SetupX - tuning and the missing indexes

after analyzing a couple of hundred sql statements in setupx I noticed that there is no real use of indexes for some reason. Why there are no indexes escapes my mind, but since we prefer higher query speed I suggest the creation of the following indexes (which are far from perfect)

create index pubdata_relatedExperimentID_index on pubdata(relatedExperimentID)
create index NCBIClassifierID_ncbiID_index on NCBIClassifierID(ncbiID)
create index formobject_question_index on formobject(question)
create index formobject_discriminator_index on formobject(discriminator)
create index formobject_value_index on formobject(value(100))
create index query_querytype_index on query(querytype)
create index query_userid_index on query(userID)
create index datafile_source_index on datafile (source)
create index cache_experiment_id_index on cache (experimentID)
create index user_password_index on user (passwd)
create index user_username_index on user (username)
create index BlockedIP_blockedIp_index on BlockedIP(blockedIP)

this should improve the performance nicely and is currently being applied to our production system.