About SampleDB


28 June 1995

SampleDB is a sample database to demonstrate features of ACEDB, especially map and sequence displays. SampleDB version 2.0, is available via ftp

Features Include

  The GMAP
   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..."

  The PMAP
   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".

  The MultiMap
   Rice chromosome 1 vs. maize chromosomes 3 and 8
   To view, examine MultiMaps "Rice 1, Maize 3,8" and "Rice 1, Maize 3,8 
   Anchored"

  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 submitting

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@greengenes.cit.cornell.edu)