Update for biom-format 1.3.1, 1.3.1-dev

Also update QIIME to use biom-format 1.3.1.
Merge pull request #84 from jrrideout/biom-1.3.1

**NOT READY FOR MERGE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!1** Update for biom-format 1.3.1, 1.3.1-dev