announcing version 2 of SampleDB
matthews at GREENGENES.CIT.CORNELL.EDU
Fri Jun 30 17:40:30 EST 1995
SampleDB 2.0 is now available in probe.nalusda.gov:pub/acedocs. Here's
SampleDB, version 2.0, 28 June 1995
A sample database to demonstrate features of ACEDB, especially map and sequence
C. elegans chromosome V and its neighbors
To view, pick Map "V".
There is a "guided tour" available via the online help; click the "Help"
button in the main window and look at "About SampleDB..."
ctg313 and ctg893, from C. elegans chromosome V, and their neighbors
To view, pick Map "V" and double-click on the yellow "Contigs" bars
The Sequence Display
C. elegans sequence B0272 and some of its neighbors
To view, pick Sequence "B0272".
Rice chromosome 1 vs. maize chromosomes 3 and 8
To view, examine MultiMaps "Rice 1, Maize 3,8" and "Rice 1, Maize 3,8
The SYN map
Human chromosome 21 and mouse 10 and 16
To view, pick Map 21.LBL
There is a guided tour available via the online help.
Improved online help
SampleDB uses the new hypertexted online help system. Much of the help,
including the guided tours, is only available via Mosaic.
Developers and documenters are encouraged to add more features to SampleDB, by
- concise .ace datasets,
- description of any models.wrm changes needed, and
- suggested objects to look at to exercise the features.
SampleDB 2.0 is distributed with a SunOS 4.x executable of xace.4.syn, 14 Jun
95, from Arun Aggarwal. All features other than the SYN map should work with
xace version 4_0b4, available from ncbi.nlm.nih.gov as executables for
several platforms and as source.
In order to make the SYN map work, wspec/options.wrm has been slightly
modified. Now when a Map object is double-clicked the SYN display is
invoked; picking a Locus object invokes the GMAP. A standard C. elegans
options.wrm is included for comparison or for alternate use.
In addition, the standard C. elegans models.wrm (as distributed with the
ACEDB v4_0b4 release) is included. The intention is to include each
models.wrm used to implement each increment of features in succeeding
releases of SampleDB, with a running log of the diff's at each step
maintained in directory wspec/models.diffs.
- Dave Matthews
matthews at greengenes.cit.cornell.edu
More information about the Acedb