Me DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Claims 1-7 are cancelled.
Claims 8-14 are pending and examined on the merits.
Priority
The instant application filed on 2/15/2022 is a 371 national stage entry of PCT/EP2020/073606 having an international filing date of 8/24/2020, and claims the benefit of priority to European Patent Application No. 19306046.4 filed on 8/29/2019. Thus, the effective filing date of the claims is 8/29/2019. The applicant is reminded that amendments to the claims and specification must comply with 35 U.S.C. § 120 and 37 C.F.R. § 1.121 to maintain priority to an earlier-filed application. Claim amendments may impact the effective filing date if new subject matter is introduced that lacks support in the originally filed disclosure. If an amendment adds limitations that were not adequately described in the parent application, the claim may no longer be entitled to the priority date of the earlier filing.
Information Disclosure Statement
The information disclosure statement (IDS) filed on 2/15/2022 has been entered and considered. A signed copy of the corresponding 1449 form has been included with this Office action.
Drawings
The drawings of the disclosure are objected to because of the following informalities: Page 2 of the drawings filed 2/15/2022 is missing a figure label. The flow chart should be labeled "[Fig. 3]".
Appropriate correction is required.
Claim Objections
Claims 10 and 11 objected to because of the following informalities:
Claim 10 lines 1-3, "gathering physico-chemical characteristics for the chemical species, on the one hand and of composition, origin and/or cost for raw materials" should read "gathering physico-chemical characteristics for the chemical species, and composition, origin and/or cost for raw materials".
Claim 11 lines 1-3, "gathering physico-chemical characteristics for the chemical species, on the one hand, and of composition, origin and/or cost for the raw materials, on the other hand" should read "gathering physico-chemical characteristics for the chemical species, and of composition, origin and/or cost for the raw materials".
Appropriate correction is required.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are:
Claim 8 recites "a performance evaluation module configured to: carry out performance estimates of said process based on the use of experimental data derived from the storage module and/or simulation results obtained by one of the functional modules of said plurality, compare at least two performance estimates with each other or with experimental results". Here the generic placeholder which is used instead of means is "configured". It is noted there is discussion of these potential performance metrics throughout the specification: para.0115 "computation of the costs and other performance assessment criteria", and para.0127 and [0133] "determine a first estimate of the performance criteria of the process based on the consumptions of raw materials and/or energy [the size and operating mode of the equipment], this criterion possibly being an economic or environmental one". To further prosecution, the performance estimates are interpreted as metrics of cost and usage of computational, raw material, and energy resources consumed for the simulated chemical process.
Claim 9 recites "an experimental data processing and analysis module allowing processing signals, performing statistical analyses, identifying model parameters". Here the generic placeholder which is used instead of means is "allowing". It is noted there is only discussion of "processing and analysing experimental data" with respect to the storage module, in the disclosed specification on page 13, para.0091. There are no further details regarding signal processing, statistical analyses, or specific model parameters. To further prosecution, the "experimental data processing and analysis module" is interpreted as being part of the storage module of claim 8, and its function may carry out any kind of signal processing, statistical analyses, and identifying model parameters.
Claims 10 and 11 recite "a database module gathering physico-chemical characteristics for the chemical species, on the one hand, and of composition, origin and/or cost for the raw materials". Here the generic placeholder which is used instead of means is "gathering". It is noted that there is discussion of these parameters with respect to data management in the disclosed specification para.0088, 0092, and 0105: "This tool brings together various functionalities such as: data management (for example experimental data relating to chemical products, physico-chemical characteristics relating to raw materials or others)", "Thus, when an assessment request has been received (1), it has been first necessary to extract the technical data (2) (nature of the process to be defined, raw materials, products, physico-chemical constraints, material constraints, cost constraints, etc.)", and "The project file could be in the form of an XML (extensible markup language) type file with three parts. A first part represents the list of the chemical species implemented in the project. Another part represents the list of raw materials with an identification and a composition with reference to the list of species. Thus, each raw material of the second part is decomposed into chemical species of the second part. A third part includes the other elements involved in the reactions such as catalysts, filter absorber resins, etc. with a respective identifier and some physico-chemical parameters". However, there is no explicit "database module" or "gathering" disclosed in the specification. Therefore, to further prosecution, the database module is interpreted as described in the instant specification paragraphs above.
