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Graphic design of combinatorial material librariesRelated Patent Categories: Data Processing: Measuring, Calibrating, Or Testing, Measurement System In A Specific Environment, Biological Or BiochemicalGraphic design of combinatorial material libraries description/claimsThe Patent Description & Claims data below is from USPTO Patent Application 20070185657, Graphic design of combinatorial material libraries. Brief Patent Description - Full Patent Description - Patent Application Claims
CROSS REFERENCE TO RELATED APPLICATIONS [0001] This is a continuation of U.S. Ser. No. 09/420,334, now issued as U.S. Pat. No. 7,199,809, which is incorporated by reference in its entirety, and which is a continuation-in-part of U.S. Ser. No. 09/174,856, filed Oct. 19, 1998, which is incorporated by reference in its entirety and which is the basis of a claim of priority under 35 U.S.C. .sctn. 120. BACKGROUND OF THE INVENTION [0002] The present invention relates to the computer-implemented design of combinatorial libraries of materials. Traditionally, the discovery and development of materials has predominantly been a trial and error process carried out by scientists who generate data one experiment at a time. This process suffers from low success rates, long time lines, and high costs, particularly as the desired materials increase in complexity. When a material is composed of multiple components, theory provides little guidance, and the large variety of possible combinations of components takes a large amount of time to prepare and analyze. [0003] Combinatorial materials science addresses some of these challenges. Combinatorial materials science refers generally to methods for creating collections or libraries of chemically diverse compounds or materials and/or to methods for rapidly testing or screening these libraries for compounds or materials having desirable performance characteristics and properties. By parallel or rapid serial testing of many compounds or materials, combinatorial techniques accelerate the speed of research, facilitate breakthroughs, and expand the amount of information available to researchers. Furthermore, the ability to observe the relationships between hundreds or thousands of materials in a short period of time enables scientists to make well-informed decisions in the discovery process and to find unexpected trends. [0004] Researchers employing combinatorial techniques design libraries or arrays containing multiple combinations of starting chemicals. It is desirable to design such libraries to explore a desired phase space of starting components and realize good experimental results at a reasonable cost and period of time. Computer programs have been used for life science libraries, and some software applications have been applied to materials. Many of these programs allow for step-by-step input of a detailed protocol for synthesizing a library of materials, but do not allow for definition of chemical ratios or process parameters. To implement such protocols, the user must manually determine the proper concentration and quantity of each starting material to achieve a desired ratio of starting materials in each library member. For large libraries with shared starting solutions, this becomes unwieldy to solve manually without significantly limiting the diversity studied within one library. Other programs allow for definition of chemical ratios or process parameters to apply to a whole library, by do not provide for high level definition of multi-dimensional variation of these ratios or parameters across the spatial dimensions of the library, also limiting the diversity that may be studied within a single library. Some of these programs have been either spreadsheet based or graphic-based. Spreadsheet-like interfaces are, for many users, non-intuitive and difficult to learn. Graphic-based interfaces are somewhat more intuitive, but are limited to supplying direct machine instructions to move volumes of liquid on a specific robotic system. Such interfaces fail to provide the comprehensive conceptual library design assistance that materials discovery chemists would find greatly beneficial. Many existing programs are limited to specific chemistries, such as those used in the pharmaceutical industry, and can only interface with a specific type of synthesis instrument. SUMMARY OF THE INVENTION [0005] The invention provides computer implemented methods and apparatus for designing combinatorial libraries of materials. The invention provides a graphical user interface through which the user designs a library conceptually, with the ability to specify the desired material composition of multiple library members in terms of a variety of interrelationships between component materials, such as multiple interdependent gradients or ratios of component materials. The resulting conceptual library design is not constrained by the physical limitations of available library substrates or equipment. The invention's graphical interface allows the user to define variation of chemical ratios or process parameters across a library or across one or more distinct, partially intersecting or completely overlapping sub-regions of the library. The invention receives the user's conceptual design and performs the detailed calculations necessary to determine the precise composition of each member of the library. The invention outputs a data file in a format suitable for manual library preparation or automated preparation using conventional material handling apparatus. The output may include a list of mappings to be performed in preparing a library. [0006] In general, in one aspect, the invention features a