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 .
Claim Status
Claims 1-20 are currently pending and under exam herein.
Priority
The instant Application claims the benefit of priority to US Provisional Application 63/407,393, filed 16 September 2022. Each of claims 1-20 have priority to the EFD of 16 September 2022.
Information Disclosure Statement
The Information Disclosure Statements filed 16 July 2024 and 13 November 2024 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action.
Drawings
The Drawings filed 7 September 2023 are accepted.
Specification
Note: All references to the Specification herein pertain to the PG publication: US20240096449.
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 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). The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) 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). The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) 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) 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) 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) 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 limitations are:
Claim 14:
a scheduling engine configured to maintain scheduling information of a state of compute resources and non-compute resources
compute resources and the non-compute resources configured to perform a sequencing task
sequencing device configured to: receive the scheduling information from the scheduling engine; determine the state of the compute resources and non-compute resources; determine a sequencing analysis priority associated with performing analysis of the at least two flow cells on the sequencing device; and perform the sequencing task related to the one or more biological samples in the at least two flow cells according to the sequencing analysis priority
a display configured to display real-time feedback associated with completion of the sequencing task for each flow cell
Because this claim limitation are being interpreted under 35 U.S.C. 112(f) they are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. In the instant Specification, disclosure of the above device is found at ([0048]-[0067]-scheduling engine); ([0003]; [0005]-[0006]; [0046]; [0048]; [0055]; [0060]; [0065]-[0066]-[0074]-(compute/non-compute resources); (Figure 1A-B; [0017]-[0018]-sequencing device); (Figure 3; [0013]; [0073]; [0076]-display).
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) applicant may: (1) amend the claim limitations to avoid them being interpreted under 35 U.S.C. 112(f) (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitations recite sufficient structure to perform the claimed function so as to avoid them being interpreted under 35 U.S.C. 112(f).
Claim Rejections - 35 USC § 112(b)-Indefiniteness
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.
Claims 1 and 14 recite, “analyzing compute resources and non-compute resources associated with the sequencing device to determine a state of the compute resources and non-compute resources”, wherein it is unclear as to the state determination in the claim as there are no actual active steps of determining recited. As such “state” may be interpreted as a relative term that not defined by the claim. Further, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Dependent claims 2-13 and 15-20 do not remedy the above and are also rejected herein. Clarification is requested through clearer claim language.
Claims 1 and 14 recite, “determining a sequencing analysis priority associated with performing analysis of the at least two flow cells on the sequencing device”, wherein the claim lacks antecedent basis for performing analysis of the at least two flow cells, as no such analysis is previously recited. Dependent claims 2-13 and 15-20 do not remedy the above and are also rejected herein. Clarification is requested through clearer claim language.
As such, Claims 1-20 are rejected under 112(b) herein.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1 Analysis: Are claims directed to process, machine, manufacture/composition of matter
With respect to step (1): yes, the claims are directed to a method for performing sequencing of one or more biological samples in at least two flow cells on a sequencing device and a sequencing system for performing sequencing of one or more biological samples in at least two flow cells on a sequencing device.
Step 2A, Prong 1 Analysis: Do claims recite abstract idea
With respect to step (2A)(1), the claims recite abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the (2A)(1) evaluation, the claims are found herein to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information).
The claim steps to abstract ideas are as follows:
Claims 1 and 14:
analyzing compute resources and non-compute resources associated with the sequencing device to determine a state of the compute resources and non-compute resources; determining a sequencing analysis priority associated with performing analysis of the at least two flow cells on the sequencing device, wherein steps directed to “analysis” and “determining” are those that are mental processes by which no other steps are recited beyond the Broadest Reasonable Interpretation (BRI) of examining available computer/non-compute resources given appropriate data. With respect to “determining” under the BRI of the claim, setting a sequencing priority is a step by which one can mentally assign the priority of any given sequencing run. As such, the claim steps are directed to abstract ideas.