Claim 12 recites "a solver module configured for solving of differential-algebraic equations". Here the generic placeholder which is used instead of means is "configured". It is noted that there is discussion of this module in the disclosed specification on para.0074-75 and para.0082-85 Therefore, to further prosecution, the solver module is interpreted as described in the instant specification paragraphs above.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 8-14 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 8 recites "carry out performance estimates of said process". The metes and bounds of "performance" are not clear (what performance metrics are being estimated, that of CPU and/or RAM usage, an economic cost, or some metric of the simulated reaction such as time to completion, etc.?). It is noted there is discussion of these potential performance metrics throughout the specification: para.0115 "computation of the costs and other performance assessment criteria", and para.0127 and [0133] "determine a first estimate of the performance criteria of the process based on the consumptions of raw materials and/or energy [the size and operating mode of the equipment], this criterion possibly being an economic or environmental one". To further prosecution, the performance estimates are interpreted as metrics of cost and usage of computational, raw material, and energy resources consumed for the simulated chemical process.
Claim 8 also recites "the decomposition into chemical species being preserved throughout the processing". It is not clear what the objective of this limitation is. There is no further discussion of what preserving a decomposition throughout the processing encompasses in the instant specification, therefore, to further prosecution, the limitation is interpreted as simply storing the files containing the chemical species of the decomposition that may be accessed by all the modules of the system.
Claims 9-11 and 13-14 rejected under 35 U.S.C. 101 due to dependency on claim 8.
Claim 12 recites "the steady-state solution of said differential-algebraic equation" in lines 16-17. There is insufficient antecedent basis for "the steady-state solution" in the claim. To further prosecution, the limitation is interpreted as "a steady-state solution of said differential-algebraic equation".
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 8-14 rejected under 35 U.S.C. 101 because the claims are is directed to non-statutory subject matter (Step 1: No). Specifically, claim 8 is rejected because “a system” does not recite any structural component and therefore equates to “software per se.” Claims that equate to “software per se” are not a statutory category of invention (See MPEP § 2106.03.1). However, claim 8 could be amended to be statutory subject matter by adding in structural components such as by replacing “a system” with the phrase “a non-transitory computer-readable medium”. Nonetheless, this amendment would still result in a rejection of the claim under 35 U.S.C. 101 for recitation of a judicial exception without significantly more. Therefore, claim 8 has been analyzed below under 35 U.S.C. 101 using the Alice/Mayo test in the interest of compact prosecution.
Claims 9-14 rejected under 35 U.S.C. 101 due to dependency on claim 8.
Claims 8-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of a mental process, a mathematical concept, organizing human activity, or a law of nature or natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claim 8: “simulation using a differential-algebraic modelling based on an equation of conservation of species” provides a mathematical calculation (differential-algebraic modeling involves mathematical calculations) that is considered a mathematical concept, which is an abstract idea.
“a simulation using an algebraic modelling relating inputs and outputs and/or initial states and final states at least of said at least one reaction” provides a mathematical calculation (algebraic modeling for comparisons involves mathematical calculations) that is considered a mathematical concept, which is an abstract idea.
“carry out performance estimates of said process based on the use of experimental data derived from the storage module and/or simulation results obtained by one of the functional modules” provides an evaluation (estimating the performance of either experimental or simulated data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“compare at least two performance estimates with each other or with experimental results” provides a comparison (comparing performance estimates) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 9: “processing signals, performing statistical analyses, identifying model parameters” provides an evaluation (processing signals, performing statistical analyses, and identifying parameters all require evaluation of data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 11: “a file structure enabling the different modules to have access either to the raw materials and to their database, or to the species and to their database, or to both depending on the needs” provides organizing information and evaluations (processing signals, performing statistical analyses, and identifying parameters all require organization and evaluation of data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 12: “solving of differential-algebraic equations” provides a mathematical calculation (solving differential-algebraic equations involves mathematical calculations) that is considered a mathematical concept, which is an abstract idea.