computer-implemented method for generating a library design for a combinatorial library of materials. The method includes defining one or more sources and one or more destinations, receiving an input defining a first mapping, using the first mapping to calculate a composition of one or materials assigned to one or more of cells of the destination, and generating a data file defining the library design. Each source is electronic data representing a component to be used in preparing the combinatorial library. Each destination is electronic data representing an arrangement of cells. The first mapping is electronic data defining a distribution pattern for assigning a component to cells in the arrangement. The distribution pattern includes a minimum and a maximum amount of the component to be assigned to any cell of the arrangement and a gradient to be applied between the minimum and maximum amounts of the component across the cells. The data file includes electronic data representing the sources, the destinations and the mapping. [0007] Implementations of the invention can include one or more of the following advantageous features. The method includes displaying a representation of the library design graphically describing the composition of one or more materials assigned to one or more of the cells. The data file includes electronic data representing one or more sets of properties, each set of properties being associated with one of the sources, the destinations or the mapping. Defining the sources and destinations includes receiving an input from a graphical input device. The input defining a first mapping includes a selection from a set of available mapping types, including a one to one mapping of a component from a source to a cell in the arrangement and a one to many mapping of a component from a source to a plurality of cells in the arrangement. The set of available mapping types also includes a many to many mapping of a plurality of components from a plurality of sources to a plurality of cells in the arrangement, a many to one mapping of a plurality of components from a plurality of sources to a cell in the arrangement, or a set of one or more user-defined equations. The gradient is selected from the group consisting of linear, logarithmic, exponential, polynomial and geometric progression. The set of properties associated with the mapping includes a source name, a source geometry, a destination name, a destination geometry, a gradient type, and a set of gradient parameters defining the gradient. The method includes receiving an input defining a second mapping, and using the first and second mappings to calculate a composition of one or more materials assigned to one or more of the cells. The second mapping is electronic data defining a second distribution pattern for distributing a second component to cells in the arrangement. The second distribution pattern includes electronic data identifying a fixed amount of the second component to be assigned to one or more cells in the arrangement. The second distribution pattern includes electronic data identifying a minimum and a maximum amount of the second component to be assigned to any of the cells of the arrangement and a second gradient to be applied between the minimum and maximum amounts of the second component across the cells. The method includes generating a modified library design by receiving an input redefining a source, a destination or a mapping, recalculating the composition of one or more materials assigned to one or more of the cells; and generating a data file defining the modified library design. The method includes receiving an input defining one or more parameters, and the data file includes electronic data representing the one or more parameters. Each parameter is electronic data corresponding to a process parameter and defines a parameter value for one or more cells of the arrangement. The parameter values vary between a minimum and a maximum amount. The arrangement comprises two or more cells, ten or more cells, or about ninety-six or more cells. [0008] In general, in another aspect, the invention features a computer-implemented method for generating a library design for a combinatorial library of materials. The method includes defining a set of one or more sources and one or more destinations, receiving an input defining a set of first mappings, using the set of equations to calculate a composition of a material assigned to one or more cells in the destination, and generating a data file defining the library design. Each source is electronic data representing a component to be used in preparing the combinatorial library. Each destination is electronic data representing an arrangement of cells. The set of first mappings is electronic data defining a set of equations for calculating an amount of one or more components to be assigned to one or more cells in the destination arrangement. The data file includes electronic data representing the sources, the destinations and the mappings. [0009] Implementations of the invention can include one or more of the following advantageous features. The method includes displaying a representation of the library design. The representation graphically describes the composition of one or more materials assigned to one or more of the cells. The component to be assigned to a cell in the arrangement is determined by the location of the cell within the arrangement. The composition of a material is determined using a subset of the set of equations, the subset of equations being determined by the location of the cell within the arrangement. The method includes generating an error indicator signal if the number of equations in the set of equations