Automated volumetric reagent delivery test

Abstract

The present disclosure relates to automated volumetric reagent delivery testing. A system includes a reagent selector valve controllable to select a reagent flow path from a plurality of reagent flow paths; and a pump coupled to the reagent flow path to draw liquid through the reagent flow path according to a prescribed test protocol. The system includes a discharge flow path for discharging the drawn liquid, and a flow meter for measuring the liquid discharged by the pump and outputting data representative of the measured flow. The system also includes a processor for accessing the data and determining a volume of liquid expelled by the pump.

Description

[0001] This application is a divisional application of the application with the filing date of December 21, 2017, application number 201780084612.5, and invention title "Automated Volume Determination Reagent Delivery Testing".

[0002] Cross - reference to related applications

[0003] This application claims the benefit of priority of U.S. Patent Application No. 15 / 841,085, filed on December 13, 2017, which claims the benefit of priority of U.S. Patent Application No. 62 / 442,736, filed on January 5, 2017, and also claims the benefit of the application No. 1704772.1, filed in the United Kingdom (GB) on March 24, 2017, which also claims the benefit of priority of U.S. Patent Application No. 62 / 442,736. All of these prior applications are hereby incorporated by reference in their entirety. Background

[0005] Instruments have been developed for sequencing molecules of interest, particularly DNA, RNA, and other biological samples, and these instruments continue to evolve. Prior to a sequencing operation, a sample of the molecule of interest is prepared to form a library or template that will be mixed with reagents and ultimately introduced into a flow cell where individual molecules will attach to sites and be amplified to enhance detectability. Then, the sequencing operation includes cycles that repeat the following steps: binding molecules at the sites, labeling the bound components, imaging the components at the sites, and processing the resulting image data.

[0006] In such a sequencing system, a fluid system (or subsystem) provides the flow of substances (such as reagents) under the control of a control system, such as a programmed computer and appropriate interfaces.

[0007] Overview

[0008] Details of one or more embodiments of the subject matter described in this specification are set forth in the accompanying drawings and the description below. Other features, aspects, and advantages will become apparent from the description, the drawings, and the claims.

[0009] In some embodiments, a system is provided that includes: a reagent selector valve controllable to select a reagent flow path from a plurality of reagent flow paths; a pump fluidly coupled to the reagent flow path to draw fluid through the selected reagent flow path according to a prescribed test protocol and then discharge the drawn fluid via a discharge flow path fluidly coupled to the pump; a flow meter configured to measure a liquid flow rate caused by the discharge of any liquid in the pump through the discharge flow path during the discharge of the drawn fluid from the pump and generate data representative of the measured liquid flow rate; and a control circuit operatively coupled to the reagent selector valve, the pump, and the flow meter, the control circuit having one or more processors and a memory storing machine-executable instructions that, when executed by the one or more processors, control the one or more processors to access the data and determine, based on the data, a volume of liquid discharged by the pump.

[0010] In some embodiments of the system, the pump can include an injection pump.

[0011] In some embodiments of the system, the flow meter can be fluidly connected in series with the discharge flow path.

[0012] In some embodiments of the system, the memory can be used to store or can store additional machine-executable instructions that, when executed by the one or more processors, further control the one or more processors to cause the one or more processors to use the data to determine a steady-state flow rate that begins after a predetermined amount of time after the start of a pumping cycle and ends before a predetermined amount of time before the end of the pumping cycle.

[0013] In some embodiments of the system, the memory can be used to store or can store additional machine-executable instructions that, when executed by the one or more processors, further control the one or more processors to cause the one or more processors to integrate the measured liquid flow rate to obtain a total volume of liquid discharged by the pump.

[0014] In some embodiments of the system, the memory can be used to store or can store additional machine-executable instructions that, when executed by the one or more processors, further control the one or more processors to cause the one or more processors to perform a low-pass filter on the measured liquid flow rate.

[0015] In some embodiments of the system, the memory can be used to store or may store additional machine-executable instructions that, when executed by one or more processors, further control the one or more processors to control the operation of the reagent selector valve and the pump to perform a plurality of reagent displacement tests, wherein for each reagent displacement test, the one or more processors are controlled to: (a) cause the reagent selector valve to select a different reagent flow path in the reagent flow path as the selected reagent flow path, (b) cause the pump to aspirate a predetermined amount of fluid while being fluidly connected to the selected reagent flow path, (c) cause the pump to discharge the fluid from (b) through the discharge flow path, and (d) obtain from the flow meter data on the measured liquid flow rate of any liquid flowing through the discharge flow path due to (c).

[0016] In some embodiments of the system, the memory can be used to store or may store additional machine-executable instructions that, when executed by one or more processors, further control the one or more processors to, for each displacement test, determine whether a fault condition exists in response to the data obtained in (d), the fault condition indicating that the total amount of liquid flowing through the discharge flow path in (c) exceeds a first predetermined threshold amount of the predetermined amount of fluid in (b), and when it is determined that a fault condition exists in one or more reagent displacement tests, provide a notification to the user.

[0017] In some embodiments of the system, the pump can be used to aspirate and discharge fluid between approximately 2000 microliters and approximately 4000 microliters.

[0018] In some embodiments of the system, the pump can be used to aspirate and discharge fluid at a fluid flow rate between approximately 1000 microliters per minute and approximately 10000 microliters per minute.

[0019] In some embodiments, a system may be provided that includes: a flow cell through which reagents from a plurality of reagent recipients will be pumped during a gene sequencing operation; a reagent selector valve controllable to select a selected reagent from the plurality of reagent recipients; a common line selector valve fluidly connected to the reagent selector valve and controllable to selectively direct the selected reagent through the flow cell or through a bypass line; a drain flow path; a flow meter fluidly coupled to the drain flow path to measure the liquid flowing through the drain flow path and generate data representative of the measured liquid flow; a pump fluidly inserted between i) the drain flow path and ii) the flow cell and the bypass line, the pump being operative to draw the selected reagent through a flow path defined by the positions of the reagent selector valve and the common line selector valve and to discharge the selected reagent through the drain flow path; and a control circuit operatively coupled to the reagent selector valve, the common line selector valve, the pump, and the flow meter, the control circuit having one or more processors and a memory for storing machine-executable instructions that, when executed by the one or more processors, control the one or more processors to access data and determine the volume of liquid discharged by the pump.

[0020] In some embodiments of the system, the memory may be used to store or may store additional machine-executable instructions that, when executed by the one or more processors, further control the one or more processors such that the reagent selector valve and the common line selector valve define a desired flow path.

[0021] In some embodiments of the system, the memory may be used to store or may store additional machine-executable instructions that, when executed by the one or more processors, further control the one or more processors to perform a plurality of reagent displacement tests, wherein for each reagent displacement test, the one or more processors are controlled to: (a) cause the reagent selector valve to select a different reagent and cause the common line selector valve to select between the flow cell or the bypass line to define a selected flow path, (b) cause the pump to draw a predetermined amount of fluid through the selected flow path, (c) cause the pump to discharge the fluid from (b) through the drain flow path, and (d) obtain from the flow meter data representative of the measured liquid flow rate of any liquid reagent flowing through the drain flow path due to (c).

