TissueInfo is distributed under the GNU General Public License (GPL)

[ necessary files ]

tisim.jar [April 29 2009]

See the ICB wiki for documentation

source code [April 29 2009]

crover.prp

The following files are updated daily:

curated_tissues

ti_to.gz

ti_dev.gz

ti_seq.gz

For users having problems downloading the large ti_seq file, it has been split up into smaller files below

ti_seq00.gz

ti_seq01.gz

ti_seq02.gz

ti_seq03.gz

ti_seq04.gz

[ optional files ]

data [April 29 2009]

tissueinfo.jar [April 29 2009]

tissueinfo.owl

The TissueInfo hierarchy is now available in OWL format. The ontology can be viewed and manipulated with an ontology editor, such as Protege. [screenshot]

[ prerequisites ]

UNIX account

Access to BLAST suite of programs via that UNIX account

Note:
This package has been written in Java 1.6. It is therefore portable, and may work on other platforms. We have tested primarily on UNIX.

Required packages:
The following third-party packages are required but are not part of TissueInfo:

- JDBC drivers (contact your DBMS vendor)

To use the tiimport and tidump and the database version of tiquery, you must obtain the JDBC drivers from your vendor. To use tisearch, timegablast and the flat file version of tiquery (you must use the -memory option), you may proceed directly with the installation files alone. Ensure that you have filled in the necessary properties in the crover.prp file.

DBMS configuration:
If you wish to use the tiimport, tidump and the database version of the tiquery executables, you will need to set up your database. The only requirement for the database is that it should support JDBC.

[ installation steps ]

1. Distribution



2. User creation



3. TissueInfo configuration



4. Creating Aliases

[ troubleshooting ]

1. Tests have been included with this distribution. To run these tests, use the command ant test. Some of these tests test the connection to the database and will fail without a correctly set up database and a correctly filled in crover.prp file.
2. If you get an OutOfMemoryException, try increasing the VMOPTIONS parameter in the relevant executable file. (eg VMOPTIONS=-mx600m means that the maximum memory available to the program is 600 Mb)
3. The most common error occurs when the TISSUEINFO environment variable is undefined or invalid. It must point to the distribution directory.
   ie. if you untarred the distribution in /home/username/tissueinfo, TISSUEINFO should be set to /home/username/tissueinfo
4. The executables are stored in the bin directory. This means that to run the programs included in this distribution, the user must use the command $TISSUEINFO/bin/executable. It is also possible to use an alias.