is not equal to the number of sources in the set of sources. At least one of the set of equations is selected from a ratio equation defining an amount of a component to be assigned to a cell as a function of an amount of another component to be assigned to the cell; a volume equation defining an amount of a component to be assigned to a cell as a function of a total volume of a plurality of components to be assigned to the cell; and a mass equation defining an amount of a component to be assigned to a cell as a function of a total mass of a plurality of components to be assigned to the cell. The set of equations includes a gradient equation defining an amount of a component to be assigned to each of a plurality of cells according to a gradient. Each of the set of equations is assigned to one or more cells of the arrangement according to the location of the cells within the arrangement. The method includes simultaneously solving a set of interdependent equations. The method includes using a matrix inversion technique to solve the set of equations. The method includes receiving an input defining a second mapping and using the first set of mappings and the second mapping to calculate a composition of a material assigned to one or more of the cells. The second mapping is electronic data defining a distribution pattern for distributing a component to cells in the arrangement. The distribution pattern includes a minimum and a maximum amount of the component to be assigned to any cell of the cells of the arrangement and a gradient to be applied between the minimum and maximum amounts of the component across the plurality of cells. [0010] In general, in another aspect, the invention features a computer-implemented method for generating a library design for a combinatorial library of materials. The method includes defining a set of one or more sources and one or more destinations, defining a plurality of mappings, receiving an input defining one or more parameters, and generating a data file defining the library design. Each source is electronic data representing a component to be used in preparing the combinatorial library. Each destination is electronic data representing an arrangement of cells. The mappings in the aggregate define a composition for each of a plurality of materials assigned to a plurality of cells in the arrangement. Each parameter is electronic data corresponding to a process parameter and defining a parameter value for one or more cells of the arrangement. The parameter value varies between a minimum and a maximum amount. The data file includes electronic data describing the source elements, the destination elements, the mappings and the parameters [0011] Implementations of the invention can include one or more of the following advantageous features. The parameter value is defined to vary over time, across two or more cells in the arrangement, or over time and across two or more cells in the arrangement. The parameter value varies according to a gradient selected from the group consisting of linear, logarithmic, exponential, polynomial and geometric progression. The parameter value corresponds to a process parameter selected from the group consisting of temperature, pressure, time, flow rate and stirring speed. [0012] In general, in another embodiment, the invention features a computer-implemented method for preparing a combinatorial library of materials on a substrate. The method includes creating a library design by defining a set of design elements, generating a data file comprising electronic data describing the set of design elements, and using the data file to cause an automated material handling apparatus to assemble the combinatorial library on a substrate. The set of design elements includes one or more sources representing components to be used in preparing the combinatorial library, one or more destinations, each of which includes an arrangement of one or more cells, and one or more elements selected from the group consisting of a mapping defining a scheme for assigning one or more amounts of a component to one or more cells of an arrangement and a parameter corresponding to a process parameter. The parameter defines a parameter value for one or more cells of the arrangement. The parameter value varies between a minimum and a maximum amount. [0013] In general, in another embodiment, the invention features a computer program product on a computer-readable medium for generating a library design for a combinatorial library of materials. The computer program includes instructions operable to cause a programmable processor to receive an input defining one or more sources and one or more destinations, receive an input defining a first mapping, use the first mapping to calculate a composition of one or materials assigned to one or more cells in the destination, and generate a data file defining the library design. Each source is electronic data representing a component to be used in preparing the combinatorial library. Each destination is electronic data representing an arrangement of cells. The first mapping is electronic data defining a distribution pattern for assigning a component to cells in the arrangement. The distribution pattern includes a minimum and a maximum amount of the component to be assigned to any cell of the arrangement and a gradient to be applied between the minimum and maximum amounts of the component across the plurality of cells. The data file includes electronic data representing the sources, the destinations and the mapping. [0014] Implementations of the invention can include one or more of the following advantageous features. The computer program includes instructions operable to cause a