Database system including computer code for predictive cellular bioinformatics

Abstract

According to the present invention, computer based techniques for using information technology in therapeutics or drug discovery. In an exemplary embodiment, computer based techniques for determining information about the properties of substances based upon information about structure of living or non-living cells exposed to substances are provided. Computer software according to the present invention enables researchers and/or scientists to identify promising candidates in the search for new and better medicines or treatments using, for example, a cellular informatics database.

1 . A computer program product for populating a database with manipulated biological information, said computer program product comprising: 
 code for providing a plurality of cells in various stages of the cell cycle, said stages of the cell cycle including at least one selected from interphase, G0 phase, G1 phase, S phase, G2 phase, M phase, prophase, prometaphase, metaphase, anaphase, and telophase;    code for manipulating said cells in said various stages of cell cycle development to form a plurality of manipulated cells;    code for capturing an image of said plurality of manipulated cells;    code for determining a descriptor from said image for said manipulated cells;    code for populating a database with said descriptor;    wherein said image includes a first component of a cell and a second component of said cell; and    a computer readable storage medium for holding the codes.    
     
     
         2 . The computer program product of  claim 1  wherein said first component and said second component are selected from a protein, a protein modification, a nucleic acid, a lipid, a carbohydrate, a sub-cellular structure and an organelle.  
     
     
         3 . The computer program product of  claim 1  wherein said image is a digitized representation of said plurality of manipulated cells.  
     
     
         4 . The computer program product of  claim 3  wherein said digitized representation provides a density value of said plurality of manipulated cells.  
     
     
         5 . The computer program product of  claim 1  wherein said descriptors comprise numeric or logical values.  
     
     
         6 . The computer program product of  claim 5  wherein said values further comprises a nucleotide.  
     
     
         6 . The computer program product of  claim 5  wherein said values further comprises an amino acid letter.  
     
     
         8 . A computer program product for determining a property of a manipulation based upon effects of said manipulation on at least two of a plurality of components of at least one of a plurality of cells, said computer program product comprising: 
 code for providing at least one of a plurality of samples of said manipulation to said at least one of a plurality of cells;    code for determining at least one of a plurality of features of said at least two of a plurality of components of at least one of a plurality of cells in the presence of said manipulation;    code for determining at least one of a plurality of descriptors, said descriptors comprising at least one of said plurality of features;    code for searching a plurality of descriptors obtained from a database to locate descriptors based upon one of said descriptors of said manipulation, said searching forming a plurality of located descriptors;    code for determining, based upon said located descriptors, properties of said manipulation based upon said located descriptors;    wherein said two of a plurality of components includes a first component and a second component of a cell, said code for determining at least one of a plurality of descriptors of a state comprises code for combining information about said first component and said second component; and    a computer readable storage medium for holding the codes.    
     
     
         9 . The computer program product of  claim 8  wherein said plurality of components are selected from a protein, a protein modification, a nucleic acid, a lipid, a carbohydrate, a sub-cellular structure and an organelle.  
     
     
         10 . The computer program product of  claim 8  wherein said code for determining said plurality of located descriptors further comprises code for determining a plurality of matching descriptors, said matching descriptors corresponding to a prior administration of said manipulation, said prior administration of said manipulation having at least one of a plurality of properties.  
     
     
         11 . The computer program product of  claim 8  wherein said code for providing a manipulation comprises code for applying a chemical factor.  
     
     
         12 . The computer program product of  claim 8  wherein said code for providing a manipulation comprises code for applying a biological factor.  
     
     
         13 . The computer program product of  claim 8  wherein said code for providing a manipulation comprises code for applying an electromagnetic factor.  
     
     
         14 . The computer program product of  claim 8  wherein said code for providing a manipulation comprises code for applying a gravitational factor.  
     
     
         15 . The computer program product of  claim 8  wherein said code for providing a manipulation comprises code for applying a mechanical factor.  
     
     
         16 . The computer program product of  claim 8  wherein said code for providing a manipulation comprises code for applying a thermal factor.  
     
     
         17 . The computer program product of  claim 8  wherein said manipulation comprises a temporal factor.  
     
     
         18 . The computer program product of  claim 8  wherein said code for providing a manipulation comprises code for applying a nuclear factor.  
     
     
         19 . The computer program product of  claim 8  wherein said properties comprises toxicity.  
     
     
         20 . The computer program product of  claim 8  wherein said properties comprises specificity against a subset of tumors.  
     
     
         21 . The computer program product of  claim 8  wherein said properties comprises a mechanism of chemical activity.  
     