[0022] In some embodiments of the system, the memory can be used to store or may store additional machine-executable instructions that, when executed by one or more processors, further control the one or more processors to determine, for each displacement test, whether a fault condition exists in response to the data obtained in (d), the fault condition indicating that the total volume of liquid flowing through the discharge flow path in (c) exceeds a first predetermined threshold amount of a predetermined amount of fluid in (b), and to provide a notification to the user when it is determined that a fault condition exists for one or more reagent displacement tests.

[0023] In some embodiments of the system, the memory can be used to store or may store additional machine-executable instructions that, when executed by one or more processors, further control the one or more processors to integrate the measured liquid flow rate from (d) to obtain the total volume of fluid discharged by the pump in (c).

[0024] In some embodiments, a method can be provided that includes implementing a stored test protocol for performing one or more reagent displacement tests, where each reagent displacement test includes: (a) selecting a reagent flow path from a plurality of reagent flow paths; (b) actuating a pump to draw a predetermined amount of fluid through the selected reagent flow path according to the stored test protocol; (c) discharging the drawn fluid from the pump and through a discharge flow path; (d) measuring the flow rate of any liquid discharged through the discharge flow path during (c) and generating data representative of the flow rate; and (e) processing the data to determine the quality of the selected reagent flow path.

[0025] In some embodiments of the method, (a) through (e) can be repeated for different reagent flow paths.

[0026] In some embodiments of the method, (e) can further include: (f) during (e), using the data to determine the total volume of liquid flowing through the discharge flow path during (c); (g) determining that the total volume of liquid flowing through the discharge path during (c) exceeds a first threshold amount of a predetermined amount of fluid and that the selected reagent flow path in (a) has a fault; and (h) in response to (g), generating a notification regarding the fault.

[0027] In some embodiments of the method, (e) can include low-pass filtering the data.

[0028] In some embodiments of the method, (f) can include integrating the data to obtain the total volume of liquid flowing through the discharge flow path during (c).

[0029] Details of one or more implementations of the subject matter described in this specification are set forth in the accompanying drawings and the description below. Other features, aspects, and advantages will become apparent from the description, the drawings, and the claims. Note that the relative dimensions in the figures below may not be drawn to scale.

[0030] Accompanying Drawings

[0031] These and other features, aspects, and advantages of the present disclosure will be better understood when the following detailed description is read with reference to the accompanying drawings, in which like characters represent like parts throughout all the figures, wherein:

[0032] Figure 1 is a schematic overview diagram of an example sequencing system in which the disclosed technology can be employed;

[0033] Figure 2 is Figure 1 a schematic overview diagram of an example fluid system of the sequencing system of

[0034] Figure 3 is Figure 1 a schematic overview diagram of an example processing and control system of the sequencing system of

[0035] Figure 4 is a flowchart showing an example of delivery test control logic for performing an automated volumetric reagent delivery test on the sequencing system of Figure 1 ;

[0036] Figure 5 is a diagram showing an example of data cutoff analysis followed by a moving average filtering analysis performed on measured flow rate data;

[0037] Figure 6 is a diagram showing an example of an integration analysis performed on the filtered flow rate data to determine flow; and

[0038] Figure 7 is a diagram showing an example of the results of an automated volumetric reagent delivery test, the results including measured flow rates, standard deviations, and calculated flows presented for each test flow path. Detailed Description

[0040] Figure 1An embodiment of a sequencing system 10 is shown that is used to process molecular samples that can be sequenced to determine their components, component orderings, and generally the sample structure. The system includes an instrument 12 that receives and processes biological samples. A sample source 14 provides a sample 16 that, in many instances, will include a tissue sample. The sample source can include, for example, an individual or subject such as a human, animal, microorganism, plant, or other donor (including environmental samples), or any other subject that includes organic molecules of interest whose sequence is to be determined. The system can be used for samples other than those taken from organisms, including synthetic molecules. In many instances, the molecules will include DNA, RNA, or other molecules with base pairs, the sequences of which can define genes and variants with specific functions of ultimate interest.

[0041] The sample 16 is introduced into a sample / library preparation system 18. This system can separate, fragment, or otherwise prepare the sample for analysis. The resulting library includes molecules of interest that are of a length amenable to sequencing operations. The resulting library is then provided to the instrument 12 where the sequencing operations are performed. In practice, the library (sometimes referred to as a template) is combined with reagents in an automated or semi-automated process and then introduced into a flow cell prior to sequencing.

[0042] In Figure 1 the illustrated embodiment, the instrument includes a flow cell or array 20 that receives the sample library. The flow cell includes one or more fluid channels that permit sequencing chemical reactions to occur, the sequencing chemical reactions including attachment of library molecules and amplification at positions or sites that can be detected during the sequencing operation. For example, the flow cell / array 20 can include sequencing templates immobilized at positions or sites on one or more surfaces. A "flow cell" can include a patterned array such as a microarray, nanoarray, etc. In fact, these positions or sites can be arranged on one or more surfaces of a support in a regularly repeating pattern, a complex non-repeating pattern, or in a random arrangement. To enable the sequencing chemical reactions to occur, the flow cell also permits introduction of substances for reaction, rinsing, etc., which substances include, for example, various reagents, buffers, and other reaction media. The substances flow through the flow cell and can contact the molecules of interest at the respective sites.

[0043] In the instrument, the flow cell 20 is mounted on a movable stage 22, which in this embodiment can be moved in one or more directions as indicated by reference numeral 24. For example, the flow cell 20 can be provided in the form of a removable and replaceable cartridge that can interface with ports on the movable stage 22 or other components of the system to allow reagents and other fluids to be delivered to or from the flow cell 20. The stage is associated with an optical detection system 26 that can direct radiation or light 28 onto the flow cell during sequencing. The optical detection system can employ various methods, such as fluorescence microscopy, to detect analytes disposed at sites in the flow cell. By way of non-limiting example, the optical detection system 26 can employ confocal line scanning to generate stepwise pixelated image data that can be analyzed to locate individual sites in the flow cell and to determine the type of nucleotide most recently attached or bound to each site. Other suitable imaging techniques can also be employed, such as techniques in which one or more radiation points are scanned along the sample, or techniques that employ a "step and shoot" imaging method. The optical detection system 26 and the stage 22 can cooperate to hold the flow cell and the detection system in a static relationship while obtaining area images, or, as described, the flow cell can be scanned in any suitable mode (e.g., point scanning, line scanning, "step and shoot" scanning).

[0044] Although many different techniques can be used for imaging, or more generally for detecting molecules at sites, the presently contemplated embodiments can utilize confocal optical imaging at wavelengths that cause excitation of fluorescent labels. Labels that are excited due to their absorption spectra return a fluorescent signal due to their emission spectra. The optical detection system 26 is configured to capture such signals, thereby processing pixelated image data at a resolution that permits analysis of the signal emission sites, and to process and store the resulting image data (or data derived therefrom).

