Abstract: Aspects of the present invention describe an apparatus and method for generating genotype calls for a sample. The genotyping initially models allelic signal response into an allelic model having one or more model parameters for an identified one or more sources of systematic variation. The model and parameters are then used to transform the allelic signals to a normalized normalized allelic space that serves to compensate for the one or more sources of systematic variation. By compensating for the systematic variation in this manner, the genotype for the sample is readily determined based upon its relationship to the representation of the allelic signals in normalized allelic space and in accordance with the allelic model.

Abstract: Aspects of the present invention describe an apparatus and method for generating genotype calls for a sample. The genotyping initially models allelic signal response into an allelic model having one or more model parameters for an identified one or more sources of systematic variation. The model and parameters are then used to transform the allelic signals to a normalized normalized allelic space that serves to compensate for the one or more sources of systematic variation. By compensating for the systematic variation in this manner, the genotype for the sample is readily determined based upon its relationship to the representation of the allelic signals in normalized allelic space and in accordance with the allelic model.

Abstract: A method of using a standard to correct for variability in sample handling, can comprise (a) adding a template of known concentration to an assay comprising a sample; (b) preamplifying the assay; (c) amplifying the assay; (d) collecting data during the amplifying; and (e) correcting the data using a comparison of data collected from the template to data collected from the sample.

Abstract: An optic device is placed in close proximity to multiple gain elements so as to selectively modify the divergence of the light from said multiple elements such that when the light is subsequently collimated and diffracted from a grating and focused into an optical fiber, it will have a predefined cross-section that matches the mode of the fiber. Using this system and method, a more efficient light transfer is achieved in an intracavity fiber coupled multigain element laser.

Abstract: An embodiment is directed to a system for dissipating cladding modes of an optical fiber. In the system, a high power light source couples optical power into the optical fiber at a fiber coupling point thereby producing the cladding modes; material is indexed-matched to the optical fiber and is optically contacted to the optical fiber near the fiber coupling point; and a substrate layer is operable to provide a thermal sink for heat generated from dissipation of cladding modes of the optical fiber.

Abstract: A tracking system and method in an optical communications system utilizing an optical communications beam. In one embodiment, the disclosed optical communications system includes a communications receiver circuit and a tracking circuit. The optical communications system generates a communications signal. The tracking system includes a tracking detector having a plurality of regions coupled to a corresponding plurality of tracking channel circuits. Each of the tracking channel circuits includes an optical detector coupled to receive the optical communications beam. The peak-to-peak amplitude modulation in the optical communications beam is measured by substantially reducing or removing a direct current (DC) offset present in the optical communications beam. In one embodiment, after the DC offset is substantially reduced or removed, the signal is then amplified, mixed with the communications signal and then filtered.

Abstract: Embodiments of the present invention are directed to method of fabrication of a broadband emitter array. Embodiments of the present invention may grown a first set of emitters possessing a first quantum well characteristic (e.g., quantum well thickness or composition). A portion of the first set of emitters is removed by etching. In place of the removed emitters, a second set of emitters is regrown with said second set of emitters possessing a different quantum well characteristic. By fabricating the emitters sets in this manner, a unitary emitter array may be fabricated that possesses an increased bandwidth, e.g., the first and second sets of emitters may be associated with different center wavelengths. Embodiments of the present invention may utilize emitter arrays fabricated in this manner in, for example, incoherently beam combined (IBC) lasers and in Raman amplifier systems.

Abstract: The present invention is directed to a system and method which utilize an incoherently beam combined (IBC) laser. The IBC laser includes a plurality of emitters with each of the emitters possessing a partially reflective surface on their front facet. The partially reflective surface causes resonant wavelengths to be defined. In certain embodiments, the system and method arrange the external cavity and emitter spacings of the IBC laser such that the center feedback wavelength provided to each emitter is an etalon resonant wavelength. In other embodiments, the range of feedback wavelengths is adapted so that it is greater than the free spectral range (the separation in wavelength space between adjacent etalon resonant wavelengths).

Abstract: The present invention is in general related to efficient operation of an external cavity laser and more particularly to a system and method of operating an external cavity laser utilizing one or more controlled linewidth gain elements. Specifically, the linewidth of an gain elements is broadened so that Brillouin scattering mechanisms in a gain medium are eliminated or reduced.