A method and system for calibrating a machine capable of automatically calibrating the axes of the machine by comparing an initial calibration state of a particular axis with a subsequent motion of the machine along the same axis. The invention specifically relates to methods and apparatus for removing gas bubbles from a reaction chamber wherein target molecules contained in a sample fluid are reacted with probe molecules immobilized on a substrate having an array of oligonucleotide binding sites. Also, the conductive material can have electrically isolated segments that are utilized as electrical jumpers for connecting circuit elements. The distal ends of the first and second pivotal support braces are adapted to be pivotally attached to a retaining assembly, mounted in relation to the table top. The method of the invention involves adding a phospholipid into a fluid composition including a lens-forming material in an amount sufficient to reduce an averaged mold separation force by at least about 40% in comparison with that without the phospholipids.