System for generating genomics data, and device, method and software product for use therein

A system 900 for generating output genomics data 970 from biological genetic material 930 includes: a genetic reading apparatus 910 which is operable to read bases included in the biological genetic material 930 to generate a genome sequence read, wherein the genome sequence read comprises at least one sequence of bases and associated quality scores; and a data processing apparatus 950 for processing the genome sequence read to generate the output genomics data 970, characterized in that the data processing apparatus 950 is operable: to determine similarity criteria (300, fig. 4a) for performing searching in a reference genome corpus (310); to perform a search of the at least one sequence of bases in the reference genome corpus (310), based upon the similarity criteria (300); to calculate (330) an adjustment for one or more of the associated quality scores, based upon results of the search (320); and to adjust one or more of the associated quality scores according to the calculated adjustment ...

SYSTEM AND METHOD FOR TRANSFORMING AND COMPRESSING GENOMICS DATA

This invention relates to the quality scores of bases produced from high throughput genomic sequencing, in particular to transforming the quality scores for improved compressibility. A method for transforming these quality scores is described whereby a quality score is modified by utilising a Bayesian model based on Coding Theory combined with search results from a genomic corpus. A related method is described for efficient searching for a Read in a genomic corpus so as to find all matching symbols up to a given Hamming-distance or Edit-distance.

System and method for compressing data using asymmetric numeral systems with probability distributions

A data compression method using the range variant of asymmetric numeral systems to encode a data stream, where the probability distribution table is constructed using a Markov model. This type of encoding results in output that has higher compression ratios when compared to other compression algorithms and it performs particularly well with information that represents gene sequences or information related to gene sequences.

SYSTEM AND METHOD FOR COMPRESSING DATA USING ASYMMETRIC NUMERAL SYSTEMS WITH PROBABILITY DISTRIBUTIONS

A data compression method using the range variant of asymmetric numeral systems to encode a data stream, where the probability distribution table is constructed using a Markov model. This type of encoding results in output that has higher compression ratios when compared to other compression algorithms and it performs particularly well with information that represents gene sequences or information related to gene sequences. 1. A method for encoding a data stream using a rANS technique , wherein the rANS technique utilizes a probability distribution table that is constructed using a Markov model.2. The method according to claim 1 , further comprising utilizing a plurality of probability distribution tables claim 1 , wherein each of the plurality of distribution tables is constructed from a subset of the data stream.3. The method according to claim 2 , wherein each of the plurality of distribution tables is used to encode another subset of the data stream.4. The method according to claim 1 , wherein the probability distribution table is extended with an escape code to form an extended probability distribution table claim 1 , wherein the escape code is used to mark a temporary switch to a secondary probability distribution table for encoding transitions or symbols in the data stream that cannot be encoded using said probability distribution table.5. The method according to claim 1 , wherein the said probability distribution table is saved in non-volatile storage in a compressed format.6. The method according to claim 1 , wherein said data stream represents information containing gene sequences or other related information.7. A system for encoding a data stream using a rANS technique claim 1 , comprising:computing hardware configured to utilize a probability distribution table in the rANS technique that is constructed using a Markov model; anda non-volatile storage.8. The system as set forth in claim 7 , wherein the computing hardware is further configured to utilize a ...

Touch Sensing Using Shadow and Reflective Modes

A touch panel is described which uses at least one infrared source and an array of infrared sensors to detect objects which are in contact with, or close to, the touchable surface of the panel. The panel may be operated in both reflective and shadow modes, in arbitrary per-pixel combinations which change over time. For example, if the level of ambient infrared is detected and if that level exceeds a threshold, shadow mode is used for detection of touch events over some or all of the display. If the threshold is not exceeded, reflective mode is used to detect touch events. The touch panel includes an infrared source and an array of infrared sensors. 1. A method of operating a touch panel system for detecting one or more objects in proximity with a touchable surface of a touch panel , the method comprising:scanning at least a portion of the touch panel to measure a level of ambient infrared radiation using at least one infrared sensor;switching to a shadow mode of operation if a level of ambient infrared radiation exceeds a first threshold,switching to a reflective mode of operation if the level of ambient infrared radiation does not exceed both the first threshold and a second threshold, wherein the switching between the shadow mode and the reflective mode changes an angle of illumination of an object adjacent to the touch panel; anddetermining the three-dimensional shape and thickness of the object based in part on the changes in the angle of illumination.2. The method of claim 1 , further comprising:determining that a battery level is below a predetermined limit while the level of ambient infrared radiation exceeds the second threshold and not the first threshold; andswitching to the shadow mode of operation after the battery level drops below the predetermined limit.3. The method of claim 2 , further comprising switching to the reflective mode of operation after the battery level rises above the predetermined limit.4. The method according to claim 1 , wherein ...