“relating a first input state vector representing initial chemical amounts of said first operation to a first vector of output state variables representing final chemical amounts of said first operation” provides organizing information (relating or assigning vector variables from inputs) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“in a first differential-algebraic equation relating: said first vector of input state variables; and a first vector of internal state variables of said first operation as an unknown of the equation” provides a mathematical relationship (relating input and internal state variables in a differential-algebraic equation) that is considered a mathematical concept, which is an abstract idea.
“set a time constant of said differential-algebraic equation thus obtained as being lower than a characteristic time of said first operation” provides an evaluation (setting a threshold requires evaluation of data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“implement the solver module on the differential-algebraic equation thus obtained to compute said first vector of output state variables” provides a mathematical calculation (solving differential-algebraic equations involves mathematical calculations) that is considered a mathematical concept, which is an abstract idea.
Claim 13: “select a simulation mode and wherein the processing module is configured to carry out said injection according to a selected mode” provides an evaluation (selecting a mode requires evaluation of the scenario being simulated) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 14: “relating: a second vector of input state variables representing initial chemical amounts of said second operation; and a second vector of internal state variables of said second operation as an unknown of the equation” provides a mathematical relationship (relating input and internal state variables in a differential-algebraic equation) that is considered a mathematical concept, which is an abstract idea.
“merge said first and second differential-algebraic equations and to implement the solver module on the merger of said first and second differential- algebraic equations” provides a mathematical calculation (merging and solving differential-algebraic equations involves mathematical calculations) that is considered a mathematical concept, which is an abstract idea.
These recitations are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or are mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Additionally, while claims 8-14 recite performing some aspects of the analysis on “a non-transitory computer-readable medium”, there are no additional limitations that indicate that this requires anything other than carrying out the recited mental processes or mathematical concepts in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then it falls within the “Mental processes” grouping of abstract ideas. As such, claims 8-14 recite an abstract idea (Step 2A, Prong 1: YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exceptions listed above are not integrated into a practical application because the claims do not recite an additional element or elements that reflects an improvement to technology. Specifically, the claims recite the following additional elements:
Claim 8: “storing experimental data relating to chemical species in a data structure usable by at least one functional module” and “storing the files containing the chemical species of the decomposition that may be accessed by all the modules of the system” provides insignificant extra-solution activities (storing and accessing data are a pre- and post-solution activities involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“a non-transitory computer-readable medium” provides insignificant extra-solution activities (running instructions on generic computer components) that do not serve to integrate the judicial exceptions into a practical application.
Claim 10: “gathering physico-chemical characteristics for the chemical species, and composition, origin and/or cost for raw materials” (as interpreted above) provides insignificant extra-solution activities (gathering data is a pre-solution activity involving data gathering steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 11: “gathering physico-chemical characteristics for the chemical species, and of composition, origin and/or cost for the raw materials” (as interpreted above) provides insignificant extra-solution activities (gathering data is a pre-solution activity involving data gathering steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 12: “receive a first explicit algebraic equation representing said first chemical or biochemical operation” provides insignificant extra-solution activities (receiving inputs is a pre-solution activity involving data gathering steps) that do not serve to integrate the judicial exceptions into a practical application.
“inject into said first differential-algebraic equation the expression of the vector of output state variables of said first operation according to said first explicit algebraic equation as a vector of internal state pseudo-variables of said first operation” provides insignificant extra-solution activities (inputting data into an equation is a pre-solution activity involving data manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“converging towards said first vector of output state variables according to the first explicit algebraic equation” provides insignificant extra-solution activities (outputting data from an equation is a post-solution activity involving data manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 14: “receive a second differential-algebraic equation representing said second chemical or biochemical operation” provides insignificant extra-solution activities (receiving inputs is a pre-solution activity involving data gathering steps) that do not serve to integrate the judicial exceptions into a practical application.
