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--- oxfordapr202009b:start [2015/02/05 15:51] – magiero
+++ oxfordapr202009b:start [2015/11/06 02:42] (current) – magiero
@@ Line 27: / Line 27: @@
 • [0099] **Output pump** 34 pumps fluids out of the sensor through **outlet channel** 36 (connected to **waste reservoir** 35 on the bottom).\\
 • [0100] **Selector valve** 45 connects the sensor to either the supply or the waste reservoir.\\
+{{ cartridge2bot.png?300}}
+{{cartridge2.png?300}}
+{{wellplate.png?200}}
 ==== - Three Sensor-on-PCB Alternatives [0148] - [0151] ====
@@ Line 51: / Line 55: @@
 An example is the [[https://thermal.ferrotec.com/index.php?id=module_detail&mod_id=69|Ferrotec Thermoelectric Module]]. It may be mounted underneath the cartridge.\\
 • [0159] The circuits two main functions are **signal processing** and **control**.\\
+=== - Signal Processing Function [0160] - [0175] ===
 • [0160] Signal processing is distributed between the internal board 50 and the embedded processor 51.\\
 {{ moduleblock.png?500}}
@@ Line 67: / Line 73: @@
 • [0166] Alternatively some readout chip on 50 could be feeding the FPGA.\\
 • [0168] The embedded computer 51 processes the digital data from each channel.  51 includes a **processing module** 73 implemented in software that includes a **pipeline** 74 in respect of each channel.\\
-• [0169]
+• [0169] The pipeline 74 processes the raw output data representing the measured electrical signal to produce output data representing the results of the biochemical analysis in respect of the corresponding channel.  Interactions between the nanopore and the sample cause characteristic changes in the electrical current that are recognizable events.  Thus, the pipeline 74 detects those events and generates output data that is event data representing those events.  Examples of such processing are disclosed in the [[oxfordfeb202007:start | Feb. 20, 2007 patent]].\\
+• [0169] The **output data** that is event data may in the simplest case represent only the fact that the event has occurred, but more typically includes other information about the event, for example the **magnitude and period of the event**.\\
+• [0170] Additionally, the pipeline may classify the event and output data may represent the classification of the event.  In the context of poly nucleotide measurements this may be referred to as **base calling**.\\
+• [0171] The pipeline also produces output data that is **quality data** representative of the quality of the output data that represents the results of the biochemical analysis.  This may represent a probability of the detection and/or classification of the events being incorrect.\\
+• [0174] The processing module 73 may also derive and store quality control metrics representing parameters of the biochemical analysis itself.\\
+• [0175] Could also do some of the pipeline work on the FPGA 72 on the internal board 50.\\
+=== - The Control Function [0176]-[0203] ===
+• [0176] The control function is distributed between the internal board 50 and embedded computer 51.\\
+• [0177] The control function includes a **controller** 58, for example a [[http://www.arm.com/products/processors/cortex-m/cortex-m3.php|Cortex M3 microcontroller]], provided on the internal board 50.\\
+• [0178] Controller 50 itself controlled by **control module** 80 implemented in embedded computer 51.  50 and 80 communicate via RS232 81.\\
+• [0201] The analysis apparatus 13 (where is this 13?!?!?!) may contain **control DNA** spiked into real samples.  Data from the control DNA can be used to adjust and refine the algorithms.
+==== - Cluster of Modules [0204] - [0243] ====
+==== - Manner of Module Networking [0244] - [0251] ====
+==== - Implementation Examples [0252] - [0260] ====
+==== - Specifics on Sequencing Example 1 [0261] - [0275] ====
+==== - Details of Biochemical Analysis that can be Performed [0276] - [0298] ====
+• [0282] nanopore-assisted sequencing by hydridisation; strand sequencing; and exonuclease-nanopore sequencing\\
+• [0284]  External circuitry can then perform measurements of DNA passing through each and every nanopore in the array **without the synchronization of base addition** to each nanopore in the array, i.e. each nanopore is free to process a single DNA strand independently of every other, for example as disclosed in [[oxforddec192007:start | Dec. 19, 2007 patent]].\\
+• [0284] Having processes one strand, each nanopore is also then free to begin processing a subsequent strand.\\