as they have the highest permission levels.
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<a name="Education"></a><H2>Education</H2>
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<P>HGMP are hosting an Acedb course in the week of 22nd-26th January 2001.
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<P>The next Sanger Centre course is likely to be in June 2001.
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<P>If you are interested in either please mail
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<A HREF="mailto:sylvia@sanger.ac.uk">Sylvia Martinelli (sylvia@sanger.ac.uk)</A>
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<a name="Future"></a><H2>Future Plans</H2>
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<P>If you wish to make suggestions about any of the below, please mail them
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to <A HREF="mailto:acedb@sanger.ac.uk">acedb@sanger.ac.uk</A>
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<a name="installRevised"></a><H3>Revised INSTALL script for Acedb</H3>
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<P>The current INSTALL script for acedb is being revised, the
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section for installing the worm database will be moved into a separate
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script (available from the
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<A HREF="http://www.sanger.ac.uk/Projects/C_elegans/">worm web site</A> in the January).
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The download site will include for each acedb release the following
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archives: compilable source code, binaries for selected platforms,
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help pages, docs and a test database.
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<a name="Enhancements"></a><H3>Enhancements to "Rename"</H3>
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<P>Discussions with a number of users have suggested that the
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"Rename" operation doesn't always so what they would like or expect.
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Currently it works like this:
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<P>Let's say we wish to rename Sequence object "A" to "B":
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<P>If the database does <b>not</b> contain a Sequence object with the name "B",
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the operation is straight forward: object "A" is simply given the new name
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of "B" and the name "A" ceases to exist.
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<P>If the database <b>does</b> contains a Sequence object with the name "B",
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things are more complicated, the two objects are combined to form a new
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"B" object following these rules:
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tag type tag in "A" ? tag in "B" ? tag in new "B"
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-------- ------------ ------------ --------------
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non-UNIQ Y N "A"s values
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Y Y (all of "A"s values
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+ all of "B"s values)
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<P>In this case the original "A" and "B" objects will be replaced with the
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single new "B" object.
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<P>The new proposal is:
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<P>Given that we want to rename object "A" to "B" and that "B" already points
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<li>The existing rename operation will combine "A" and "B" as before.
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<li>New variants of rename will be provided:
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<li>safe-rename: will fail because "B" points to an existing object
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<li>replace-rename: will delete "B" and then rename "A" to "B"
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<li>overwrite-rename: will combine "A" and "B", where tags exist in
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both "A" will take preference.
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<li>augment-rename: as for overwrite-rename, but where tags exist in
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both "B" will take preference.
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When implemented, the third and fourth operations will probably be called
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<P>This would allow users to do renames and choose how this should work. They
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could for instance do a "safe-rename" which would avoid any loss of data, or
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conversely do a "replace-rename" which would avoid any combining of objects.
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<P>A question remains about whether these operations should be inclusive or
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exclusive for non-UNIQ tags, i.e. should they be combined as before, or should
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one set of tags overwrite another. If you are regularly parsing in data to an Acedb
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database and have thoughts about how you would like Rename to work, then please
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mail <A HREF="mailto:acedb@sanger.ac.uk">acedb@sanger.ac.uk</A>.
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<H2>December monthly build available in first week of January 2001</H2>
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<P>Sorry, not time to do this before Christmas, build has been done
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and will be distributed first week in January.
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<P>You can pick up the monthly builds from:
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<dt><b>Sanger users</b>
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<dd>~acedb/RELEASE.DEVELOPMENT
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<dt><b>External users</b>
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<dd>ftp://ftp.sanger.ac.uk/pub/acedb/Sanger-release.2000_12_22.tar.gz
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<H2>Next User Group Meeting - D319, 2.30pm, Thursday 18th January 2001</H2>
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<ADDRESS><A href="mailto:edgrif@sanger.ac.uk">Ed Griffiths <edgrif@sanger.ac.uk></A></ADDRESS>
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