     
         22 . The computer program product of  claim 8  wherein said properties comprises a mechanism of biological activity.  
     
     
         23 . The computer program product of  claim 8  wherein said properties comprises a target protein.  
     
     
         24 . The computer program product of  claim 8  wherein said properties comprises a mechanism of action.  
     
     
         25 . The computer program product of  claim 8  wherein said properties comprises a structure.  
     
     
         26 . The computer program product of  claim 8  wherein said properties comprises at least one of a plurality of adverse biological effects.  
     
     
         27 . The computer program product of  claim 8  wherein said properties comprises at least one of a plurality of biological pathways.  
     
     
         28 . The computer program product of  claim 8  wherein said properties comprises at least one of a plurality of adverse clinical effects.  
     
     
         29 . The computer program product of  claim 8  wherein said properties comprises at least one of a plurality of cellular availability.  
     
     
         30 . The computer program product of  claim 8  wherein said properties comprises at least one of a plurality of pharmacological properties.  
     
     
         31 . The computer program product of  claim 8  wherein said properties comprises a gene expression profile.  
     
     
         32 . The computer program product of  claim 30  wherein said pharmacological properties comprises absorption.  
     
     
         33 . The computer program product of  claim 30  wherein said pharmacological properties comprises excretion.  
     
     
         34 . The computer program product of  claim 30  wherein said pharmacological properties comprises distribution.  
     
     
         35 . The computer program product of  claim 30  wherein said pharmacological properties comprises metabolism.  
     
     
         36 . The computer program product of  claim 8  wherein said properties comprises pharmacodynamic properties.  
     
     
         37 . The computer program product of  claim 8  wherein said properties can be selected from clinical uses and indications, human and veterinary diagnostic uses and tests, or human and veterinary prognostic uses and tests.  
     
     
         38 . The computer program product of  claim 8  wherein said descriptor comprises a scalar.  
     
     
         39 . The computer program product of  claim 8  wherein said descriptor comprises a vector.  
     
     
         40 . A computer program product of mapping a manipulation of cells based upon a morphological value, said computer program product comprising: 
 code for capturing a morphological value from said plurality of cells said cells being manupulated;    code for assigning a degree of presence of said morphological value; and    code for storing said morphological value and said degree of presence;    wherein said morphological value is derived from a first component of a cell and a second component of said cell, said code for capturing said morphometric value from said plurality of cells comprises code for determining a relationship between said first component and said second component; and    a computer readable storage medium for holding the codes.    
     
     
         41 . The computer program product of  claim 40  wherein said first component and said second component are selected from a protein, a protein modification, a nucleic acid, a lipid, a carbohydrate, a subcellular structure and an organelle.  
     
     
         42 . The computer program product of  claim 40  wherein said manipulation occurs in a manner selected from a electrical source, a chemical source, a thermal source, a gravitational source, a nuclear source, a temporal source, and a biological source.  
     
     
         43 . The computer program product of  claim 42  wherein said chemical source is selected from a pharmacological candidate and a drug screening library.  
     
     
         44 . The computer program product of  claim 40  wherein said morphological value is selected from a count, an area, a perimeter, a length, a breadth, a fiber length, a fiber breadth, a shape factor, a elliptical form factor, an inner radius, an outer radius, a mean radius, an equivalent radius, an equivalent sphere volume, an equivalent prolate volume, an equivalent oblate volume, an equivalent sphere surface area, an average gray value, a total gray value, and an optical density.  
     
     
         45 . The computer program product of  claim 40  wherein said degree of presence is multiple of a quantized value.  
     
     
         46 . A computer program product of predicting properties of an unknown compound based upon information about effects of at least one of a plurality of known compounds on a first cell population, said computer program product comprising: 
 code for populating a database with descriptors for known compounds, wherein said descriptors are determined from imaging said first cell population;    code for determining descriptors for cells subjected to the unknown compound, wherein said descriptors are determined from imaging a second cell population;    code for determining a relationship between said descriptors of said unknown compound with said descriptors of said known compounds;    code for making an inference about said unknown compound based upon said descriptors of said known compounds; and    a computer readable storage medium for holding the codes.    
     
     
         47 . The computer program product of  claim 46  wherein said code for determining descriptors comprises code for determining a relationship between said first component and said second component.  
     
     
         48 . The computer program product of  claim 47  wherein said first component and said second component are selected from a protein, a protein modification, a nucleic acid, a lipid, a carbohydrate, a sub-cellular structure and an organelle.