[0045] In a sequencing operation, cyclic operations or processes can be implemented in an automated or semi-automated manner, where, for example, reactions are facilitated with single nucleotides or oligonucleotides, followed by washing, imaging, and de-blocking to prepare for subsequent cycles. A library of samples that is prepared for sequencing and immobilized on a flow cell can undergo many such cycles before all useful information is extracted from the library. An optical detection system can generate image data during each cycle of the sequencing operation by scanning the flow cell (and its sites) using an electronic detection circuit (e.g., a camera or imaging electronics circuit or chip). The resulting image data can then be analyzed to locate individual sites in the image data and to analyze and characterize the molecules that appear at those sites, for example, by reference to a specific color or specific wavelength of light (the characteristic emission spectrum of a specific fluorescent tag) detected at a particular location, as indicated by a group or cluster of pixels at that location in the image data. For example, in DNA or RNA sequencing applications, the four common nucleotides can be represented by distinguishable fluorescent emission spectra (wavelength or range of wavelengths of light). Each emission spectrum can then be assigned a value corresponding to that nucleotide. Based on this analysis and tracking the periodic values determined for each site, the individual nucleotides and their order can be determined for each site. These sequences can then be further processed to assemble longer fragments, including genes, chromosomes, etc. As used in this disclosure, the terms "automated" and "semi-automated" mean that once an operation is initiated, or once a process that includes the operation is initiated, the operation is performed through system programming or configuration with little or no human interaction.

[0046] In the illustrated embodiment, reagent 30 is drawn or aspirated into the flow cell through valving 32. The valve can obtain the reagent, for example, from a receptacle or vessel storing the reagent through a pipette or straw (not shown). Valve 32 can allow selection of the reagent based on a specified sequence of operations performed. The valve can also receive commands to direct the reagent through flow path 34 into flow cell 20. An outlet or effluent flow path 36 directs the used reagent from the flow cell. In the illustrated embodiment, pump 38 is used to move the reagent through the system. The pump can also be used for other useful functions, such as measuring the reagent or other fluid passing through the system, aspirating air or other fluids, etc. An additional valve 40 downstream of pump 38 allows the used reagent to be appropriately directed to a disposal vessel or receptacle 42. Figure 1 The instrument also includes a series of circuits that facilitate commanding the operation of the various system components, monitoring their operation through feedback from sensors, collecting image data, and at least partially processing the image data. In

[0047] Figure 1In the illustrated embodiment, the control / supervision system 44 includes a control system 46 and a data acquisition and analysis system 48. Both systems will include one or more processors (e.g., digital processing circuitry such as a microprocessor, multi-core processor, FPGA, or any other suitable processing circuitry) and associated memory circuitry 50 (e.g., solid-state memory devices, dynamic memory devices, on-board and / or off-board memory devices, etc.), which can store machine-executable instructions for controlling, for example, one or more computers, processors, or other similar logic devices to provide certain functions. A dedicated or general-purpose computer can at least partially constitute the control system and the data acquisition and analysis system. The control system can include, for example, circuitry that is (e.g., programmed to) process commands for the jets, optics, stage control, and any other useful functions of the instrument. The data acquisition and analysis system 48 interacts with the optical detection system to command: movement of the optical detection system or the stage or both, emission, reception, and processing of return signals for cycle detection, etc. The instrument can also include various interfaces as shown by reference numeral 52, such as an operator interface, which allows for control and monitoring of the instrument, loading of samples, initiation of automated or semi-automated sequencing operations, generation of reports, etc. Finally, in Figure 1 the embodiment, an external network or system 54 can be coupled to and cooperate with the instrument, for example, for analysis, control, monitoring, maintenance, and other operations.

[0048] It can be noted that while a single flow cell and jet path and a single optical detection system are shown in Figure 1 , more than one flow cell and jet path can be accommodated in some instruments. For example, in currently contemplated embodiments, two such arrangements are provided to enhance sequencing and throughput. In fact, any number of flow cells and paths can be provided. These can utilize the same or different reagent containers, disposal containers, control systems, image analysis systems, etc. Multiple jet systems (if provided) can be controlled individually or in a coordinated manner. It should be understood that the phrase "fluidly connected" can be used herein to describe a connection between two or more components that places these components in fluid communication with each other, in much the same way that "electrically connected" can be used to describe an electrical connection between two or more components. The phrase "fluidly inserted" can be used, for example, to describe a particular ordering of components. For example, if component B is fluidly inserted between component A and component C, then the fluid flowing from component A to component C will flow through component B before reaching component C.

[0049] Figure 2 is shown Figure 1An example jet system of a sequencing system. In the illustrated embodiment, the flow cell 20 includes a series of passageways or lanes 56A and 56B, which can be grouped in pairs for receiving fluid substances (such as reagents, buffers, reaction media) during a sequencing operation. Lane 56A is coupled to a common line 58 (the first common line), while lane 56B is coupled to a second common line 60. A bypass line 62 is also provided to allow fluid to bypass the flow cell without entering it. As described above, a series of vessels or receivers 64 allow the storage of reagents and other fluids that may be used during a sequencing operation. A reagent selector valve (RSV) 66 is mechanically coupled to a motor or actuator (not shown) to allow the selection of one or more reagents to be introduced into the flow cell. The selected reagent then advances to a common line selector valve (CLSV) 68, which similarly includes a motor (not shown). The common line selector valve can be commanded to select one or more of the common lines 58 and 60, or both common lines, so that the reagent 64 flows to lanes 56A and / or 56B in a controlled manner, or to select the bypass line 62 to allow one or more reagents to flow through the bypass line. It can be noted that the bypass line can enable other useful operations, such as the ability to prime all reagents (and liquids) into the reagent selector valve (and the common line selector valve) without drawing air through the flow cell, the ability to clean the reagent channels and pipettes independently of the flow cell (e.g., automatically or semi-automatically), and the ability to perform diagnostic functions on the system (e.g., pressure and volume delivery tests).

[0050] Used reagents leave the flow cell through a line coupled between the flow cell and the pump 38. In the illustrated embodiment, the pump includes an injection pump having a pair of syringes 70, which are controlled and moved by an actuator 72 to aspirate reagents and other fluids and to eject or dispense reagents and fluids during different operations of testing, validation, and sequencing cycles. The pump assembly can include various other parts and components, including valves, instruments, actuators, etc. (not shown). In the illustrated embodiment, pressure sensors 74A and 74B sense the pressure on the inlet line of the pump, while a pressure sensor 74C is provided to sense the pressure output by the injection pump.

[0051] The used fluid of the system enters a used reagent selector valve (URSV) 76 from the pump. This valve allows the selection of one of multiple flow paths for the used reagents and other fluids. In the illustrated embodiment, the first flow path leads to a first used reagent container 78, while the second flow path passes through a flow meter 80 to a second used reagent container 82. Depending on the reagents used, it may be advantageous to collect the reagents or certain reagents in separate vessels for disposal, and the used reagent selector valve 76 allows this control.

[0052] It should be noted that the valves within the pump assembly can allow various fluids - including reagents, solvents, cleaners, air, etc. - to be pumped by the pump and to be ejected or circulated through one or more common pipelines, bypass pipelines, and flow cells. Additionally, as described above, in the currently contemplated embodiments, Figure 2 two parallel embodiments of the jet system shown are provided under common control. Each jet system can be part of a single sequencing instrument and can perform functions including sequencing operations on different flow cells and sample libraries in parallel.

