ChIPMonk is a java application. This means that in order to run ChIPMonk you need to have installed a java runtime environment (JRE). If you do not have a JRE installed then ChIPMonk will not start.
There are a number of freely (no cost) available JREs. ChIPMonk has been tested to work with Sun JRE v 1.5 running under windows, linux and MacOSX. If you don't have this JRE already you can get it from java.sun.com. Other java environments/versions may also work, but we haven't tested them.
The nature of the data ChIPMonk has to deal with is that it is very large. Both genome annotations and array data take up huge amounts of memory. ChIPMonk requires at least 512Mb of RAM for small experiments, and large experiments may require >1Gb RAM. If you're having problems with memory usage then look at the notes on configuration to see how you can reduce the amount of memory ChIPMonk requires.
If ChIP Monk fails to import new genomes it's probably because it was unable to contact the web server which provides this data. In order to do this your machine needs to be able to access the internet.
If your machine is networked and genome importing still doesn't work then the most common cause is the proxy server settings (under Network from Edit > Preferences). If your network uses a proxy server you should enter its details here. If not then the proxy server name should be left blank.
If you are using a data file generated by version 1.0 of ChIPMonk or earlier it is possible that the name of the genome you're using has been changed. We have changed some of the mouse genomes to a more standard form in later ChIP
If your mouse genome is called NCBI## (where ## is a number), then you need to change this to NCBIM## (add an extra M) in the second line of the .cmk file. The genome should then be recognised and will work as before.