programmable processor to display a representation of the library design graphically describing the composition of one or more materials assigned to one or more of the cells. The data file includes electronic data representing one or more sets of properties, each set of properties being associated with one of the sources, the destinations or the mapping. The input defining the sources and destinations includes an input from a graphical input device. [0015] The input defining a first mapping includes a selection from a set of available mapping types. The set of available mapping types includes a one to one mapping of a component from a source to a cell in the arrangement and a one to many mapping of a component from a source to a plurality of cells in the arrangement, a many to many mapping of a plurality of components from a plurality of sources to a plurality of cells in the arrangement, a many to one mapping of a plurality of components from a plurality of sources to a cell in the arrangement, or a set of one or more user-defined equations. The gradient is selected from the group consisting of linear, logarithmic, exponential, polynomial and geometric progression. The set of properties associated with the mapping comprises a source name, a source geometry, a destination name, a destination geometry, a gradient type, and a set of gradient parameters defining the gradient. The computer program includes instructions operable to cause a programmable processor to receive an input defining a second mapping and use the first and second mappings to calculate a composition of one or more materials assigned to one or more of the cells. The second mapping is electronic data defining a second distribution pattern for distributing a second component to cells in the arrangement. The second distribution pattern includes electronic data identifying a fixed amount of the second component to be assigned to one or more cells in the arrangement. The second distribution pattern includes electronic data identifying a minimum and a maximum amount of the second component to be assigned to any of the cells of the arrangement and a second gradient to be applied between the minimum and maximum amounts of the second component across the cells. The computer program includes instructions operable to cause a programmable processor to generate a modified library design by receiving an input redefining a source, a destination or a mapping; recalculating the composition of one or more materials assigned to one or more of the cells; and generating a data file defining the modified library design. The computer program includes instructions operable to cause a programmable processor to receive an input defining one or more parameters and the data file includes comprises electronic data representing the one or more parameters. Each parameter is electronic data corresponding to a process parameter and defining a parameter value for one or more cells of the arrangement. The parameter value varies between a minimum and a maximum amount. The arrangement comprises two or more cells, ten or more cells, or about ninety-six or more cells. [0016] In general, in another embodiment, the invention features a computer program product on a computer-readable medium for generating a library design for a combinatorial library of materials. The computer program includes instructions operable to cause a programmable processor to receive an input defining a set of one or more sources and one or more destinations, receive an input defining a set of first mappings, use the set of equations to calculate a composition of a material assigned to one or more of cells of the destination, and generate a data file defining the library design. Each source is electronic data representing a component to be used in preparing the combinatorial library. Each destination is electronic data representing an arrangement of cells. The set of first mappings is electronic data defining a set of equations for calculating an amount of one or more components to be assigned to one or more cells in an arrangement. The data file includes electronic data representing the sources, the destinations and the mappings. [0017] Implementations of the invention can include one or more of the following advantageous features. The computer program includes instructions operable to display a representation of the library design graphically describing the composition of one or more materials assigned to one or more of the cells. The component to be assigned to a cell in the arrangement is determined by the location of the cell within the arrangement. The composition of a material is determined using a subset of equations determined by the location of the cell within the arrangement. The computer program includes instructions operable to generate an error indicator signal if the number of equations in the set of equations is not equal to the number of sources in the set of sources. At least one of the set of equations is selected from a ratio equation defining an amount of a component to be assigned to a cell as a function of an amount of another component to be assigned to the cell, a volume equation defining an amount of a component to be assigned to a cell as a function of a total volume of a plurality of components to be assigned to the cell, and a mass equation defining an amount of a component to be assigned to a cell as a function of a total mass of a plurality of components to be assigned to the cell. The set of equations includes a gradient equation defining an amount of a component to be assigned to each of a plurality of cells according to a gradient. The set of equations is assigned to one or more cells of the arrangement according