Claims 2 and 15:
the sequencing analysis priority comprises prioritizing a makespan of a sequencing process comprising the sequencing task, a power consumption for performing the sequencing task, or a priority of a flow cell of the at least two flow cells, wherein with respect to “prioritizing”, under the BRI of the claim, setting a sequencing priority makespan is a step by which one can mentally assign the start and stop task time prioritization. As such, the claim steps are directed to abstract ideas.
Claims 3 and 16:
determining the sequencing analysis priority further comprising determining that a first flow cell is associated with a first priority and a second flow cell is associated with a second priority, wherein the first priority is a relatively higher priority than the second priority, wherein prioritization schemes may be set in a mental fashion and represents nothing more that abstract mental activity.
Claims 4-13 and 15-20 further limit the prioritization steps whereby said operations are mental activity as above. The allocation of compute and non-compute resources is a mental activity that is an assignment of allocation based on mental input of particular data that includes, for example, a workflow operation.
Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined herein to each cover performance in the mind (calculations by hand or pen and paper), save for computing devices. There are no specifics as to the methodologies involved in “analyzing” or in “determining” and thus, under the BRI, one could simply, for example, perform said steps with pen and paper, or, alternatively with the aid of a generic computer as a tool to perform said operations. These recitations are similar to the concepts of collecting information, analyzing it and providing certain results from the collection and analysis (Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations (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 with pen and paper, and can include mathematical concepts.
Further, see MPEP § 2106.04(a)(2), subsection III. The courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (see, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674: noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016): holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper"). Nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind" (see Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016): holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
Step 2A, Prong 2 Analysis: Integration to a Practical Application
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements:
Claims 1 and 14:
Computer-implemented; performing a sequencing task related to the one or more biological samples in at least one of the at least two flow cells…compute resource controlled…; displaying real-time feedback associated with completion of the sequencing task for each flow cell on a display; system; device, wherein said operations are performed using generic computing and laboratory equipment (sequencer) to perform said judicial exception task assignments.
Dependent claims further limit the task as performed by generic computing operations for the same reasons.
The courts have recognized the following laboratory techniques as insignificant extra-solution activity. See further, the MPEP at 2106.05(d)II.): determining the level of a biomarker in blood by any means (Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017)); detecting DNA or enzymes in a sample (Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017)).
Further, the devices, system, processor, memory and instructions are part of a general purpose computer system and there are no details herein wherein of how the specific computer structures are used to implement the judicial exceptions beyond generic computing operations, i.e., the computer elements of the claims do not provide improvements to the functioning of the computer itself (see: DDR Holdings, LLC v. Hotels.com LP); they do not provide improvements to any other technology or technical field (see: Diamond v. Diehr); nor do they utilize a particular machine (see: Eibel Process Co. v. Minn. & Ont. Paper Co.). Hence, these are mere instructions to apply the judicial exception using a computer, and therefore the claim does not provide integration into a practical application of any judicial exception.
Step 2B Analysis: Do Claims Provide an Inventive Concept
The claims are lastly evaluated using the (2B) analysis, wherein it is determined that because the claims recite abstract ideas, and do not integrate that abstract ideas into a practical application, the claims also lack a specific inventive concept. Applicant is reminded that the judicial exception alone cannot provide the inventive concept or the practical application and that the identification of whether the additional elements amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the prior art systems and devices, such as those described in: Camerlengo et al. ( 2012, AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science:10 pages) include next generation sequencers that are operational for task performances, such as the Illumina Genome Analyzer II (abstract). Further, the prior art to Ambardar et al. (Indian J Microbiol (Oct–Dec 2016) 56(4):394–404) discloses high-throughput sequencing wherein multiple flow cells are utilized in a sequencing environment (p. 397). As such, said devices and systems are laboratory step devices (sequencers with two flow cells) that are routine, well-understood and conventional in the art.
The courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)II.): determining the level of a biomarker in blood by any means (Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017)); detecting DNA or enzymes in a sample (Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017)).
