Max-Planck-Institut für Informatik
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User manual, GOTaxExplorer, Version 1.0


GOTaxExplorer is available with a command line interface and a graphical user interface. Both interfaces can be used to issue queries using the query language or SQL and to see the results in a table. A configuration file is used to provide details on the database access and to change program behavior.

System requirements

GOTaxExplorer needs JavaTM 1.5 or later to be installed. It requires a database to be accessible either locally or over a network link. GOTaxExplorer is configured to use a MySQL database. If another database is used, it is very likely that it is necessary to rewrite some SQL commands used by GOTaxExplorer. The database access information and driver can be changed in the configuration file.

GOTaxExplorer should run reasonably fast on a computer with a CPU with more than 2GHz. The amount of main memory required depends on the size of the data sets returned by the queries. Performance is in large parts restricted by the database server since database queries are the most common and costly operations. Due to the fact that the comparison of sets of GO terms and functional equivalents are implemented multi-threaded, they can benefit from a client computer with more than one CPU. However, the database will be the limiting factor in such a setting. Using more than one thread on a single CPU increases execution speed because it helps to operate the database at full capacity. The database load generated by GOTaxExplorer can be adjusted with the number of threads used for a GO set comparison or a functional equivalence calculation. Since all queries are cached during a functional equivalence calculation, the database is released by the client. However, the caching uses large amounts of memory and there should be available at least 1024MB of main memory or virtual memory.

In order to use the 3D visualization of graphs, the Java3D libraries and the WilmaScope libraries have to be installed. GOTaxExplorer needs up to 1024MB of memory for this visualization. Furthermore, it needs a high performance graphics card with OpenGL rendering capabilities.

The command line interface is faster than the GUI. It also requires 512MB of memory for the comparison of sets of GO terms of a functional equivalence calculation.