acedb-3.0

Danielle et Jean Thierry-Mieg mieg at kaa.cnrs-mop.fr
Mon Jan 10 23:06:52 EST 1994


ACEDB version 3 data and code
=============================

ACEDB, written for the needs of the C.elegans community is now
being used for several other organisms and it has become necessary
to devise a more versatile structure to accomodate these data.

One has to handle and compare various partial genetic and physical
maps, usually less accurate than in the case of the nematode, and
often contradictory. To face this situation, we have introduced in
collaboration with Otto Ritter a generalised construction which
allows one to assign to a vertical map objects belonging to any
class. In this way, we can handle YAC/STS physical data, cytogenetic
maps, restriction fragment maps, as well as all the usual nematode
data (genetic maps, clones, sequence, bibliography etc).

To allow rapid development of these new concepts, it was decided to
distribute the nematode data in a different version: acedb-2 which
is available on the same servers and has been used in Cambridge
since april. However, we recommend that

ALL DEVELOPERS USING ACEDB should port their data into ACEDB-3

rather than acedb-2. The present acedb-3-0 distribution
comes with data on human chromosome 21 collected in collaboration
with 
  Otto Ritter                   oritter at dkfz-heidelberg.de
  Nicole Creau-Goldberg         creau at arthur.citi2.fr
  Jean-Maurice Delabar          delabar at arthur.citi2.fr
from the data produced by the 4th International Workshop on Chromosome 21 
(Genomics,1993,18,735-744) and from the data provided by or taken from the
following databases and data repositories:
  GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB.

Code 2 and 3 differ only at the level of the displays. The database
manager, graphic library and most of the rest of the code is shared.
However, because the map data are stored in a different way, code 2
would not correctly display the c21 data and vice-versa, the
nematode data should be slightly modified to be viewed with acedb-3.

As of this release, the main difference is the creation of a new
class, the multi-map, which allows direct comparison of an arbitrary
number of maps sharing some common markers, and easy navigation
between them. This structure is democratic, not hierarchic as in the
case of the nematode genetic/physical/sequence maps which can be
seen as various levels of zooms on the same map. On chromosome 21,
for example, the multimap clearly shows the contradictions between the
various available maps obtain by yac/sts mapping, classical
genetics and restriction fragments.

In the future, we will probably remove from ace3 the horizontal
physical map display inherited from Sulston's CONTIG9 program which
has proved quite useless on other sets of data such as the genethon
yac map. Some of the analysis tools provided in ace2 and 3 will also
differ, although the bulk of the code will remain shared. Possibly,
the nematode data will be transferred into this structure at a later
date.

Recompilation:
-------------

We provide the source code of acedb-3, and some of the binaries. To
recompile on other machines, you must set 2 environment variables: setenv
ACEDB_MACHINE xxx where xxx is one of SUN, SGI, IBM etc, describing
your platform and setenv ACEDB_SRC `pwd` make xace3 in case of
difficulty, contact mieg at kaa.cnrs-mop.fr

The command make xace2 would make the acedb-2 version, but you should
do that in a different directory because otherwise, our makefile is
a little naive and would forget to recompile with the proper options
some of the object modules.

Display Modifications:
---------------------

Multimap: 
The multimap is a composite display, showing in a comparative way a
set of maps sharing some markers. It can be invoked by selecting a
member of the MultiMap class or from the keyset menu. Only those
loci present on at least 2 maps will be displayed, but you can then
pass to a specific map as usual by double clicking. You can recentre
or zoom either all the maps at once or a single one by selecting the
appropriate button. Only the direct connection between one map and
its immediate neighbour are materialised by lines, but the switch
button lets you exchange the columns, and the flip button can be used
to flip a given column vertically.

Vertical map: Here lies the main difference with acedb versions 1
and 2. A generalisation of the Map models now allows to display, in
the manner of the nematode genetic map, objects belonging to those
classes one wishes, rather than only genes and rearrangements. This
is the reason why we recommend acedb-3 for the other organisms. The
way to rearrange the data is explained in the documentation:
wdoc/Porting.Data and you can contact (mieg at kaa.cnrs-mop.fr) for
help. We hope that the new models will accomodate in a natural way
all organisms and are very interested to have your feedback.

The rest of the display differ at present very little from the ace-2
version.


Query Windows:
-------------

Note that acedb allows several ways to search the database: 
navigation by mouse pick, text search in main window, long text
search to also scan the paper abstracts or OMIM documents. 

Three different interfaces allow to pass complex queries:
1) query by example, friendly, but slow and not very powerful;
2) query builder, friendly and rather general;
3) direct query interface, complete, but unfriendly.
The third system requires that you know the acedb query syntax and
the models of the database, whereas the other 2 prompt you with the
models in a nice way. However only the third system allows you to
save and load files of queries, and use the full syntax.

We are grateful to the LBL-group headed by John MacCarthy for
providing the two friendly interfaces.

The table maker has been improved. It allows you to construct and
export spreadsheets, or relational tables, out of acedb and is used
in the construction of the multimaps.

At last to search the dna for motifs, use the DNA tool.

The queries, table maker and DNA tools are all available from the
main menu.

Kernel Changes with respect to acedb-1-10:
-----------------------------------------

These changes are common to the ace2 and ace3 versions.  The system
has been globally accelerated and has become less disk greedy. The
table maker is improved. The vt-100 version, called tace, has been
improved. It can now initialise the database, read the models and
read the update files. The dialog on initialisation has been
streamlined. There is also a possibility to make and use the pair
aceserver/aceclient which allows remote batch mode interrogations
and updates of the database.
If you are missing the lockf call on your machine, add a line NOLOCK
in passwd.wrm

Two changes may affect your code:
The first call to lexNext() will now avoid the model, which are now
attached to Model class. This means that, to see the models, you
must now go the Model class. But also that if you yourself had a
special trick to jump the model, you should remove it.

Portability:
-----------

Acedb now runs on Sun-OS, Solaris, Silicon Graphics, Dec, Dec-alpha,
HP, IBM, Next, Macintosh and PC running Linux.  If you have problems
or queries about any of these there may be more information in the
file NOTES at the ftp sites.

How to get ACEDB:
=================

To install acedb-3 with together with the human-chromosome 21
database, you need all the datafile human.21.ace.Z for the data, and
either the source code or one of the bin file bin.*.tar.Z for the
programs, and doc.*.tar.Z for the documentation.

All the files are available in the following public access accounts
(anonymous ftp sites) accessible over internet:

  cele.mrc-lmb.cam.ac.uk (131.111.84.1) in England, in pub/acedb
  lirmm.lirmm.fr (193.49.104.10) in France, in directory pub/acedb
  ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb

In each case, log in as user "anonymous" and give a user identifier
as password.  Remember to transfer the files in BINARY mode by
typing the word "binary" at the start of your ftp session.  Many
thanks to NCBI for letting us share in their excellent resource.

Always get files README and NOTES.  If at all uncertain, quit at that
point and read them before continuing.

Example:

ftp 130.14.20.1
login: anonymous
password 'whatever you want'
cd repository/acedb/ace3    (or ace2)
binary
mget *
get README  y/n   answer yes   etc
..
..

quit

Always get a copy of the INSTALL script.  Move it and the .tar.Z files
into the home directory in which you are installing ACEDB.  Type
"source INSTALL". 

If you have a problem making the program work, look at the section
on problems in NOTES, and if that fails to help, let us know.

******************************************************************

Please send any comments, especially about anything you think is
wrong (program or data), to

Danielle and Jean Thierry-Mieg (mieg at kaa.cnrs-mop.fr)

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