Further with respect to the claims to the system, devices and processor, memory and instruction, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. Further, the specification also discloses that computer processors and systems, as example, are generic computing systems [0074]; [0077]; [0078]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer and equipped sequencer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than an abstract idea (see MPEP 2106.05(b)I-III).
The dependent claims have been analyzed with respect to step 2B and none of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception.
For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim 1-2 and 14-15 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wratten et al. (Nature Methods (October 2021) Vo1. 18:1161–1168).
Instant claims 1 and 14 are directed to:
A computer-implemented method for performing sequencing of one or more biological samples in at least two flow cells on a sequencing device, the method comprising (The prior art to Wratten et al. discloses workflow managers for sequencing operations [abstract]:
analyzing compute resources and non-compute resources associated with the sequencing device to determine a state of the compute resources and non-compute resources (Wratten et al. disclose workflow managers that allow for analysis of scheduling that includes queue and adaptive input-p.1162, col. 2-interpreted as the analysis of compute and or non-compute resources, as the instant claims do not include limitations thereof);
determining a sequencing analysis priority associated with performing analysis of the at least two flow cells on the sequencing device (Wratten et al. disclose determinations of priority of workflow operations as a set of rules for defining said pipelines wherein rules herein are interpreted as priority establishment for a device-p. 1165, col. 1);
performing a sequencing task related to the one or more biological samples in at least one of the at least two flow cells according to the sequencing analysis priority, wherein the sequencing task is performed by controlling at least one compute resource or at least one non-compute resource in accordance with the sequencing analysis priority, and wherein the at least one compute resource or the at least one non-compute resource is controlled based on the state of the compute resources and non-compute resources; and (Wratten et al. disclose re-entrance capability that allows pipeline operation to run based on the state of the last executed step, therefore disclosing control by at least one compute/non-compute resource as claimed-p.1163).
displaying real-time feedback associated with completion of the sequencing task for each flow cell on a display (Wratten et al. disclose display of task completion-Figure 1).
Claim 14 is further directed to the sequencing system configured for the operations as above, wherein the art discloses said systems performing those operations at Figure 1 (software implementation that inherently run on systems).
Thus the prior art to Wratten et al. discloses the framework for bioinformatic analysis of sequencing tasks related to a sample as performed in flow cell sequencing and wherein the tasks are according to a set priority.
With respect to claims 2 and 15, Wratten et al. disclose prioritizing a makespan (scheduling; timeframe etc) at p. 1163, col. 1 [automatically manage the scheduling and deployment of containers, further enabling the effective utilization of available resources].
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 3-13 and 16-20 are rejected under 35 U.S.C. 103 as being unpatentable over Wratten et al. (Nature Methods (October 2021) Vo1. 18:1161–1168) in view of Molder et al. (F1000Research (2021) Vol. 10, No.33:25 pages).
Instant claims 1 and 14 are directed to:
A computer-implemented method for performing sequencing of one or more biological samples in at least two flow cells on a sequencing device, the method comprising (The prior art to Wratten et al. discloses workflow managers for sequencing operations [abstract]:
analyzing compute resources and non-compute resources associated with the sequencing device to determine a state of the compute resources and non-compute resources (Wratten et al. disclose workflow managers that allow for analysis of scheduling that includes queue and adaptive input-p.1162, col. 2-interpreted as the analysis of compute and or non-compute resources, as the instant claims do not include limitations thereof);
determining a sequencing analysis priority associated with performing analysis of the at least two flow cells on the sequencing device (Wratten et al. disclose determinations of priority of workflow operations as a set of rules for defining said pipelines wherein rules herein are interpreted as priority establishment for a device-p. 1165, col. 1);
performing a sequencing task related to the one or more biological samples in at least one of the at least two flow cells according to the sequencing analysis priority, wherein the sequencing task is performed by controlling at least one compute resource or at least one non-compute resource in accordance with the sequencing analysis priority, and wherein the at least one compute resource or the at least one non-compute resource is controlled based on the state of the compute resources and non-compute resources; and (Wratten et al. disclose re-entrance capability that allows pipeline operation to run based on the state of the last executed step, therefore disclosing control by at least one compute/non-compute resource as claimed-p.1163).
displaying real-time feedback associated with completion of the sequencing task for each flow cell on a display (Wratten et al. disclose display of task completion-Figure 1).
