Databases and Systems

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table of 13 columns and 1 million lines in 16 minutes. For the IGD project, we were
able to load on a DEC alpha a large data set consisting of GDB, GenBank, SwissProt
and several dozen smaller databases into acedb. Once loaded, Acedb was able to
complete a test suite of queries on this data set in 3 minutes as opposed to 30 minutes
for a Sybase server on the same machine.
It is crucial, however, to run the database on a local disk. If the database disk is
mounted over NFS, or on a RAID system, performance easily degrades by a factor of
10. In such a case, to produce a very large table, it is much faster to ftp the whole
database onto a local disk, run the table query and destroy the database, than to run
the query off the remote disk.
How does the storage capacity of Acedb compare to other database management
systems? Comparisons with relational systems are difficult because of the
impossibility of relating relational tables to objects. However, we can compare
Acedb to other object oriented systems. The present C.elegans data set contains 500
thousand objects and uses half a Gigabyte of disk space. Direct comparisons of
storage capacity by counting the number of objects may be misleading because it
depends on the expressive power of the grammar. For example, Gilles Lucato and
Isabelle Mougenot at LIRMM wrote an automatic Acedb to Matisse translator. Extra
classes were needed in Matisse to store the Acedb structured tags and as a result, the
C.elegans dataset in Matisse is spread over several million objects and takes several
times more disk space. Illustra also uses more diskspace. We have been told that 02
performance degrades at around 50 thousand objects on similar machines.
Objectstore databases are memory mapped to disk, this places a strict limit of 4
gigabytes on conventional 32-bit architecture machines. Acedb has no such hard
limit, but typically one needs 50 bytes of memory and 1 kilobyte of disk space per
object, effectively limiting acedb to one million objects and 1 gigabyte of disk on a
128 Mb machine.
How to get the software
The whole Acedb system, including the Java and Perl tools and demos, and the
Acembly package are available from our Web page http://alpha.crbm.cnrs-mop.fr.
The C.elegans data and Acedb source code may be downloaded from
ftp://ncbi. nlm.nih.gov/repository/acedb/ in the US
ftp://Airmm.lirmm. fr/pub/acedb/ in France
ftp://ftp.sanger.ac. uk/pub/acedb/ in England
Documentation, tutorials and examples are maintained by Sam Cartinhour and Dave
Matthews on the US site http:probe.nalusda.gov:8000/acedocs/index.html