An apparatus and method for generating a modified maximum-likelihood description of a system having a parent population of entities of different classes that includes collecting a sample population of the entities and measuring a statistical distribution of the sample population. The method further includes determining a modified maximum-likelihood estimate of the parent population based on the statistical distribution of the sample population and calculating a diversity measure of the estimated parent population to describe the system.

Systems and methods for creating fully custom products from scratch without exclusive use of off-the-shelf or pre-specified components. A system for creating custom products includes an image capture device for capturing image data and/or measurement data of a user. A computer is communicatively coupled with the image capture device and configured to construct an anatomic model of the user based on the captured image data and/or measurement data. The computer provides a configurable product model and enables preview and automatic or user-guided customization of the product model. A display is communicatively coupled with the computer and displays the custom product model superimposed on the anatomic model or image data of the user. The computer is further configured to provide the customized product model to a manufacturer for manufacturing eyewear for the user in accordance with the customized product model. The manufacturing system is configured to interpret the product model and prepare instructions and control equipment for the manufacturing of the customized product.

The invention describes an explicit solvent all-atom molecular dynamics methodology (SILCS: Site Identification by Ligand Competitive Saturation) that uses small aliphatic and aromatic molecules plus water molecules to map the affinity pattern of a large molecule for hydrophobic groups, aromatic groups, hydrogen bond donors, and hydrogen bond acceptors. By simultaneously incorporating ligands representative of all these functionalities, the method is an in silico free energy-based competition assay that generates three-dimensional probability maps of fragment binding (FragMaps) indicating favorable fragment:large molecule interactions. The FragMaps may be used to qualitatively inform the design of small-molecule ligands or as scoring grids for high-throughput in silico docking that incorporates both an atomic-level description of solvation and the large molecule's flexibility.

Method, systems and apparatus to determine the suitability of parts or protocols to perform unit operations in the context of a biological process, comprising recording of a user score associated with an instance of use of a protocol or part, wherein the context of the use is recorded along with the rating, and wherein the context is defined as the value of factors that may affect the performance of the unit operation in which the part or protocol was used. The method may be implemented as a web service.

Various embodiments select markers for modeling epistasis effects. In one embodiment, a processor receives a set of genetic markers and a phenotype. A relevance score is determined with respect to the phenotype for each of the set of genetic markers. A threshold is set based on the relevance score of a genetic marker with a highest relevancy score. A relevance score is determined for at least one genetic marker in the set of genetic markers for at least one interaction between the at least one genetic marker and at least one other genetic marker in the set of genetic markers. The at least one interaction is added to a top-k feature set based on the relevance score of the at least one interaction satisfying the threshold.

Computer-implemented methods for providing improvements in genome-scale metabolic models are described. The methods identify and optimize metabolic flux states that minimize the cost of enzyme production while maximizing a desired cellular phenotype. The computer-implemented methods may maximize cellular phenotypes such as growth (biomass) or production of a metabolite, such as a commercially valuable chemical compound, through the selection of metabolic pathways that maximize these phenotypes while minimizing metabolic costs associated with production of the proteomic constituents of individual metabolic pathways. The computer implemented methods may be useful for computationally designing microbial strains for the production of chemicals.

A system and method for automatically navigating an in vivo imaging capsule in a body lumen. The system comprises an imaging capsule including an imager, optional pressure sensor for producing data of forces acting on the imaging capsule in vivo, and a transmitter to transmit image, positioning and pressure data from the capsule to an external unit. A positioning system for providing current position data of the capsule in vivo may be included in the capsule and/or external to it. External magnets may generate a magnetic field to scan a body lumen by causing a predetermined motion pattern of the imaging capsule within a region proximate to its current position, and generate a driving force to propel the imaging capsule according to a calculated target direction vector. A processor may calculate a target direction vector for propelling the imaging capsule based, on unique patterns identifiable in one or more images.

Embodiments include a system for determining cardiovascular information for a patient. The system may include at least one computer system configured to receive patient-specific data regarding a geometry of the patient's heart, and create a three-dimensional model representing at least a portion of the patient's heart based on the patient-specific data. The at least one computer system may be further configured to create a physics-based model relating to a blood flow characteristic of the patient's heart and determine a fractional flow reserve within the patient's heart based on the three-dimensional model and the physics-based model.

The present invention relates, in general, to an HIV-1 vaccine and, in particular, to a B cell lineage-based vaccination protocol.

The orthogonal space random walk (OSRW) algorithm is generalized to be the orthogonal space tempering (OST) method via the introduction of the orthogonal space sampling temperature. Moreover, a double-integration recursion method is developed to enable practically efficient and robust OST free energy calculations, and the algorithm is augmented by a novel -dynamics approach to realize both the uniform sampling of order parameter spaces and rigorous end point constraints. In the present work, the double-integration OST method is employed to perform alchemical free energy simulations, specifically to calculate the free energy difference between benzyl phosphonate and difluorobenzyl phosphonate in aqueous solution, to estimate the solvation free energy of the octanol molecule, and to predict the nontrivial Barnase-Barstar binding affinity change induced by the Barnase N58A mutation. As demonstrated in these model studies, the DI-OST method can robustly enable practically efficient free energy predictions, particularly when strongly coupled slow environmental transitions are involved.