[0053] The jet system operates under the command of a control system 46 that implements a prescribed protocol for testing, validation, sequencing, etc. The prescribed protocol will be pre-established and will include a series of events or activity operations such as pumping reagents, pumping air, pumping other fluids, ejecting these reagents, air, and fluids, etc. The protocol will allow such fluid operations to be coordinated with other operations of the instrument such as reactions occurring in the flow cell, imaging of the flow cell and its sites, etc. In the illustrated embodiment, the control system 46 employs one or more valve interfaces 84 and a pump interface 86, where the valve interface 84 is used to provide command signals to the valves and the pump interface 86 is used to command the operation of the pump actuators. Various input / output circuits 88 can also be provided for receiving and processing feedback, for example, from pressure sensors 74A-C and flow meters 80.

[0054] Figure 3 An example of certain functional components of the control / supervision system 44 is shown. As shown, the memory circuit 50 stores prescribed routines executed during testing, debugging, troubleshooting, repair, and sequencing operations. Many such protocols and routines can be implemented and stored in the memory circuit, and these protocols and routines can be updated or changed from time to time. As Figure 3 shown, these protocols and routines can include a jet control protocol 90 for controlling various valves, pumps, and any other jet actuators, as well as for receiving and processing feedback from jet sensors (such as valves) and flow and pressure sensors. The stage control protocol 92 allows the flow cell to be moved as needed, for example, during imaging. The optics control protocol 94 allows commands to be issued to the imaging components to illuminate some parts of the flow cell and receive the returned signals for processing. The image acquisition and processing protocol 96 allows the image data to be at least partially processed to extract useful data for sequencing. As indicated by reference numeral 98, other protocols and routines can be provided in the same or different memory circuits. In fact, the memory circuit can be provided as one or more memory devices, such as volatile and non-volatile memory. The memory can be within the instrument, and some can also be outside the instrument.

[0055] One or more processors 100 access the stored protocols and implement them on the instrument. As described above, the processing circuitry can be a dedicated computer, a general-purpose computer, or part of any suitable hardware, firmware, and software platform. The operation of the processor and the instrument can be commanded by a human operator via the operator interface 101. The operator interface can allow testing, debugging, troubleshooting, and repair, as well as allow reporting of any problems that may occur in the instrument. The operator interface can also allow starting and monitoring of the sequencing operation.

[0056] As elaborated above, in order for sequencing to occur, reagents are introduced for reaction based on a prescribed sequence of operations performed. Diagnostic tests may be required to check for leaks or blockages in the fluid system during manufacturing, commissioning, or use, so as to avoid delivering inaccurate reagent volumes. To avoid manual operations for precisely determining reagent delivery, an automated volumetric reagent delivery test as described below is provided.

[0057] Figure 4 FIG. is a flowchart showing an example of delivery test control logic 104 for an automated volumetric reagent delivery test that can be performed on a sequencing system 10. One or more events of the delivery test control logic 104 can be executed by a control / supervision system 44 (e.g., control system 46 and data acquisition and analysis system 48). In the illustrated embodiment, the delivery test control logic 104 can include a process 106 that executes a suction sequence (including 112 to 122), a process 108 that executes a delivery sequence (including 124 to 130), and a process 110 that executes a data processing / analysis sequence (including 132 to 144). The delivery test control logic 104 can also include a logic 146 for exiting the delivery test control logic 104, and a process 148 for repeating the delivery test control logic 104 to test another flow path (reagent) of interest.

[0058] When the conveyance test control logic 104 is initiated, the control system 46 may verify various “home” states of the sequencing system 10 in block 112. For example, the sequencing system 10 may already be in an idle state such that when the conveyance test control logic 104 is initiated, the control system 46 may first verify whether various valves (e.g., RSV 66, CLSV 68, URSV 76) are in the home position and whether a pump (e.g., pump 38) is in the home position, and so on. As used herein, the term home refers to the process of returning an adjustable component to a default or “home” position, e.g., to a particular operational limit or predefined setting. At 114, the control system 46 may move the URSV 76 to a first position to fluidly connect the discharge flow path (which may be downstream of the pump 38) to the receiver 82. In certain embodiments, the control system 46 may move the URSV 76 to a second position different from the first position to fluidly connect the discharge flow path to the receiver 78. At 116, the control system 46 may move the CLSV 68 to a position or port corresponding to a respective flow path. For example, the flow path may include one or more of a passage or channel 56A fluidly connected to the first common line 58 or a passage or channel 56B fluidly connected to the second common line 60, and the flow path may further include a bypass line 62. Different positions or ports of the CLSV 68 may each correspond to one of the flow paths set forth above, and thus, by moving the CLSV 68 to a particular position, a corresponding flow path may be selected.

[0059] At 118, the control system 46 may actuate one or more valves that may be part of one or more pumps 38 such that the pump is fluidly connected to a respective reagent flow path either through the flow cell 20 or through the bypass line 62. For example, the control system 46 may cause a valve to fluidly couple the output / input of the pump 38 to a first port of the pump 38 that is fluidly connected to a reagent flow path connected to the flow cell 20, or the control system 46 may cause a valve to fluidly couple the output / input of the pump 38 to a second port of the pump 38 that is fluidly connected to a reagent flow path connected to the bypass line 62. At 120, the control system 46 may move the RSV 66 to allow a particular reagent to be aspirated from a variety of different reagents. For example, the RSV 66 may be moved to different positions or ports, where each position or port corresponds to a respective reagent. It will be appreciated that the processes 114 to 120 may or may not be performed in the same order as described above. In certain embodiments, the processes 114 to 120 may be performed in parallel or simultaneously with each other.

[0060] At 122, the control system 46 controls the pump 38 to aspirate a volume of reagent or other liquid or fluid from a reagent source or other source via a flow path through the RSV 66 and the CLSV 68. After processes 112 to 120 are completed, the flow path of interest will be established, thereby selecting the corresponding reagent of interest, and the control system 46 can start aspirating the volume according to the protocol, for example, aspirating the specified volume of the selected reagent of interest determined by a specific protocol (such as a test protocol or an analysis protocol). The aspiration sequence 106 ends here. Next, the delivery test control logic 104 can proceed to the delivery sequence 108 (including processes 124 to 130). At 124, the control system 46 can actuate the valve that is part of the pump 38 to a dispensing configuration such that when the pump 38 is actuated to discharge the aspirated reagent from the pump 38, the dispensed fluid flows to the designated port. For example, the valve position of the valve of the pump 38 can be changed to "dispense" at the pump 38 so that the fluid is dispensed to the URSV 76 instead of to the flow cell 20 or the bypass line 62. In other words, during the delivery sequence 108, the fluid drawn by the pump 38 from the aspiration sequence 106 is dispensed to the URSV 76. The URSV 76 can be controlled to route the dispensed fluid through the discharge flow path, which passes through the flow meter 80 to the used reagent receiver 82.