“output state variables representing final chemical amounts of said second operation” and “compute a vector of output state variables of the process” provides insignificant extra-solution activities (outputting data from an equation is a post-solution activity involving data manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
The steps for receiving, storing, accessing, inputting, and outputting data are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application because they are pre- and post-solution activities involving data gathering, data manipulation, and sample manipulation steps (see MPEP 2106.04(d)(2)). Furthermore, the limitations regarding implementing program instructions do not indicate that they require anything other than mere instructions to implement the abstract idea in a generic way or in a generic computing environment. As such, this limitation equates to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. Therefore, claims 8-14 are directed to an abstract idea (Step 2A, Prong 2: NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application, or equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
As discussed above, there are no additional elements to indicate that the claimed “a non-transitory computer-readable medium” requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. Additionally, the limitations for receiving, storing, accessing, inputting, and outputting data are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application. Furthermore, no inventive concept is claimed by these limitations as they are well-understood, routine, and conventional.
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 8-14 are not patent eligible.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 8-11 rejected under 35 U.S.C. 103 as being unpatentable over Paxson et al. (US-7769576).
Regarding claim 8, Paxson teaches a system for simulating a chemical or biochemical process, comprising at least one reaction or a separation transforming at least one raw material (Figure 2C and Abstract "A system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical system comprising a plurality of chemical reactions").
Paxson also teaches a functional module enabling a simulation using a differential-algebraic modeling based on an equation of conservation of species, and at least one functional module enabling a simulation using an algebraic modeling relating inputs and outputs and/or initial states and final states at least of said at least one reaction (Para.0064 "the analysis tool 120 does this by setting the derivative of all differential equations to 0 and solving the system algebraically. In others of these embodiments, the analysis engine performs a flux-balance analysis").
Paxson also teaches at least one storage module for storing experimental data relating to chemical species in a data structure usable by at least one functional module of said plurality a performance evaluation module configured to: carry out performance estimates of said process based on the use of experimental data derived from the storage module and/or simulation results obtained by one of the functional modules of said plurality, compare at least two performance estimates with each other or with experimental results (Page 15 col 2 line 53 "the analysis environment 130 interfaces with data acquisition hardware (not shown in FIG. 1) which allows the analysis environment 130 to compare the generated results with experimental data").
Paxson also teaches said process is defined by a set of files shared by all of the modules of the system, each file including a description of said at least one raw material and a description of a decomposition of said at least one raw material into chemical species (Page 10 col 1 line 53 "The modeling environment 110 accepts input to create a model of the chemical or biochemical reaction to be simulated. In some embodiments, the modeling environment 110 accepts input contained in a file, such as a file in Systems Biology Markup Language (SBML)", an SBML file contains the components and relationships of a biological model, including compartments (like cells or a cell's organelles), species (molecules or entities), reactions (processes where species change), and parameters (constants and variables used in reaction rate equations)”).
Paxson also teaches said files are the inputs and the outputs of said modules of the system, the decomposition into chemical species being preserved throughout the processing (Page 15 col 2 line 10 "Once putative reactions times are computed for each reaction in the system using a probability distribution particular to each reaction, the times are sorted, by putative occurrence time, into a state array (step 604). In one embodiment, the state array is an array of pointers sorted by occurrence time, each of the pointers pointing to the object to be executed at that point in model simulation. Once sorted, the object identified by the first entry in the array is executed (step 606). Because execution of the top object may affect the amount of species present in the modeled system or the putative reaction times for specific reactions in the table, the putative time for each of the entries in the state array is recalculated (step 608) and the state array is resorted (step 610)").