VIRTUALISATION SYSTEM

This invention relates to virtualised systems, in particular to portable virtualised systems whereby a user is able to transfer their desktop environment from one computing machine to another. A method of providing a transferable computing environment between a computing machine and a portable storage device is described whereby the operational state of the computing environment is maintained after the transfer. A virtual machine is portioned into a common portion and a second portion, the second portion storing a state of operation of the virtual machine and the state of applications. The second portion is transferred to a computing machine to be used in combination with the common portion of the virtual machine already residing on the computing machine. 1. A method of providing a transferable computing environment , wherein said computing environment is operable on a first , computing machine and is able to be transferred to a second , portable device , and wherein said transfer retains an operational state of said computing environment , the method comprising:providing a said first computing machine, wherein said first computing machine has a host operating system and a virtual machine monitor running on said host operating system;providing a plurality of virtual machines each able to run on said virtual machine monitor, wherein each said virtual machine includes a guest operating system to run using said virtual machine and an application residing in said virtual machine;portioning each said virtual machine into first and second portions, wherein said first portion of said virtual machine comprises at least a common portion of said virtual machines shared between said plurality of virtual machines, said common portion including at least a common part of said guest operating system, and wherein said second portion of said virtual machine comprises application state data defining a state of operation of said application specific to operation of the application in ...

SYSTEM AND METHOD FOR STORING AND ACCESSING DATA

A method of structuring data in a virtual file system, includes using the file system to apply specific handling of data that represents genomic sequence information or information that is related to genomic sequences. The method also concerns portioning the data into a collection of storage devices that have different cost and performance characteristics, wherein the splitting policy is based on a cost model. The method is executable by employing a computing device functioning under software control. 1. A method of providing data by utilising a virtual file system , wherein the data represents genome sequence information or information related to genome sequences , wherein the virtual file system includes a front-end and a back-end , wherein the method includes:(i) presenting the data in one or more file formats to the front-end of the virtual file-system; and(ii) recording the data in one or more machine readable data storage media of the back-end of the virtual file-system, wherein the data when stored is structured in a different file format in comparison to the one or more file formats used in the front-end of the virtual file-system.2. A method of portioning data and recording the portioned data in a plurality of machine readable data storage media , wherein the data represents genome sequence information or information related to genome sequences , wherein the method comprises:(i) portioning the data into a plurality of data portions according to a cost model that utilises genomic attributes;(ii) assigning each portion into one or more of the plurality of machine readable data storage media; and(iii) recording the data portions into each assigned machine readable data storage media.3. A method as claimed in claim 2 , wherein in step (ii) claim 2 , the method includes compressing the data portions.4. A method as claimed in claim 2 , wherein the method includes using a virtual file system that includes a front-end and a back-end claim 2 , wherein the method ...

SYSTEM FOR GENERATING GENOMICS DATA, AND DEVICE, METHOD, AND SOFTWARE PRODUCT FOR USE THEREIN

There is provided a system () for generating output genomics data () from biological genetic material (). The system () includes: (i) a genetic reading apparatus () which is operable to read bases included in the biological genetic material () to generate a genome sequence read, wherein the genome sequence read comprises at least one sequence of bases and associated quality scores; and (ii) a data processing apparatus () for processing the genome sequence read to generate the output genomics data (), characterized in that the data processing apparatus () is operable: (a) to determine similarity criteria () for performing searching in a reference genome corpus (); (b) to perform a search of the at least one sequence of bases in the reference genome corpus (), based upon the similarity criteria (); (c) to calculate () an adjustment for one or more of the associated quality scores, based upon results of the search (); and (d) to adjust one or more of the associated quality scores according to the calculated adjustment from (c). 1900970930900. A system () for generating output genomics data () from biological genetic material () , wherein the system () includes:{'b': 910', '930, '(i) a genetic reading apparatus () which is operable to read bases included in the biological genetic material () to generate a genome sequence read, wherein the genome sequence read comprises at least one sequence of bases and associated quality scores; and'}{'b': 950', '970, '(ii) a data processing apparatus () for processing the genome sequence read to generate the output genomics data (),'}{'b': '950', 'characterized in that the data processing apparatus () is operable{'b': 300', '310, '(a) to determine similarity criteria () for performing searching in a reference genome corpus ();'}{'b': 310', '300, '(b) to perform a search of the at least one sequence of bases in the reference genome corpus (), based upon the similarity criteria ();'}{'b': 330', '320, '(c) to calculate () an adjustment ...