Claim 14 is further directed to the sequencing system configured for the operations as above, wherein the art discloses said systems performing those operations at Figure 1 (software implementation that inherently run on systems).
Thus the prior art to Wratten et al. discloses the framework for bioinformatic analysis of sequencing tasks related to a sample as performed in flow cell sequencing and wherein the tasks are according to a set priority.
With respect to claims 3-13 and 16-20, Wratten et al. do not specifically disclose operations whereby tasks are performed according to flow cell prioritization as detailed in the claims. However, the prior art to Molder et al. disclose the workflow analysis system Snakemake wherein optimal scheduling of jobs may be performed (Figure 4). The includes that not all jobs in a workflow may be performed at the same time and wherein Snakemake enables scheduling based on solving select subsets that lead to efficient execution of workflow while not exceeding a given resource (e.g., hard drive space, I/O capacity, CPU cores) (p. 8). The further entails criteria wherein execution should be as fast as possible, high-priority jobs will be preferred (based on prioritization of jobs by definition and command line), and temporary output files will be deleted once a job is complete (Figure 4; p. 8, col. 2; p. 9, col. 1 at paragraph 2; Table 1). Constraints ensure that the schedule does not violate resource constraints (p. 9, col. 1-2). Further to operation, Snakemake enables caching between workflows to entail the handling of multiple datasets (tasks) that are particular to a specific need. In addition Snakemake is able to include conditional execution whereby if a quality step is performed whereby quality values are not suitable for a sample to pass the quality thresholds, workflows can be parsed using conditional execution analysis (p. 13).
As such, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing data of the claimed invention to have utilized the methods of workflow prioritization in the context of sequencing analysis as in Wratten et al. with the detailed framework as disclosed by Molder et al. for the purposes of efficiently streamlining sequence analysis priories tasks as claimed. One would have been motivated to do so because Snakemake provides a generic structured approach to leverage workflow-inherent information (p. 10-Molder et al.) and is customizable as such. In addition, Adaptable data analyses can not only be repeated on the same data, but also be modified and extended for new questions or scenarios and can support all aspects of workflow including from data analysis of raw data processing, quality control and interactive exploration, and plotting of final results (p. 15, col. 1-Molder et al.). Last, because both references are in the same field of endeavor, one would have had a reasonable expectation of success in so doing.
Conclusion
No claims are allowed.
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Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting following form via EFS-Web or Central Fax (571-273-8300): PTO/SB/439. Applicant is encouraged to do so as early in prosecution as possible, so as to facilitate communication during examination.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowronek can be reached on (571) 272-9047.
Any inquiry of a general nature or relating to the status of this application or proceeding should be directed to (571) 272-0547.
Patent applicants with problems or questions regarding electronic images that can be viewed in the Patent Application Information Retrieval system (PAIR) can now contact the USPTO’s Patent Electronic Business Center (Patent EBC) for assistance. Representatives are available to answer your questions daily from 6 am to midnight (EST). The toll free number is (866) 217-9197. When calling please have your application serial or patent number, the type of document you are having an image problem with, the number of pages and the specific nature of the problem. The Patent Electronic Business Center will notify applicants of the resolution of the problem within 5-7 business days. Applicants can also check PAIR to confirm that the problem has been corrected. The USPTO’s Patent Electronic Business Center is a complete service center supporting all patent business on the Internet. The USPTO’s PAIR system provides Internet-based access to patent application status and history information. It also enables applicants to view the scanned images of their own application file folder(s) as well as general patent information available to the public.
/Lori A. Clow/ Primary Examiner, Art Unit 1687
Prosecution Insights