Patents by Inventor Roger Dean Chamberlain

Roger Dean Chamberlain has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 11789965
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a structured format such as a fixed field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Grant
    Filed: April 13, 2020
    Date of Patent: October 17, 2023
    Assignee: IP Reservoir, LLC
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Publication number: 20210304848
    Abstract: Apparatuses and methods are disclosed for comparing a first biosequence string with a second biosequence string to assess similarity between those biosequence strings. For example, a field programmable gate array (FPGA) can be used to (1) detect substrings of the second biosequence string that are matches to substrings of the first biosequence string, and (2) map the detected substrings of the second biosequence string to corresponding positions in the first biosequence string where the detected substrings are located based on a data structure that links substrings of the first biosequence string to positions in the first biosequence string where the substrings of the first biosequence string are located. These operations can be used to seed an alignment between the first and second biosequence strings that permits comparisons to be performed over longer substrings of the first and second biosequence strings so that similarities between those longer substrings can be quantified.
    Type: Application
    Filed: March 23, 2021
    Publication date: September 30, 2021
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Patent number: 10957423
    Abstract: Apparatuses and methods are disclosed for comparing a first biosequence string with a second biosequence string to assess similarity between those biosequence strings. For example, a field programmable gate array (FPGA) can be used to (1) detect substrings of the second biosequence string that are matches to substrings of the first biosequence string, and (2) map the detected substrings of the second biosequence string to corresponding positions in the first biosequence string where the detected substrings are located based on a data structure that links substrings of the first biosequence string to positions in the first biosequence string where the substrings of the first biosequence string are located. These operations can be used to seed an alignment between the first and second biosequence strings that permits comparisons to be performed over longer substrings of the first and second biosequence strings so that similarities between those longer substrings can be quantified.
    Type: Grant
    Filed: February 28, 2020
    Date of Patent: March 23, 2021
    Assignee: WASHINGTON UNIVERSITY
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Patent number: 10949442
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a mapped variable field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Grant
    Filed: November 29, 2018
    Date of Patent: March 16, 2021
    Assignee: IP Reservoir, LLC
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Publication number: 20200251185
    Abstract: Apparatuses and methods are disclosed for comparing a first biosequence string with a second biosequence string to assess similarity between those biosequence strings. For example, a field programmable gate array (FPGA) can be used to (1) detect substrings of the second biosequence string that are matches to substrings of the first biosequence string, and (2) map the detected substrings of the second biosequence string to corresponding positions in the first biosequence string where the detected substrings are located based on a data structure that links substrings of the first biosequence string to positions in the first biosequence string where the substrings of the first biosequence string are located. These operations can be used to seed an alignment between the first and second biosequence strings that permits comparisons to be performed over longer substrings of the first and second biosequence strings so that similarities between those longer substrings can be quantified.
    Type: Application
    Filed: February 28, 2020
    Publication date: August 6, 2020
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Publication number: 20200242126
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a structured format such as a fixed field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Application
    Filed: April 13, 2020
    Publication date: July 30, 2020
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Patent number: 10621192
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a fixed field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Grant
    Filed: April 17, 2017
    Date of Patent: April 14, 2020
    Assignee: IP Resevoir, LLC
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Patent number: 10580518
    Abstract: A system and method for performing similarity searching is disclosed wherein programmable logic devices such as field programmable gate arrays (FPGAs) can be used to implement Bloom filters for identifying possible matches between a query and data. The Bloom filters can be implemented in a parallel architecture where the different parallel Bloom filters share access to the same memory units. Further, a hash table may be generated to map a set of strings to keys. In other examples, the hash table may be used to map a set of substrings to a position in a larger string.