Touch sensing using shadow and reflective modes

A touch panel is described which uses at least one infrared source and an array of infrared sensors to detect objects which are in contact with, or close to, the touchable surface of the panel. The panel may be operated in both reflective and shadow modes, in arbirary per-pixel combinations which change over time. For example, if the level of ambient infrared is detected and if that level exceeds a threshold, shadow mode is used for detection of touch events over some or all of the display. If the threshold is not exceeded, reflective mode is used to detect touch events. The touch panel includes an infrared source and an array of infrared sensors.

Touch sensing using shadow and reflective modes

A touch panel is described which uses at least one infrared source and an array of infrared sensors to detect objects which are in contact with, or close to, the touchable surface of the panel. The panel may be operated in both reflective and shadow modes, in arbirary per-pixel combinations which change over time. For example, if the level of ambient infrared is detected and if that level exceeds a threshold, shadow mode is used for detection of touch events over some or all of the display. If the threshold is not exceeded, reflective mode is used to detect touch events. The touch panel includes an infrared source and an array of infrared sensors.

System for generating genomics data, and device, method, and software product for use therein

There is provided a system (900) for generating output genomics data (970) from biological genetic material (930). The system (900) includes: (i) a genetic reading apparatus (910) which is operable to read bases included in the biological genetic material (930) to generate a genome sequence read, wherein the genome sequence read comprises at least one sequence of bases and associated quality scores; and (ii) a data processing apparatus (950) for processing the genome sequence read to generate the output genomics data (970), characterized in that the data processing apparatus (950) is operable: (a) to determine similarity criteria (300) for performing searching in a reference genome corpus (310); (b) to perform a search of the at least one sequence of bases in the reference genome corpus (310), based upon the similarity criteria (300); (c) to calculate (330) an adjustment for one or more of the associated quality scores, based upon results of the search (320); and (d) to adjust one or more of the associated quality scores according to the calculated adjustment from (c).

Communication with a touch screen

A touch panel is arranged to enable communication using infrared signals with nearby devices. The touch panel includes an array of infrared sensors, arranged parallel to the touchable surface of the panel and at least one of the sensors is capable of detecting an infrared signal received from a nearby device.

System and method for storing and accessing data

A method of structuring data in a virtual file system, includes using the file system to apply specific handling of data that represents genomic sequence information or information that is related to genomic sequences. The method also concerns portioning the data into a collection of storage devices that have different cost and performance characteristics, wherein the splitting policy is based on a cost model. The method is executable by employing a computing device functioning under software control.

Sistema y método para transformar y comprimir datos genómicos

Un método implementado en ordenador para ajustar la puntuación de calidad de una base de secuencia genómica (Sj) en una lectura de secuencia genómica (S), comprendiendo el método: realizar una búsqueda de secuencias dentro de una distancia determinada o preseleccionada de la lectura de secuencia genómica (S) en un cuerpo genómico que comprende n-meros (R) de un genoma de referencia para dicha lectura genómica, en donde dicha distancia es una distancia de Hamming o una distancia de edición; basándose en los resultados de dicha búsqueda, realizar cálculos de una nueva puntuación de calidad para dicha base de secuencia genómica (Sj) en dicha lectura (S) estimando la probabilidad de que la base (Sj) en la lectura (S) tenga un error de secuenciación (Pr(Sj ≠ Zj | S)) como: **(Ver fórmula)** en donde L indica el conjunto de n-meros (Rk€L) dentro de dicha distancia, m indica una probabilidad de mutación, ej indica la probabilidad de un error de lectura en la base (Sj) y β es una estimación de la contribución de n-meros que no están dentro de dicha distancia; y sustituir la puntuación de calidad antigua con la nueva puntuación de calidad si la nueva puntuación de calidad es mejor que la puntuación de calidad antigua.

System and method for transforming and compressing genomics data

Communication with a touch screen

A touch panel is arranged to enable communication using infrared signals with nearby devices. The touch panel includes an array of infrared sensors, arranged parallel to the touchable surface of the panel and at least one of the sensors is capable of detecting an infrared signal received from a nearby device.