Add default use_ndex value
Add default use_ndex value

Closes #284
bgyori/indra,johnbachman/belpy,sorgerlab/belpy,sorgerlab/indra,johnbachman/indra,bgyori/indra,bgyori/indra,johnbachman/indra,pvtodorov/indra,johnbachman/indra,sorgerlab/indra,johnbachman/belpy,pvtodorov/indra,johnbachman/belpy,sorgerlab/indra,sorgerlab/belpy,pvtodorov/indra,sorgerlab/belpy,pvtodorov/indra