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Paxson in order to ease the development of new drugs, chemical substances, nanomachinery by simulation of reaction processes to yield cost and safety data (page 8 col 1 line 18 "The development of new drug targets by the pharmaceutical industry is time-consuming and expensive because a large number of possible targets need to be tested before the molecule or compound with the desired properties is found or formulated. Along the same argument, but not for the purpose of new drug development, are the activities or synthetic biology", page 8 col 1 line 37 "Development of chemical substances and nanomachinery, in addition to being time-consuming, can generate potentially dangerous intermediate substances"). One skilled in the art would have a reasonable expectation of success because Paxson takes a similar approach of differential-algebraic equations for modeling complex processes, including chemical and biochemical reactions.
Regarding claim 9, Paxson teaches the methods of Claim 8 on which this claim depends/these claims depend, respectively. Paxson also teaches an experimental data processing and analysis module allowing processing signals, performing statistical analyses, identifying model parameters (Page 10 col 1 line 39 "The analysis environment 130 may provide refinements to a model in the modeling environment 110 and may provide parameters for use by the simulation engine 120 when executing a model").
Regarding claims 10 and 11, Paxson teaches the methods of Claim 8 on which this claim depends/these claims depend, respectively. Paxson also teaches a database module gathering physico-chemical characteristics for the chemical species, and of composition, origin and/or cost for the raw materials (Page 9 col 1 line 22 "The probability distributions may be defined by a user, automatically calculated based on kinetics of the first chemical reaction, and/or derived through data collected from at least one experiment").
Paxson also teaches a central module configured to generate a composition vector representing a decomposition of said at least one raw material into a plurality of chemical species; and a file structure enabling the different modules to have access either to the raw materials and to their database, or to the species and to their database, or to both depending on the needs (Page 11 col 2 line 18 "the reaction table 310 may include a distribution column 319, which indicates a suitable probability distribution for the associated reaction. The probability distribution may be specified using a MATLAB vector or through another suitable format" and Figure 2C showing the reaction table and the chemical species of each reaction available for simulation).
Claims 12 rejected under 35 U.S.C. 103 as being unpatentable over Paxson et al. (US-7769576) as applied to claims 8-11 above, and further in view of Neto et al. (Neto, Ataíde S. Andrade, Argimiro R. Secchi, and Príamo A. Melo. "Nonlinear dynamic analysis of chemical engineering processes described by differential-algebraic equations systems." Computer Aided Chemical Engineering. Vol. 46. Elsevier, 2019. 769-774).
Paxson et al. is applied to claims 8-11.
Regarding claim 12, Paxson teaches the method of Claim 8 on which this claim depends/these claims depend. Paxson also teaches a reception module for the simulator (Figure 1 and Page 10 col 1 line 24 "The simulation engine 120 receives models of chemical reactions or biological processes generated using the modeling environment 110").
Paxson also teaches set a time constant of said differential-algebraic equation thus obtained as being lower than a characteristic time of said first operation, and implement the solver module on the differential-algebraic equation thus obtained to compute said first vector of output state variables (Page 14 col 2 line 5 "At any given instant of time, these equations may be viewed as relationships between the system's output response ("outputs"), the system's input stimuli ("inputs") at that time, the current state of the system, the system parameters, and time").
Paxson does not explicitly teach a processing module configured to: in a first differential-algebraic equation relating: said first vector of input state variables; and a first vector of internal state variables of said first operation as an unknown of the equation; nor inject into said first differential-algebraic equation the expression of the vector of output state variables of said first operation according to said first explicit algebraic equation as a vector of internal state pseudo-variables of said first operation, a steady-state solution of said differential-algebraic equation thus obtained thus converging towards said first vector of output state variables according to the first explicit algebraic equation.
