I would like to (try to) publish a software I have been developing; the software is for analyzing and integrating data from ENCODE, and of course will be open source.

I know about Bioinformatics APPLICATIONS NOTES as a possible venue, but I would like to evaluate alternatives.

Can anyone point me to some valid journal accepting this kind of publications?
Here are few journals to consider,

 - BMC Bioinformatics
 - Briefings in Bioinformatics
 - Molecular systems biology
 - PLOS Computational Biology
 - GigaScience
 - Nucleic Acids Research
 - Genome Biology (Software)