[0061] At 126, the control system 46 begins to record data (such as flow rate data) via the flow meter 80. The data can be recorded continuously or at any suitable time interval. It can be appreciated that the data recording interval can be as short as the flow response time of the flow meter 80 (for example, about 20 milliseconds). In process 128, the control system 46 causes the pump 38 to start dispensing a fluid volume, and the dispensed fluid flows into the receiver 82. At 130, the control system 46 stops recording data (such as flow rate data). In some embodiments, data recording can occur until the syringe 70 of the pump 38 completes the dispensing action, that is, during the entire dispensing cycle of the pump 38. In some embodiments, data recording can be terminated when the flow rate reaches a steady state or at any other suitable time according to the test protocol.

[0062] Once data has been collected regarding a given reagent / flow path, the volumetric flow rate data can be analyzed in one or more ways to perform various diagnostic checks. For example, in some embodiments, the flow rate data can be analyzed to determine how much liquid has been dispensed from pump 38 after a given amount of liquid (reagent) has been aspirated, and if the total amount dispensed is less than (or greater than) the total amount aspirated, an error condition can be determined. For example, a test protocol can include driving pump 38 to aspirate 2000 μL of a particular reagent via a selected flow path and then actuating pump 38 to completely dispense all of the aspirated liquid through flow meter 80. If flow meter 80 collects data indicating that only 1500 μL has flowed through flow meter 80, then this may indicate some type of system error, such as a leak in the flow path resulting in the loss of 500 μL of liquid reagent, an insufficient amount of reagent in the reagent receiver (as may occur when the reagent receiver is damaged), or improper actuation of pump 38 (which may occur in situations such as, for example, if the pump actuation is incorrectly calibrated - syringe pumps can typically be actuated to dispense a precise amount of liquid based on a sensor that measures how much travel the syringe plunger undergoes during actuation; if the sensor is incorrectly calibrated, the plunger may travel insufficiently and aspirate less liquid than expected, and in a similar manner, syringe pumps can also be incorrectly calibrated in the opposite direction, e.g., it may aspirate more liquid than expected, in which case the flow meter may measure a volume of liquid greater than what the protocol specifies should be aspirated). It should be understood that the volumetric flow rate test involving the syringe pump can be started and ended when the pump is in the home position (as described above), e.g., the syringe plunger is in the bottom-most position such that no more fluid can be expelled from the syringe.

[0063] It should be understood that references to the phrase "aspirate a predetermined amount of liquid" or similar phrases used herein refer to an aspiration intended to obtain a predetermined amount of liquid. In an ideal state, the amount of liquid obtained will be equal to the volume of liquid aspirated. However, if there is a leak or some other factor that reduces the amount of liquid actually obtained by such aspiration, then the actual amount of liquid obtained by such aspiration will be less than the desired amount of liquid. It should be understood that, for greater clarity, references to aspirating an amount of liquid can be replaced in this document by the phrase "aspirate an amount of fluid". For example, if 2000 μL of fluid is aspirated from a receiver that contains only 1500 μL of liquid, then the resulting 2000 μL of aspirated fluid can include 1500 μL of liquid and 500 μL of air.

[0064] Another aspect of the system performance that can be tested is checking the volumetric flow rate. For example, pump 38 can be operated at one or more specified dispense rates according to a test protocol. Flow meter 80 can be used to monitor the volumetric flow rate of the liquid pumped out of pump 38 during a dispense operation and can confirm that pump 38 is dispensing the liquid at a rate consistent with the specified volumetric flow rate of the protocol. As previously described, this volumetric flow rate measurement / determination can be performed concurrently with the overall volumetric flow determination.

[0065] As part of a diagnostic test, the reagents for multiple or all of the flow paths of the analytical instrument can be tested. For example, this can also include testing each flow path to each reagent receptacle. While a larger portion of the flow paths leading to the various reagents can be shared in common, e.g., portions of the flow paths along bypass line 62 or through flow channels A and / or B of flow cell 20, the flow paths for each reagent can branch downstream of RSV 66. Testing each such flow path can allow for the identification of potential leaks that may exist in the downstream region of RSV 66, e.g., if a pipette that is fluidly connected to RSV 66 and is used to aspirate liquid from a reagent receptacle is damaged, e.g., cracked or otherwise impaired, or has become loose (e.g., the pipette can be a tube with a threaded fitting at the end that can be screwed into a larger manifold that routes fluid from the pipette to RSV 66), and allows fluid to enter the pipette at a location other than the pipette tip, which can allow air to be aspirated into the flow path through such an entry point, thereby reducing the amount of liquid aspirated.

[0066] In some embodiments, this volumetric flow rate and volume testing can be performed using a portion of the reagent that is used during an actual analysis. In other embodiments, the reagent can be replaced with another liquid that is less expensive or has fewer issues, such as distilled water (e.g., this liquid can be selected or modified to simulate the various fluid properties of the reagent, such as viscosity if needed). The flow rate and / or volumetric flow testing can be performed at different intervals and using different frequencies. In some embodiments, for example, one or both types of tests can be performed when the analytical instrument is first turned on and loaded with reagents. In some additional embodiments, one or both types of tests can be performed when a kit or source is removed and replaced with a new kit or source. In some additional or alternative embodiments, one or both types of tests can be performed periodically, e.g., according to a regular schedule or in response to a predetermined number of analysis cycles being performed, etc.

[0067] Back to Figure 4, after completion of the delivery sequence 108, the data acquisition and analysis system 48 can proceed to the data processing / analysis sequence 110 (including processes 132 to 144), during which, as discussed above, one or more types of data processing can be performed on the data from the volumetric flowmeter. For example, at 132, the data acquisition and analysis system 48 can optionally perform data truncation on the data collected during the delivery sequence 108. Data truncation can include applying "upper" and "lower" truncation filters to the collected flow rate data, as will be discussed in Figure 5 . At 134, the data acquisition and analysis system 48 can perform another filtering on the filtered flow rate data (from 132). For example, a "moving average filter" can be applied to the flow rate data, as will be discussed in Figure 5 . At 136, the data acquisition and analysis system 48 can integrate the filtered flow rate data to calculate the total flow rate of a given flow. For example, the filtered flow rate data can be trapezoidally integrated to calculate the total flow rate, as will be discussed with reference to Figure 6 .

[0068] At 138, the data acquisition and analysis system 48 can optionally calculate the average flow rate and / or the standard deviation of the flow rate based on the filtered data (at 134); this can be omitted if the pump speed test is not performed. The data acquisition and analysis system 48 can also calculate the flow rate based on the data analyzed in process 136, as mentioned above, and as will be further discussed with reference to Figure 7 . At 140, the data acquisition and analysis system 48 can determine the pass / fail status of the flow path (reagent) being tested. For example, the pass / fail determination can be based on a comparison between the calculated total flow rate and a predetermined flow rate, as will be discussed in Figure 7As discussed. The predetermined flow rate can be a reagent-specific value (depending on the specific gene sequencing protocol), or it can be based on the pumping capacity of the pump 38 (e.g., pumping volume). For example, if a 2000 μL amount of a specific reagent is to be used during an analysis protocol, then the predetermined amount can be 2000 μL to simulate the amount used during the execution of the analysis protocol. In another example, if the syringe pump has a maximum displacement of 1500 μL, then the predetermined amount can be 1500 μL even if the amount used during the analysis protocol (which requires multiple syringe aspiration cycles) exceeds this amount. If the calculated total flow rate is greater than or less than the predetermined flow rate, and the difference is greater than a predetermined threshold or tolerance, then the sequencing system 10 can be considered to have failed the qualified volumetric determination reagent delivery test for the selected flow path (reagent), and the delivery test control logic 104 can proceed to block 142 to record the test result. If the calculated average flow rate is equal to the predetermined flow rate or within a predetermined threshold or tolerance of the predetermined flow rate, then the sequencing system 10 can be considered to have passed the qualified volumetric determination reagent delivery test for the selected flow path (reagent), and the delivery test control logic 104 can proceed to 144 to record the test result. It can be appreciated that the threshold or tolerance can be 0.01%, 0.1%, 1%, 5% or 10% of the predetermined flow rate, or it can be any suitable value, depending on the selected reagent, gene sequencing protocol, inherent accuracy of the pump 38, inherent measurement accuracy of the flow meter 80, and other factors.

