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Old 06-15-2009, 03:38 AM   #25
Roald
Director at CLC bio
 
Location: Denmark

Join Date: Aug 2008
Posts: 26
Default CLC Genomics 3.5

Disclaimer: I work at CLC bio
Hi Arne,

I have added some comments to your post here that I hope may be of use:
You are right that the Java side of our software uses a lot of memory. In order to utilize the full potential of the hardware and get things done as fast as possible we allow the program to use as much memory as is safe. This is done by checking the hardware specifications during startup.
If you are using the .sh installer the vmoptions should automatically be set to around 75%. However, if you think this is too much you can change the memory settings from the vmoptions file in the installation directory (e.g. clcgenomicswb3.vmoptions).

We have an ongoing effort to optimize our algorithms and data structures such that the software will run smoothly on even moderately equipped hardware and will fit the use case of doing big jobs on a large machine and then delegating the inspection to e.g. labtops.
On my MacBook Pro labtop I can quite comfortably view very large contigs of all human chromosomes. However, when the reference sequence of the contig is heavily decorated with annotations the machine can get a bit slow and unresponsive. This is something that we will address over the next couple of months as part of a major restructuring of our annotation handling framework. Stay tuned for that.

Regarding the missing search functionalities for RNA-seq results, we actually offer some quite advanced but also quite well hidden options for filtering and searching the result table (as well as most other tables). Please, have a look at http://www.clcbio.com/index.php?id=1...th_tables.html

I hope this helps, otherwise please get back here or try our support folks.

With best regards

Roald Forsberg
Director of Scientific Software Solutions, CLC bio


Disclaimer: I work at CLC bio
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