Abstract: A method and system for interpreting experimental data with automated reasoning. Domain specific knowledge is acquired from one or more pharmaceutical information sources. A semantic representation of the domain specific knowledge is created meeting a desired set of criteria. Pharmaceutical data from a knowledge database is classified with the semantic representation, allowing construction of a set of reasons for any classified pharmaceutical data. The set of reasons may help interpret the classified pharmaceutical data to remove errors, such as “physical errors” and “biological errors”. Removing such errors helps improve fusion of knowledge from multiple data, information and knowledge sources which incorporates activity and selectivity against a target, desired pharmacokinetic and toxicity properties enabling selection of potential pharmaceutical compounds.

Abstract: Synthetic versions of a full length and termini truncated humanized green fluorescent protein based on Ptilosarcus gurneyi are disclosed which have been modified to the favored or most favored codons for mammalian expression systems. The disclosed encoded protein has 239 amino acid residues compared with the wild type Ptilosarcus gurneyi which has 238 amino acids. In the present invention, a valine residue has been added at the second position from the amino terminus and codon preference bias has been changed in a majority of the wild type codons of Ptilosarcus gurneyi fluorescent protein. The humanized Ptilosarcus gurneyi green fluorescent protein is useful as a fluorescent tag for monitoring the activities of its fusion partners using imaging based approaches.

Abstract: A method and system for creating and using knowledge patterns. One or more patterns derived from one or more pharmaceutical data sources are acquired. A knowledge map is created using the one or more patterns. The knowledge map, such as a self-organizing knowledge map, includes a selected representation of a pattern space. A set of selected regions from the knowledge map are annotated. Others patterns are classified with annotated regions of the knowledge map, thereby adding additional knowledge to the knowledge map. The knowledge map is used for recognizing previously unseen or unknown patterns from large amounts of pharmaceutical data obtained by automated screening systems. The knowledge map includes knowledge for a new real or virtual drug compounds or drug therapies. The knowledge patterns may be used to select new known pharmaceutical compounds, or model new virtual pharmaceutical compounds.

Abstract: Methods and system for efficient collection and storage of experimental data. These methods and system allow experimental data from high-throughput, feature-rich data collection systems, such as high-throughput cell data collection systems to be efficiently collected, stored, managed and displayed. The methods and system can be used, for example, for storing managing and displaying cell image data and cell feature data collected from microplates including multiple wells and a variety of bio-chips in which an experimental compound has been applied to a population of cells. The methods and system provide a flexible and scalable repository of experimental data including multiple databases at multiple locations including pass-through databases that can be easily managed and allows cell data to be analyzed, manipulated and archived. The methods and system may improve the identification, selection, validation and screening of new drug compounds that have been applied to populations of cells.

Abstract: The present invention provides systems, methods, and screens to measure receptor internalization in a single step with appropriate automation and throughput. This approach involves luminescent labeling of the receptor of interest and the automated measurement of receptor internalization to a perinuclear location.

Abstract: The present invention provides systems, methods, screens, reagents and kits for optical system analysis of cells to rapidly determine the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for those that specifically affect particular biological functions.

Abstract: The present invention provides systems, methods, and screens to measure receptor internalization in a single step with appropriate automation and throughput. This approach involves luminescent labeling of the receptor of interest and the automated measurement of receptor internalization to a perinuclear location.

Abstract: The present invention provides systems, methods, and screens for an optical system analysis of cells to rapidly determine the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for those that specifically affect particular biological functions. The invention involves providing cells containing fluorescent reporter molecules in an array of locations and scanning numerous cells in each location with a high magnification fluorescence optical system, converting the optical information into digital data, and utilizing the digital data to determine the distribution, environment or activity of the fluorescently labeled reporter molecules in the cells. The array of locations may be an industry standard 96 well or 384 well microtiter plate or a microplate which is microplate having cells in a micropaterned array of locations.

Abstract: The present invention provides automated systems, methods, screens, and software for the analysis of cell spreading. The invention involves providing cells containing fluorescent reporter molecules in an array of locations, contacting the cells with a test stimulus, acquiring images from the cells, and automatically calculating one or more morphological features that provide a measure of cell spreading.