[0069] The data and / or results recorded in processes 142 and 144 can be stored in the memory circuit 50 and / or can be provided to an authorized user (upon request or according to a protocol) through the interface 52. It can be appreciated that knowing the pass / fail result of the volumetric determination reagent delivery test can help verify the accuracy of the instrument 12 and perform calibration. In addition, the data and / or results recorded in processes 142 and 144 can also help troubleshoot problems in the case where one or more flow paths fail the volumetric determination reagent delivery test.

[0070] At 146, the delivery test control logic 104 has completed a volumetric flow delivery test of the selected flow path (reagent) of interest, and the control system 46 can advance to the next flow path (reagent) of interest at 148 based on the test protocol. For example, the control system 46 can return to 120 to set the RSV to the next location or port specified in the protocol and can perform the process (122 to 146) on another reagent of interest. If only a flow rate test is performed, for example, to determine whether the pump 38 is operating correctly, it may not be necessary to test all reagent flow paths because the dispensing action of the pump can utilize the same flow path leading to the flow meter 80 regardless of which reagent is selected. However, if a volumetric delivery test is performed, each reagent flow path can be tested. In this way, the delivery test control logic 104 can continue until each flow path (reagent) of interest has been tested. Alternatively, the control system 46 can end the volumetric flow delivery test and exit the delivery test control logic 104 upon completion of the flow path (reagent) test or upon receiving an instruction from the user.

[0071] Figure 5 is a diagram showing an example of the data cutoff analysis and data filtering (moving average) analysis mentioned at 132 and 134 in Figure 4 The diagram includes an original flow rate data chart 152, a filtered flow rate data chart 162, and an average analysis chart 168, which have a vertical axis 154 representing the flow rate in microliters per minute (μL / min) and a horizontal axis 156 representing time in seconds (sec). In the original flow rate data chart 152, the original trace 160 is plotted at time steps 158 when the original flow rate data is collected by the flow meter 80. It can be appreciated that the time step 158 can be any suitable time interval selected for the test protocol (e.g., 0.5, 1, 2, 3, 4, 5, or 10 seconds) and cannot be less than the response time of the flow meter 80 (e.g., 20 milliseconds). There can be one or more spikes 166, which may be noise that has a negligible effect on the measurement accuracy but significantly deviates from the norm or trend of the original trace 160. However, in some cases, it may be desirable to remove one or more spikes 166 from the analysis to improve the accuracy.

[0072] Values (corresponding to one or more spikes) can be removed from the original trace 160 based on a specified upper cut-off limit and a lower cut-off trace. In one example, if a value is outside the specified cut-off limits, the value can be replaced with a previous value (e.g., a value in a previous time step) to produce a trace 164 (e.g., a filtered trace) as shown in the filtered flow rate data graph 162. In some embodiments, the lower cut-off value can be approximately 0 μL / min, and the upper cut-off value can be approximately 5000 μL / min. Alternatively, depending on the test protocol, the lower and upper limits can be any suitable values specific to the reagent. It should be noted that after the cut-off analysis 150 as described above, the trace 164 can be clearer (e.g., have reduced data noise) compared to the trace 150. In one aspect, the "removed values" can also be used to provide information about the fluid characteristics. For example, the number of points removed or truncated (e.g., one or more spikes) can be proportional to the number of bubbles in the fluid system. Thus, the number of spikes can be summed, and the total number of microbubbles in the fluid system can be estimated based on the number of spikes observed for a given sample. If desired, the estimated number of microbubbles obtained in this way can be compared to a predetermined threshold amount of microbubbles, and if the estimated number of microbubbles exceeds such a threshold, a warning or notification can be generated to alert the user of an undesired high frequency of microbubble generation or presence.

[0073] After the cut-off analysis 150, an averaging (moving average) analysis 168 can be performed, where a data filtering process is applied to the trace 164 using a specified moving average filter to produce an average trace 170 (e.g., a filtered trace) as shown in the averaging analysis graph 168. It can be appreciated that a moving average filter (or a low-pass filter) is a filter commonly used to smooth any sampled data / signal array. In some embodiments, the window size of the moving average analysis can be 50 data points for a 0.1-second time step (e.g., 50 flow rate data points are averaged to produce an average flow rate value). Alternatively, any other suitable window size can be used. Alternatively, any other suitable averaging analysis can be used, such as a frequency-based Fourier transform, e.g., using the Fourier transform to transform the data into the frequency domain, removing high-order harmonics and frequencies from the frequency domain data set, and then transforming the adjusted frequency domain data set back into the time domain to produce a filtered data set that does not include high-frequency noise.

[0074] Figure 6 is shown at Figure 4Illustration of an example of integral analysis referred to at 136. The illustration includes a filtered flow rate data graph 174 and a truncated flow rate data graph 190, which graphs have a vertical axis 176 representing flow rate in μL / min and a horizontal axis 178 representing time in seconds. In the filtered flow rate data graph 174, multiple complete traces 182 are plotted according to time steps 180, where each of the multiple complete traces 182 represents filtered flow rate data obtained for a corresponding flow path (reagent) (e.g., filtered by processes 132 and 134). It should be noted that each of the multiple complete traces 182 includes a rising trace 184 where the flow rate rapidly increases with time, a falling trace 186 where the flow rate rapidly decreases with time, and a steady-state trace 188 between the rising trace 184 and the falling trace 186, where the flow rate in the steady-state trace remains relatively constant. The rising trace 184 and the falling trace 186 can be attributed to fluid inertia (e.g., the pressure difference in the fluid required to cause the volumetric flow rate to vary with time) and fluid capacitance, as well as the start of flow after a command is issued to the pump 38 (e.g., on the order of a few milliseconds to several tens of milliseconds).

[0075] In some embodiments, it may be desirable to remove the flow rate data in the rising trace 184 and the falling trace 186 from the data processing / analysis being performed to improve accuracy, e.g., during flow rate measurement rather than during total volumetric flow rate measurement. For example, the data acquisition and analysis system 48 may have a predetermined "start delay" time (e.g., roughly spanning the rising trace 184) and / or a predetermined "length" time (e.g., roughly spanning the steady-state trace 188) specified in a protocol such that the flow data from the rising trace 184 and the falling trace 186 can be removed, truncated, or ignored, and only the flow rate data measured after the flow meter 80 has reached a steady state is retained for further analysis, which results in the truncated flow rate data graph 190. It should be noted that the average flow rate and the corresponding standard deviation can be calculated based on the flow rate data in the steady-state trace 188.