However, Neto teaches a methodology for the direct computation of Hopf bifurcation points in differential-algebraic equations systems, which takes as input vectors of state variables for computing a steady-state output (page 2 paragraph 4 "Knowing beforehand the precise location where nonlinear phenomena, such as bifurcation points, occur is of great importance in real-life applications, as not only safety but also economic issues may be avoided. Also, because the DAE approach is the current paradigm in the theoretical analysis of chemical processes, computational methods that efficiently handle DAE systems becomes necessary" and page 3 section 2.3 "Hopf bifurcation points can be detected by an indirect method by tracing a branch of steady state solutions of an ODE [ordinary differential equations] system, usually done by homotopy continuation methods, while monitoring the eigenvalues of Jacobian matrix at the fixed points. When a single pair of eigenvalues crosses the imaginary axis a trapping method, such as the bisection or the secant method, can be used to refine the HBP. This procedure, despite being effective and easily extended to handle DAE systems, has a high computational cost").
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Paxson as taught by Neto in order to analyze nonlinear processes for design and operation of chemical plants for safety and/or cost (page 1 abstract "the theoretical analysis of processes prone to nonlinear responses plays a key role in design and operation of chemical plants either for safety or economic purposes"). One skilled in the art would have a reasonable expectation of success because both approaches utilize differential-algebraic equations for modeling chemical processes.
Claims 13 and 14 rejected under 35 U.S.C. 103 as being unpatentable over Paxson et al. (US-7769576) in view of Neto et al. (Neto, Ataíde S. Andrade, Argimiro R. Secchi, and Príamo A. Melo. "Nonlinear dynamic analysis of chemical engineering processes described by differential-algebraic equations systems." Computer Aided Chemical Engineering. Vol. 46. Elsevier, 2019. 769-774) as applied to claims 8-12 above, and further in view of Greenwood et al. (US-20170147722).
Paxson et al. in view of Neto et al. are applied to claims 8-12.
Regarding claim 13, Paxson and Neto teach the method of Claim 12 on which this claim depends/these claims depend.
Paxson nor Neto explicitly teach a selection module configured to select a simulation mode and wherein the processing module is configured to carry out said injection according to a selected mode.
However, Greenwood teaches a selection module configured to select a simulation mode and wherein the processing module is configured to carry out said injection according to a selected mode (Figure 5B step 550, Abstract "selecting a combination of model units using the fitness values of each model unit, the combination of model units representing a collective model that models the system behaviour", and para.0021 "Typically the method includes: [0022] a) selectively isolating a number of model units in an isolated population; and, [0023] b) selectively reintroducing model units from the isolated population").
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Paxson and Neto as taught by Greenwood in order to identify the best model, according to fitness in the case of Greenwood (para.0024 "Typically the method includes, modifying the model units at least one of: [0025] a) iteratively over a number of generations; [0026] b) by at least one of inheritance, mutation, selection, and crossover; [0027] c) in accordance with the fitness value of each model unit; and, [0028] d) in accordance with speciation constraints"). One skilled in the art would have a reasonable expectation of success because both approaches are using models based on differential equations for predicting chemical processes (Para.0161 and 0635 "Whilst the system can be used for a range of different applications, some specific medical applications include []. Forensic pathology, including using time-series measurements to reconstruct earlier dynamics of chemical, biochemical and biological processes" and para.0331 "The models can be of any suitable form and could include ordinary differential equations, difference equations, stochastic differential equations, partial differential equations, or fractional-order differential equations").
Regarding claim 13, Paxson and Neto teach the method of Claim 12 on which this claim depends/these claims depend. Neto also teaches, as shown for claim 12, the differential-algebraic equations, and it would have been obvious to try multiple equations/models because Greenwood suggests using multiple models. As such, combining or merging differential-algebraic equations would be obvious for Paxson as it is a routine procedure in many engineering and scientific fields.
Paxson nor Neto explicitly said processing module is further configured to merge said first and second differential-algebraic equations and to implement the solver module on the merger of said first and second differential- algebraic equations thus obtained to compute a vector of output state variables of the process
However, Greenwood does teach combining models, which are sets of differential-algebraic equations in the case of both Greenwood and Neto (Figure 5B step 575 and para.0416 "Combinations of candidate model units can then be determined at step 575, with this being assessed to select the best candidate model unit at step 580").
Conclusion
No claims are allowed.
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/R.A.P./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686