to the location of the cells within the arrangement. The instructions operable to cause a programmable processor to use the set of equations to calculate a composition of a material assigned to one or more of the cells include instructions simultaneously to solve a set of interdependent equations. The instructions simultaneously to solve the set of interdependent equations include instructions to use a matrix inversion technique to solve the set of equations. The computer program includes instructions operable to receive an input defining a second mapping and use the first set of mappings and the second mapping to calculate a composition of a material assigned to one or more of the cells. The second mapping is electronic data defining a distribution pattern for distributing a component to cells in the arrangement. The distribution pattern includes a minimum and a maximum amount of the component to be assigned to any cell of the cells of the arrangement and a gradient to be applied between the minimum and maximum amounts of the component across the plurality of cells. [0018] In general, in another embodiment, the invention features a computer program product on a computer-readable medium for generating a library design for a combinatorial library of materials. The computer program includes instructions operable to cause a programmable processor to receive an input defining a set of one or more sources and one or more destinations, receive an input defining a plurality of mappings, receive an input defining one or more parameters, and generate a data file defining the library design. Each source is electronic data representing a component to be used in preparing the combinatorial library. Each destination is electronic data representing an arrangement of cells. The mappings in the aggregate define a composition for each of a plurality of materials assigned to a plurality of cells in the arrangement. Each parameter is electronic data corresponding to a process parameter and defining a parameter value for one or more cells of the arrangement. The parameter value varies between a minimum and a maximum amount. The data file includes electronic data describing the source elements, the destination elements, the mappings and the parameters. [0019] Implementations of the invention can include one or more of the following advantageous features. The parameter value is defined to vary over time, across two or more cells in the arrangement, or over time and across two or more cells in the arrangement. The parameter value varies according to a gradient selected from the group consisting of linear, logarithmic, exponential, polynomial and geometric progression. The parameter value corresponds to a process parameter selected from the group consisting of temperature, pressure, time, flow rate and stirring speed. [0020] In general, in another aspect, the invention features a computer program product on a computer-readable medium for generating a library design for a combinatorial library of materials. The computer program includes instructions operable to cause a programmable processor to create a library design by defining a set of design elements, generate a data file including electronic data describing the design and use the data file to cause an automated material handling apparatus to assemble the combinatorial library on a substrate. The set of design elements includes one or more sources representing components to be used in preparing the combinatorial library, one or more destinations, and one or more elements selected from the group consisting of a mapping defining a scheme for assigning one or more amounts of a component to one or more cells of an arrangement and a parameter corresponding to a process parameter. Each destination includes an arrangement of one or more cells. The parameter defines a parameter value for one or more cells of the arrangement, the parameter value varying between a minimum and a maximum amount. [0021] Advantages that can be seen in implementations of the invention include one or more of the following. The invention allows users to design combinatorial libraries conceptually, while automatically performing a large number of detailed calculations required for the exact assignment of materials at each library member in a process that is preferably invisible to the user, although it may be shown if desired. The user can visualize a conceptual library design and identify potential errors before undertaking actual library synthesis. Separation of library design from library synthesis allows the user to lay out a library design conceptually, without regard for the physical limitations of a particular destination substrate or synthesis apparatus. The library design can flexibly define variation of chemical composition across library members by specifying multiple, interdependent material gradients or ratios defining the composition of each library member. The library design can also include variation of process parameters over time or across library members, which enables the user combinatorially to explore the effect of changing process conditions on material composition. The output of the design process is a recipe file that allows the automated synthesis of a library corresponding to the conceptual design. Maintaining databases of chemical information, library designs and composition data speeds up library design, avoids the repetition of old experiments, and assists in the overall planning and execution of experiments necessary to explore the preparation and properties of diverse materials. Continue reading about Graphic design of combinatorial material libraries... 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