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Home >> Research >> Bioinformatics
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9. System Requirements & Performance Issues

There are very few system requirements for RescueNet, aside from the obvious observation that a faster computer will bring down running time. RescueNet normally operates using less than 2MB of free RAM, but in the case of a user choosing to generate long format (ordered) results in the probability scores step (see Section 5.1), then memory requirements will be substantially higher. To order the results, RescueNet requires approximately 650bytes for every gene in the file under test (i.e: 650Kb free RAM for analysing 1000 genes). This only becomes a substantial figure when dealing with extremely large datasets, and even then should not cause any memory issues for the typical computer.

The user should also be aware of free disk space requirements. This is especially an issue when using RescueNet in the annotation process. To find the required amount of disk space for an annotation run, the following formula may be used:
(window size*3) * (genome size in base-pairs)/(window offset * 3)

This gives the number of bytes needed for one reading frame file. The figure should be multiplied by 6 to give the figure for all reading frames, and then multiplied by 4 to include the requirements of the RSCU and observed/expected files needed by the program. This will be a fairly substantial figure, but the actual results files only take up a small fraction of this space. I suggest deleting all files with extension “.seq”, “.rscu” and “.obsexp” after the program exits. These files are not deleted automatically by RescueNet in case the user wishes to inspect any of the intermediate sliding window sequences.

Running times vary not only from machine to machine, but also due to different program settings like training time, SOM size and dataset size. Some applications, such as integrating RescueNet into an annotation workbench, may be time-critical. As a guideline, such users should be aware that an entire annotation run (including SOM training) on a 2.5Mbp genome and using typical program settings takes about 5 minutes on a Pentium 4 PC.

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