Notes from ACEDB Workshop, part I

John L. McCarthy jlmccarthy at lbl.gov
Wed Sep 8 11:42:17 EST 1993


By popular request, here are some very rough outline notes I took at the
ACEDB Workshop in Boston last month. I cannot vouch for their accuracy, but
hope I have not misquoted anyone too badly. Please post corrections and
clarifications to this newsgroup.

The full set of notes are about 20 pages long. I have broken them into two
parts to accomodate my news reader and mail software.

If you have questions about particular points, you probably should send
them directly to the people who made those points at the workshop.  A list
of workshop attendees with Email addresses was posted to this newsgroup a
few weeks ago.

A copy of this document is available via anonymous ftp
on weeds.mgh.harvard.edu  under pub/acedb-dev/doc

-John McCarthy, Lawrence Berkeley Laboratory


==================================================================
ACEDB Workshop  Wed 28-31 July 1993 Boston, MA 
Highlight notes from John McCarthy (LBL) jlmccarthy at lbl.gov 

more or less in chronological order, with TOPICS IN CAPS
see list of attendees for full names, addresses, etc.

Wed 28 July 
=================================
COMMUNICATIONS, GOPHER
Mike Cherry is providing ACEDB archive on his gopher server at
Stanford -- genome.stanford.edu.

Mike asks if people could please send notes to bionet.software.acedb
another thing that would be nice to have is FAQ - Brad will do this

weeds.mgh.harvard.edu has anonymous gopher+  login/server
Also experimenting with remote anonymous AATDB login aatdb
user name c-aatdb used for MacX
Mike used Richard's acedump to create gopher files.
WAIS paragraph format / from acedump    also textace

Brad notes that his gopher archive includes USDA sysad archive.

Brad Sherman did research for secure anonymous ftp

Mike: weeds is a separate machine, not cross mounted to anything, and
not used for anything else

stty script --  Otto points out that you can trap interupts with Bourne
shell
Brad points out that most vulnerable spot is within application.

anonymous FTP setup instructions,  
thor.ece.uc.edu
/pub/sun-faq/anon-ftp.script
guidelines:  . cert.org   /pub/tech.tips/anonymous.ftp

=========================================================
PRINTING FOR REMOTE USERS
richard: set ACEDB_LPR to null -- code checks for this.
maybe could do a script that turns print script into Email.
Michelle: also may want to print to a file  
(richard:  currently always goes into /PS directory).  
Stan: might be nice to have switch to disable all writing
could do changeroot to keep people restricted to specified area.

=================================
ACEDB NEW DEVELOPMENTS - Richard Durbin: 
ORGANIZATIONAL STATUS, what Richard and Jean are doing:
RD  -worm sequencing (2,5,10 Mb/yr)
      -sanger Centre  (RD joint head of informatics)
      -CGC map -> Cambridge  (worm cytogenetics center)
            Mary O'Callaghan doing this (moc at mrc-lmb.cam.ac.uk)
      -in house use: sequence (worm, yeast, human)
                             worm genetic map
   so RD will have less time for kernal development

Jean:  -Human mapping - Frensal (Genethon)
          -IGD
          -ports to various unix systems
          - management of kernal  (want to keep unified version)
             incorporate changes from others & redistribute
             also would like to make other's tools & modules available

RELEASES:
        1-10  now  (still backwards compatible with old databases)
        2-0 September? (model changes for maps, sequences)
                             running this in Cambridge now
                      but want to make other changes before release
              would like to get some feedback from this workshop first
     developers can get 2-0 code but should not use for databases
          that will be distributed, etc.
Will have AWK scripts for database restructuring from 1-10 to 2-0
Extra things in specifications directories, PS fonts, Xfonts.wrm,


NEW ARCHITECTURE FOR MAP DISPLAY-- RD
  columnar architecture/format will help
  would also be nice to have developers style guide

Stan: would be nice to have another level of indirection, so people
could map different names to std display code names -- intermediate
layer to make it easier to change models and yet maintain
compatibility with display modules.

RD: not convinced that another layer of indirection is good idea
may slow things down

RD: people should not expect that all the good ideas that get
suggested here will get implemented.  Commitment to maintain kernal.

------------------- break-----------------------
NEW DEVELOPMENTS (mostly in 1-10)
SUBCLASSES 
  -can appear on main window
  -can use in queries, .ace files
  -no code change required
specification
  -wspec/subclasses.wrm
  -read after models.wrm
  -ace file
      class genome_Sequence
      Subclass-of Sequence  //can be a subclass  (can have 2 parents?)
      Visible            //indicates whether displayed on main window
      Filter     "Genomic_canonical"  query
  How it works:
       Have 8 bits free per key in memory 
       -uses 1 bit per filter
       checks on object save
       when filter changes -- rescans entire class with query
       can't change entries in class class directly, reads from
subclasses.wrm
        
May be possible in future:
      to have different default display type for different subclasses
      
Used in 2.0
?Map   -  Chromosome
?Locus - gene, RFLP, etc.
?Interval - rearrangement, Chrom_Band, Hybrid cell line, ...
?Df_dup_defic     Inside
                           Outside
?Probe

2-0 has a models class 
so won't have ?class as part of keyset
you will get this type of info in other ways

2 possible ways to do sub-maps
  1 scale with some linear transformation
  2 interpolate between shared loci (now done in 1-10 physical map)

Otto: IGD has used clone grid as general model for 2-D maps

RD: map display now automatically transforms contig info in this way
 maybe could do some graphic to indicate where there are conflicts
  between different versions of maps

GRAPH PACKAGE additions
   filled arcs
   filled polygons (from Suzanna)

IMAGES (grey level: 256-->128)
      (a) in subwindow    graphPixels()
      (b) PIXEL_SCROLL graph type   (coordinates are pixels) 
            graph Pixel Background()

Possible Development
      -ASCII dump format for draw stack
      -stand alone drawing editor
 full color images will require more thought!
now easier to attach sub-menus to boxes

Otto: can pick up X colors and coordinates to use from XV
Suzanna: has done some things to display TIFF images

MAP PACKAGE
map.h     w7/mapcontrol.c
A. drawing coordinates  (zoom, centre, scroll, etc.)
B. columns of data (user toggleable)
C Cursor

MAP  *map
Look -> map -> mapCreate(column, ...         )
{float   min, max
Coordinate Functions
Locator (small green bar)

Stan: is this the way you would draw multiple (synteny) maps?
RD: not yet..., in the meantime can use TableMaker multi-map

Planned Enhancements
1. add a help line per column for display control
2. allow >32 columns
3. give names to sets of columns
4  ?   Multiple ?MAP's per window

Code:
     separate columns further
             ==>library of columns
     separate SEG's array per column    (convert (store),  destroy)
   put PICK control in MAP package
          -select   /  follow
          - neighbor       on/off  (key)  [e.g., to light up related
objects]

Sequence Fetch/Align
--------------------------
a. summon up SwissProt/PIR entry(s)
b. show multiple alignment based on BLAST segments  =BLIXEM
uses unix command
   fetch  -Bdbname (SP,PIR,EMBL,GB)
             -a accession number
             -P Pearson (FASTA) format
             -s  just  sequence ... no new line
   our version uses the EMBL CDROM index structu



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