[0076] Next, data acquisition and analysis system 48 can perform integration on the rising trace 184, steady-state trace 188, and falling trace 186 over corresponding time periods to determine the total flow rate as shown in the integrated data graph 192. Although any suitable numerical integration method can be used for the integration process (e.g., at 136), in the illustrated embodiment, trapezoidal integration is performed on the steady-state trace 188 to produce the integrated data graph 192. The integrated data graph 192 has a vertical axis 194 representing the flow rate delivered during the volume determination reagent delivery test in μL and a horizontal axis 178 representing time in seconds. Multiple volume traces 196 are plotted at time steps 180, where each of the multiple volume traces 196 represents the total flow rate data obtained for a corresponding flow path (reagent). As shown in the multiple volume traces 196, the flow rate of each flow path (reagent) continues to increase with time before saturating to a value that represents the integrated flow rate, which is used to determine the pass / fail result of the volume determination reagent delivery test as discussed in process 140 as Figure 4 discussed in process 140.

[0077] Figure 7A diagram showing examples of the results of a volume determination reagent delivery test, with the measured flow rates, standard deviations, and calculated flows presented for each of the tested flow paths. The diagram includes bar chart 198, bar chart 208, and bar chart 212, each having multiple values corresponding to multiple flow paths (reagents) tested in accordance with the above-described delivery test control logic 104. In bar charts 198 and 208, the vertical axis 200 represents the average flow rate in μL / min (e.g., calculated based on the flow rate measured after reaching steady-state delivery), and the horizontal axis 202 represents the tested flow paths (reagents). In the illustrated embodiment of bar chart 198, the average flow rate data includes multiple normal / expected flow rate data 204 and some anomalies 206. For example, according to the test protocol, for some flow paths (the four flow paths labeled VB2 on the right side of bar chart 198), the average flow rate can be approximately 4000 μL / min, while for other flow paths, the average flow rate can be approximately 2000 μL / min. For flow paths that should have a flow rate of approximately 2000 μL / min, values of approximately 1500 μL / min and approximately 500 μL / min are outside the normal range, e.g., ±10% of 2000 μL, and are thus considered anomalies 206. It should be noted that the test protocol can be established at least in part based on the sensing accuracy of the flow meter 80. For example, the flow rate can be selected such that the flow rate remains at a level where the flow meter has acceptable accuracy. For example, a recommended flow rate can be approximately 1000 μL / min. In another example, the recommended flow rate can be lower than the theoretical flow rate of approximately 40000 μL / min and lower than, or approximately 10000 μL / min of the actual flow rate. In this context, the term "about" is intended to indicate that the indicated value may not be precise, and the actual value may differ from the indicated value in a manner that does not materially change the operation involved. For example, as understood by those skilled in the art, the term "about" as used herein is intended to convey a suitable value within a specific tolerance (e.g., ±10%, ±5%, or ±1%) of the indicated value.

[0078] Standard deviation values corresponding to each average flow rate (e.g., 204 and 206) can be calculated, and this value is shown as value 210 in bar chart 208. In some embodiments, the pass / fail determination discussed in Figure 4 process 140 can also be based on the above standard deviation values.

[0079] Finally, in bar graph 212, the vertical axis 200 represents the average flow rate in μL, and the horizontal axis 202 represents the tested flow paths (reagents). In bar graph 212, the integrated flow rate data includes a plurality of normal / expected flow rate data 214 (corresponding to the normal / expected flow velocity data 204 - in this example, the data represents the total volume flowing through in a one-minute interval) and several anomalies 216 (caused by anomalies 206). For example, according to the test protocol (which may involve a volume flow of 1 minute for each reagent / flow path), for some flow paths, the integrated flow rate may be approximately 4000 μL, while for other flow paths, the integrated flow rate may be approximately 2000 μL. For a flow path that should have an integrated flow rate of approximately 2000 μL, values of approximately 1500 μL and approximately 500 μL can be considered outside the acceptable range (e.g., the difference between these values and the expected value is greater than a predetermined threshold), and are thus considered anomalies 216. Based on the results of the automated volumetric delivery test (e.g., Figure 7 )(e.g., if the volumetric delivery test indicates that one or more reagent flows are outside the acceptable limits), a diagnostic sequence or test can be performed to check for leaks or blockages in the instrument 12 that may cause incorrect reagent volumes to be delivered during sequencing.

[0080] It can be appreciated that the expected integrated flow rate can depend at least in part on the capacity of the pump 38. Based on the fluid system described above, it is expected that the integrated flow rate is equal to the volume of fluid discharged by the pump 38. For a pump 38 having two pairs of syringes 70 (e.g., the capacity of each pair of syringes is approximately 1000 μL), the volume of fluid discharged by the pump 38 is between approximately 2000 μL and approximately 4000 μL (e.g., if only one pair of syringes 70 is dispensed, the fluid volume is approximately 2000 μL, and if two pairs of syringes 70 are dispensed, the fluid volume is approximately 4000 μL). In some embodiments, syringes 70 having a capacity greater than or less than approximately 1000 μL (e.g., approximately 1250 μL, approximately 500 μL, approximately 250 μL) can be used, and the expected integrated flow rate will change accordingly.

[0081] The use of sequence indicators (if any) in this disclosure and the claims - such as (a), (b), (c), etc. - should be understood not to convey any particular order or sequence, unless such an order or sequence is explicitly indicated. For example, if there are three steps labeled (i), (ii), and (iii), it should be understood that these steps can be performed in any order (or even simultaneously, if not otherwise conflicting) unless otherwise stated. For example, if step (ii) involves processing an element created in step (i), then step (ii) can be considered to occur at some time after step (i). Similarly, if step (i) involves processing an element created in step (ii), then the reverse should be understood.

[0082] It should also be understood that the use of "for" - e.g., "a valve for switching between two flow paths" - can be replaced with language such as "configured to" - e.g., "a valve configured to switch between two flow paths".

[0083] Unless otherwise stated, terms such as "about", "approximately", "substantially", "nominal", etc. when used in reference to a quantity or a similar quantifiable attribute should be understood to include values within 10% of the specified value.

[0084] In addition to the claims listed in this disclosure, the following additional embodiments should be understood to be within the scope of this disclosure:

[0085] Embodiment 1: A system, comprising: a reagent selector valve that can be controlled to select a reagent flow path from a plurality of reagent flow paths; a pump coupled to the reagent flow path to draw liquid through the reagent flow path according to a specified test protocol; a discharge flow path for discharging the drawn liquid; a flow meter for measuring the liquid discharged by the pump and generating data representing the measured flow; and a processor for accessing the data and determining the volume or mass of the liquid discharged by the pump.

[0086] Embodiment 2: The system according to Embodiment 1, wherein the pump comprises an injection pump.

[0087] Embodiment 3: The system according to Embodiment 1, wherein the flow meter is coupled in the discharge flow path.