    Type: Grant
    Filed: January 11, 2017
    Date of Patent: March 3, 2020
    Assignee: WASHINGTON UNIVERSITY
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Publication number: 20190108177
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a mapped variable field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Application
    Filed: November 29, 2018
    Publication date: April 11, 2019
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Patent number: 10146845
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a mapped variable field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Grant
    Filed: October 22, 2013
    Date of Patent: December 4, 2018
    Assignee: IP RESERVOIR, LLC
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Publication number: 20170220655
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a fixed field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Application
    Filed: April 17, 2017
    Publication date: August 3, 2017
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Publication number: 20170124255
    Abstract: A system and method for performing similarity searching is disclosed wherein programmable logic devices such as field programmable gate arrays (FPGAs) can be used to implement Bloom filters for identifying possible matches between a query and data. The Bloom filters can be implemented in a parallel architecture where the different parallel Bloom filters share access to the same memory units. Further, a hash table may be generated to map a set of strings to keys. In other examples, the hash table may be used to map a set of substrings to a position in a larger string.
    Type: Application
    Filed: January 11, 2017
    Publication date: May 4, 2017
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Patent number: 9633093
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a fixed field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Grant
    Filed: October 22, 2013
    Date of Patent: April 25, 2017
    Assignee: IP Reservoir, LLC
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Patent number: 9547680
    Abstract: A system and method for performing similarity searching is disclosed wherein programmable logic devices such as field programmable gate arrays (FPGAs) can be used to implement Bloom filters for identifying possible matches between a query and data. The Bloom filters can be implemented in a parallel architecture where the different parallel Bloom filters share access to the same memory units.
    Type: Grant
    Filed: August 19, 2013
    Date of Patent: January 17, 2017
    Assignee: Washington University
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Publication number: 20140114908
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a fixed field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Application
    Filed: October 22, 2013
    Publication date: April 24, 2014
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Publication number: 20140114929
    Abstract: Various methods and apparatuses are described for performing high speed format translations of incoming data, where the incoming data is arranged in a delimited data format. As an example, the data in the delimited data format can be translated to a mapped variable field format using pipelined operations. A reconfigurable logic device can be used in exemplary embodiments as a platform for the format translation.
    Type: Application
    Filed: October 22, 2013
    Publication date: April 24, 2014
    Inventors: Michael John Henrichs, Joseph M. Lancaster, Roger Dean Chamberlain, Jason R. White, Kevin Brian Sprague, Terry Tidwell
  • Publication number: 20140067830
    Abstract: A system and method for performing similarity searching is disclosed wherein programmable logic devices such as field programmable gate arrays (FPGAs) can be used to implement Bloom filters for identifying possible matches between a query and data. The Bloom filters can be implemented in a parallel architecture where the different parallel Bloom filters share access to the same memory units.
    Type: Application
    Filed: August 19, 2013
    Publication date: March 6, 2014
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Patent number: 8515682
    Abstract: A system and method for performing similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of data strings and a plurality of substrings of a query string. The pipeline may further include an ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.
    Type: Grant
    Filed: March 11, 2011
    Date of Patent: August 20, 2013
    Assignee: Washington University
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Publication number: 20110231446
    Abstract: A system and method for performing similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of data strings and a plurality of substrings of a query string. The pipeline may further include an ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.
    Type: Application
    Filed: March 11, 2011
    Publication date: September 22, 2011
    Applicant: Washington University
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster
  • Patent number: 7917299
    Abstract: An apparatus and method for performing similarity searching on a data stream with respect to a query string are disclosed, where the data stream comprises a plurality of data substrings, and where the query string comprises a plurality of query substrings. A programmable logic device is used to filter the data stream to find a plurality of possible matches between the data substrings and a plurality of the query substrings, wherein the data substrings and the query substrings comprise a plurality of characters. From these possible matches, a determination can be made as to a similarity between the query string and at least a portion of the data stream.
    Type: Grant
    Filed: February 22, 2006
    Date of Patent: March 29, 2011
    Assignee: Washington University
    Inventors: Jeremy Daniel Buhler, Roger Dean Chamberlain, Mark Allen Franklin, Kwame Gyang, Arpith Chacko Jacob, Praveen Krishnamurthy, Joseph Marion Lancaster