Abstract: The present invention provides systems, methods, and screens for an optical system analysis of cells to rapidly determine the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for those that specifically affect particular biological functions. The invention involves providing cells containing fluorescent reporter molecules in an array of locations and scanning numerous cells in each location with a high magnification fluorescence optical system, converting the optical information into digital data, and utilizing the digital data to determine the distribution, environment or activity of the fluorescently labeled reporter molecules in the cells. The array of locations may be an industry standard 96 well or 384 well microtiter plate or a microplate which is a microplate having a cells in a micropaterned array of locations.

Abstract: The present invention provides systems, methods, and screens for an optical system analysis of cells to rapidly determine the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for those that specifically affect particular biological functions. The invention involves providing cells containing fluorescent reporter molecules in an array of locations and scanning numerous cells in each location with a high magnification fluorescence optical system, converting the optical information into digital data, and utilizing the digital data to determine the distribution, environment or activity of the fluorescently labeled reporter molecules in the cells. The array of locations may be an industry standard 96 well or 384 well microtiter plate or a microplate which is a microplate having a cells in a micropaterned array of locations.

Abstract: The invention relates to an optical system for determining the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for specific biological activity. The invention involves providing cells containing fluorescent reporter molecules in an array of locations and scanning numerous cells in each location with a fluorescent microscope, converting the optical information into digital data, and utilizing the digital data to determine the distribution, environment or activity of the fluorescently labeled reporter molecules in the cells. The array of locations may be an industry standard 96 well or 384 well microtiter plate or a microplate which is a microplate having a cells in a micropaterned array of locations.

Abstract: The invention relates to an optical system for determining the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for specific biological activity. The invention involves providing cells containing fluorescent reporter molecules in an array of locations and scanning numerous cells in each location with a fluorescent microscope, converting the optical information into digital data, and utilizing the digital data to determine the distribution, environment or activity of the fluorescently labeled reporter molecules in the cells. The array of locations may be an industry standard 96 well or 384 well microtiter plate or a microplate which is a microplate having a cells in a micropaterned array of locations. The invention includes apparatus and computerized method for processing, displaying and storing the data.

Abstract: The present invention provides novel recombinant fusion proteins for detecting binding of a molecule of interest containing a detection domain, a first and optionally a second localization domain, and a binding domain. The invention also provides recombinant nucleic acid molecules and recombinant expression vectors encoding these novel fusion proteins, genetically engineered host cells containing these expression vectors, and kits for the use of these fusion proteins, nucleic acid molecules, expression vectors, and host cells. Additionally, the present invention provides methods for identifying compounds that alter the binding of a molecule of interest in a cell.

Abstract: The invention relates to an optical system for determining the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for specific biological activity. The invention involves providing cells containing fluorescent reporter molecules in an array of locations and scanning numerous cells in each location with a fluorescent microscope, converting the optical information into digital data, and utilizing the digital data to determine the distribution, environment or activity of the fluorescently labeled reporter molecules in the cells. The array of locations may be an industry standard 96 well or 384 well microtiter plate or a microplate which is a microplate having a cells in a micropaterned array of locations. The invention includes apparatus and computerized method for processing, displaying and storing the data.

Abstract: The present invention provides systems, methods, screens, reagents and kits for optical system analysis of cells to rapidly determine the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for those that specifically affect particular biological functions.

Abstract: The present invention describes novel methods for making a substrate for selective cell patterning, and the substrates themselves, wherein the method comprises contacting reactive hydroxyl groups on the surface of a substrate with a hydroxyl-reactive bifunctional molecule to form a monolayer, and using stencils to deposit cell repulsive or cell adhesive moieties in controlled locations on the cell culture substrate. Methods comprising selective differentiation of stem cells to create tissue specific and organ-specific cell substrates, as well as the cell substrates themselves are also provided.

Abstract: The present invention provides automated methods and associated software for determining the organization of a component of interest in individual cells by determining the amount or distribution of the cellular component of interest as a function of position relative to a reference component in the individual cells.

Abstract: The present invention provides methods and software for tracking individual cells during a kinetic cell screening assay.

Abstract: The invention provides a method for a method for determining a best initial focal position estimate for a current sample location on a substrate comprising multiple sample locations, comprising determining the best initial focal position estimate by using a result from one or more techniques selected from the group consisting of linear regression analysis of focal positions determined for at least two other sample locations on the substrate and quadratic regression analysis of focal positions determined for at least three other sample locations on the substrate.