[0088] Embodiment 4: The system according to Embodiment 1, wherein the flow meter measures the flow rate at a plurality of time steps during the test protocol.

[0089] Embodiment 5: The system according to Embodiment 4, wherein the processor is configured to integrate the measured flow rate to obtain the total volume or mass of the liquid discharged by the pump.

[0090] Embodiment 6: The system according to Embodiment 1, wherein the processor is configured to perform low-pass filtering on the measured flow rate.

[0091] Embodiment 7: The system according to Embodiment 1, comprising a control circuit configured to control the operation of the reagent selector valve and the pump and to automatically and continuously perform another displacement test by selecting different reagent flow paths.

[0092] Embodiment 8: The system according to Embodiment 7 of the implementation system, wherein the control circuit is configured to provide a result output of the displacement test to the user.

[0093] Embodiment 9: The system according to Embodiment 1, wherein the volume of the fluid discharged by the pump is between approximately 2000 microliters and approximately 4000 microliters.

[0094] Embodiment 10: The system according to Embodiment 1, wherein the flow rate of the fluid discharged by the pump is between approximately 1000 microliters per minute and approximately 10000 microliters per minute.

[0095] Embodiment 11: A system, comprising: a flow cell through which a plurality of reagents are pumped during a gene sequencing operation; a reagent selector valve controllable to select a reagent from a plurality of reagents disposed in respective reagent containers; and a common line selector valve controllable to select to direct the reagent from the reagent selector valve through the flow cell or through a bypass line; a pump coupled downstream of the flow cell and the bypass line to draw liquid through a flow path defined by the positions of the reagent selector valve and the common line selector valve according to a predefined test protocol; a discharge flow path for discharging the drawn liquid; a flow meter coupled to at least one of the flow paths to measure the liquid discharged by the pump and to generate data representative of the measured flow; and a processor configured to access the data and determine the volume or mass of the liquid discharged by the pump.

[0096] Embodiment 12: The system according to Embodiment 11, comprising a control circuit configured to control the operation of the reagent selector valve and the common line selector valve to define a desired reagent flow path.

[0097] Embodiment 13: The system according to Embodiment 12, wherein the control circuit is configured to continuously perform another displacement test by selecting different reagent flow paths.

[0098] Embodiment 14: The system according to Embodiment 11, wherein the flowmeter is configured to measure the flow rate at a plurality of time steps during a test protocol.

[0099] Embodiment 15: The system according to Embodiment 14, wherein the processor is configured to integrate the measured flow rate to obtain the total volume or mass of the liquid discharged by the pump.

[0100] Embodiment 16: A method comprising: implementing a stored test protocol that includes: selecting a desired reagent flow path from a plurality of reagent flow paths; actuating a pump to draw liquid through the selected reagent flow path according to the stored test protocol; discharging the drawn liquid through a discharge flow path; and measuring the flow rate of the liquid and generating data representative of the flow rate; and processing the data to determine the mass of at least one of the flow paths.

[0101] Embodiment 17: The method according to Embodiment 16, comprising repeating the stored test protocol for different reagent flow paths and processing the resulting data to separately determine the mass of each reagent flow path.

[0102] Embodiment 18: The method according to Embodiment 16, wherein the flow rate is measured at a plurality of consecutive time steps.

[0103] Embodiment 19: The method according to Embodiment 18, wherein processing the data includes low-pass filtering the data over more than one of the plurality of time steps.

[0104] Embodiment 20: The method according to Embodiment 18, wherein processing the data includes integrating the measured flow rate over the plurality of time steps to obtain the volume of liquid discharged during the stored test protocol.

[0105] It should be recognized that all combinations of the foregoing concepts (assuming these concepts are not mutually inconsistent) are considered to be part of the inventive subject matter disclosed herein. In particular, all combinations of the claimed subject matter appearing at the end of this disclosure are considered to be part of the inventive subject matter disclosed herein. It should also be recognized that terms explicitly employed herein that also appear in any disclosure incorporated by reference should be accorded a meaning most consistent with the particular concepts disclosed herein.

Claims

1. A system, comprising: a reagent selector valve controllable to select a reagent flow path from a plurality of reagent flow paths; a pump fluidly coupled to the reagent flow path to draw fluid through the selected reagent flow path according to a prescribed test protocol and then discharge the drawn fluid via a discharge flow path fluidly coupled to the pump; a flow meter configured to measure a liquid flow rate caused by the discharge of any liquid in the pump through the discharge flow path during the discharge of the drawn fluid and to generate data representative of the measured liquid flow rate; and a control circuit operably coupled to the reagent selector valve, the pump, and the flow meter, the control circuit having one or more processors and a memory for storing machine-executable instructions, the machine-executable instructions when executed by the one or more processors controlling the one or more processors to access the data and determine a volume of liquid discharged by the pump based on the data.

2. The system according to claim 1, wherein, the pump includes an injection pump.

3. The system according to claim 1, wherein, the flow meter is fluidly connected in series with the discharge flow path.

4. The system according to claim 1, wherein, the memory is for storing additional machine-executable instructions which, when executed by the one or more processors, further control the one or more processors such that the one or more processors use the data to determine a steady-state flow rate that begins a predetermined amount of time after the start of a pumping cycle and ends a predetermined amount of time before the end of the pumping cycle.

5. The system according to claim 4, wherein, the memory is for storing additional machine-executable instructions which, when executed by the one or more processors, further control the one or more processors such that the one or more processors integrate the measured liquid flow rate to obtain a total volume of liquid discharged by the pump.

6. The system according to claim 1, wherein, the memory is for storing additional machine-executable instructions which, when executed by the one or more processors, further control the one or more processors such that the one or more processors perform low-pass filtering on the measured liquid flow rate.

7. The system according to claim 1, wherein, the memory is for storing additional machine-executable instructions which, when executed by the one or more processors, further control the one or more processors to control the operation of the reagent selector valve and the pump to perform a plurality of reagent displacement tests, wherein for each reagent displacement test, the one or more processors are controlled to: a) cause the reagent selector valve to select a different reagent flow path from the reagent flow paths as the selected reagent flow path, b) cause the pump to draw a predetermined amount of fluid while fluidly connected to the selected reagent flow path, c) cause the pump to discharge the fluid from (b) through a discharge flow path, and d) obtain data from the flow meter on the measured liquid flow rate of any liquid flowing through the discharge flow path due to (c).

8. The system according to claim 7, wherein, the memory is used to store additional machine-executable instructions that, when executed by the one or more processors, further control the one or more processors to determine, for each displacement test, whether a fault condition exists in response to the data obtained in (d), the fault condition indicating that the total amount of liquid flowing through the discharge flow path in (c) exceeds a first predetermined threshold amount of the predetermined amount of fluid in (b), and to provide a notification to the user when it is determined that one or more of the reagent displacement tests have the fault condition.

9. The system according to claim 1, wherein, the pump draws and discharges a fluid between approximately 2000 microliters and approximately 4000 microliters.

10. The system according to claim 1, wherein, the pump draws and discharges fluid at a fluid flow rate between approximately 1000 microliters per minute and approximately 10000 microliters per minute.

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