ChIPMonk has to deal with potentially enormous amounts of data, both in ters of array data and genome annotation. The amount of data held can require enormous amounts of memory on your system for the program to work efficiently. To help keep things moving we've included a number of configuration options which can help memory usage and improve performace of the program.
ChIPMonk comes with a default set of settings which are appropriate for small to medium sized projects and work on the assumption that you're running on a machine with 1Gb of RAM (the recommended minimum for all but the smallest of experiments). You may find that altering these defaults will improve performance on your machine.
Most settings are stored per-user in a file called chipmonk_prefs.txt in your home directory.
Under Edit > Preferences there are a few settings which you can change to improve the usage of both RAM and hard drive space on your system.
This value is an approximate estimate of the number of probes which are going to be in your array. The value doesn't have to be exact and it doesn't really matter if you get it wrong. It's merely used when creating the data structure which holds your array data. Setting the value too high will cause your program to consume slightly more RAM than it needs to. Setting it too low will slow down the loading of your data.
This option allows you to save RAM by only loading certain types of genome annotation. If you put anything into this list only those types of features will be loaded - saving memory. If you don't put anything in then all features will be loaded. Note that you can still change which loaded features are displayed under View > Set Annotation Tracks, but that only loaded features will be listed there.
To allow you to make more efficient use of your filespace you can configure where ChIPMonk expects to find certain files.
Each genome available in ChIPMonk comes as a set of EMBL format sequence files (just the annotation, not the sequence). These can be quite large so you may want to move them to make efficient use of disk space, or allow them to be shared between users.
The initial genome base is the "Genomes" folder of your ChIPMonk installation, and you can copy this folder to anywhere else and then update your genome base preference to make it available again.
This simply sets the default location which is selected when you choose to import new data.
This sets the default location used when you load/save ChIPMonk project files, reports and probe lists.
In order to download new genomes into the program ChIPMonk needs to be able to contact a web server to get the list of available genomes and the compressed genome data. If your network doesn't allow direct connection to the internet, but instead uses a proxy server then you can specify the details here to allow ChIPMonk to connect.
The host name of your proxy server. This should be provided without an http:// prefix (eg wwwcache.example.com). Simply leave this blank if you're not using a proxy.
The port on which your proxy server is listening. The usual ports used by proxies are 80 or 8080 so those are worth a try if you're not sure what your server uses! This value will be ignored if you don't specify a proxy host name.
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