There were two novels, you did not have to read one before the other but they were connected. There was an attic lab. Large bones that you could walk through. A city enclosed in glass. A junkyard where robots/automatons "hid". A floating island made of ships. The protagonist was a young woman who escaped a ship, I think she has some kind of power. The science lab had some kind of flying bat like monkey and strange animals in cages. Her sister (?) lived in a prison type castle but she was not locked in a cell, she was attached to a chain that was connected to a complex system of bars that ran through out the building. On these ships were people charged with some crime and condemned to be mechanically modified for slave work. The setting is dirty, muddy, a lot of crime and starvation. I want these in my home library and to read again. Thank you!