renamed from zmap_lace.2006_11_10..oops...

ZMAP_LACE_PROJECT/zmap_lace.2006_10_11

+==============================================================================
+ZMap/Otterlace Development
+
+
+Date:  Wens 11th October 2006
+
+Attendees: th, jla1, jgrg, kj2, edgrif
+
+
+1) otterlace + zmap progress
+============================
+
+
+new features
+------------
+
+- Bug that led to blixem freezing for reverse complemented sequence
+is fixed.
+
+
+- We will do a complete acedb/zmap build this week and after it is
+integrated into lace we will do the following:
+
+	1) with each new release of the lace/zmap system we (a lace
+	person and a zmap person) will sit with one of the annotators
+	to check that everything is working
+
+	2) publish a list of the changes/fixes for that release
+
+
+- 3 frame translation is done.
+
+
+- Navigator with clickable locus names and a display of the clone assembly
+is high priority. We need to allow the user to search for locus names within
+the navigator window. The locus names will also be displayed in the main
+column. Roy is working on this now and it should be ready for the next release. 
+
+
+- bumping of homols: Matches from the same est will have a background colour
+painted between them to make it obvious which matches go with which and perfect
+alignments will have "intron" connectors drawn between them. The intron conector
+code still needs to be written. This is a high priority item.
+
+
+- the release notes for each release and the code version numbers will be
+put in a web page that will be viewable from either the lace or zmap
+programs as a main menu item. This will help the annotators to be sure of
+which version they are using and of the changes/updates made. This release
+will be the first time we have this.
+
+
+- glyph for single base features is done.
+
+
+- alternative translations: edgrif about half way through code to do this.
+
+
+- multiple alignments: edgrif is about a third of the way through implementing
+a more general way of displaying arbitrary blocks. This is a high priority item.
+
+
+- zmap needs to get sequences that are in acedb from there for blixem, means
+issuing a call to the server to get them but this is possible. NOTE that some
+sequences are _only_ in acedb.
+
+
+- we need a "back" button
+
+
+- DNA searching in zmap is done.
+
+
+- There is still a problem with the shutting down of the ace server which
+leads to a broken pipe message. edgrif will check that server shuts down
+in a timely way.
+
+
+Builds
+------
+
+- universal binaries: we have an updated mac laptop with the latest XCode set up
+which will allow us to produce the binaries. edgrif is pursuing both nfs mounts
+for automated builds and how to import our standard build system into XCode.
+
+
+
+Blixem/pfetch
+--------------
+
+- blixem: dna searching is NOT DONE, edgrif to expedite.
+
+
+- pfetch: caching? NOT DONE + where should we cache ?
+
+
+
+multiple species
+----------------
+
+- James and Ed need to discuss how this will be done. Zmap can display
+multiple sequences in one zmap window but there will need to changes to
+the supporting infrastructure including:
+
+	- should the species go in one or multiple acedb databases
+
+	- the lace <-> zmap protocol needs to allow specification of
+	multiple sequence display.
+
+	- lace needs to allow the user to pick multiple species
+
+
+Acedb
+-----
+
+- Treeview has a bug whereby if you click on an item, the window is no longer
+preserved. This is because of a fix by Ed and now needs to be refixed.
+
+- need to make sure that both acedb and zmap use the Mac "open" command to
+show urls.  DONE
+
+
+
+2) Other matters
+================
+
+
+sorry, this section is rather sparse...give me more information if you need to.
+
+- das - NOT DONE (th)
+
+
+- interface for tags: NOT DONE but Leo working on related code for import of
+Ensemble genes that will be directly applicable.
+
+
+- submit button for EMBL dumping: not done.
+
+
+==============================================================================