SG11201610126RA - Systems and methods for synthetic biology design and host cell simulation - Google Patents

Systems and methods for synthetic biology design and host cell simulation

Info

Publication number
SG11201610126RA
SG11201610126RA SG11201610126RA SG11201610126RA SG11201610126RA SG 11201610126R A SG11201610126R A SG 11201610126RA SG 11201610126R A SG11201610126R A SG 11201610126RA SG 11201610126R A SG11201610126R A SG 11201610126RA SG 11201610126R A SG11201610126R A SG 11201610126RA
Authority
SG
Singapore
Prior art keywords
systems
methods
host cell
synthetic biology
cell simulation
Prior art date
Application number
SG11201610126RA
Inventor
Premkumar Jayaraman
Chueh Loo Poh
hui juan Wang
Original Assignee
Univ Nanyang Tech
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Univ Nanyang Tech filed Critical Univ Nanyang Tech
Publication of SG11201610126RA publication Critical patent/SG11201610126RA/en

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Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/11—Complex mathematical operations for solving equations, e.g. nonlinear equations, general mathematical optimization problems
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/30—Dynamic-time models
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Physiology (AREA)
  • General Physics & Mathematics (AREA)
  • Mathematical Physics (AREA)
  • Computational Mathematics (AREA)
  • Mathematical Analysis (AREA)
  • Pure & Applied Mathematics (AREA)
  • Mathematical Optimization (AREA)
  • Data Mining & Analysis (AREA)
  • Biochemistry (AREA)
  • Computing Systems (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Library & Information Science (AREA)
  • General Engineering & Computer Science (AREA)
  • Algebra (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Operations Research (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
SG11201610126RA 2014-06-27 2015-06-19 Systems and methods for synthetic biology design and host cell simulation SG11201610126RA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201462018078P 2014-06-27 2014-06-27
PCT/SG2015/050169 WO2015199614A1 (en) 2014-06-27 2015-06-19 Systems and methods for synthetic biology design and host cell simulation

Publications (1)

Publication Number Publication Date
SG11201610126RA true SG11201610126RA (en) 2017-01-27

Family

ID=54938549

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201610126RA SG11201610126RA (en) 2014-06-27 2015-06-19 Systems and methods for synthetic biology design and host cell simulation

Country Status (5)

Country Link
US (1) US20170147742A1 (en)
EP (1) EP3161697A4 (en)
CN (1) CN106663146A (en)
SG (1) SG11201610126RA (en)
WO (1) WO2015199614A1 (en)

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* Cited by examiner, † Cited by third party
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US9988624B2 (en) 2015-12-07 2018-06-05 Zymergen Inc. Microbial strain improvement by a HTP genomic engineering platform
CA3007635A1 (en) 2015-12-07 2017-06-15 Zymergen Inc. Promoters from corynebacterium glutamicum
US11208649B2 (en) 2015-12-07 2021-12-28 Zymergen Inc. HTP genomic engineering platform
WO2018005655A2 (en) 2016-06-30 2018-01-04 Zymergen Inc. Methods for generating a bacterial hemoglobin library and uses thereof
KR102345898B1 (en) 2016-06-30 2022-01-03 지머젠 인코포레이티드 Methods for generating glucose permeabilization enzyme libraries and uses thereof
US11359234B2 (en) 2016-07-01 2022-06-14 Microsoft Technology Licensing, Llc Barcoding sequences for identification of gene expression
US10892034B2 (en) 2016-07-01 2021-01-12 Microsoft Technology Licensing, Llc Use of homology direct repair to record timing of a molecular event
WO2018005117A1 (en) 2016-07-01 2018-01-04 Microsoft Technology Licensing, Llc Storage through iterative dna editing
KR20190113800A (en) * 2017-02-15 2019-10-08 지머젠 인코포레이티드 Bioreachable Prediction Tool
GB201810636D0 (en) * 2018-06-28 2018-08-15 Microsoft Technology Licensing Llc Dynamic characterisation of synthetic genetic circuits in living cells
WO2020005628A1 (en) * 2018-06-28 2020-01-02 Microsoft Technology Licensing, Llc Dynamic characterization of synthetic genetic circuits in living cells
US11393555B1 (en) * 2018-09-06 2022-07-19 X Development Llc Dynamic coordinating framework for model cell simulations
GB201900742D0 (en) 2019-01-18 2019-03-06 Microsoft Technology Licensing Llc Modelling ordinary differential equations using a variational auto encoder
CN110656121B (en) * 2019-10-29 2022-04-29 江南大学 Method for regulating and controlling cell size of escherichia coli
US20220036975A1 (en) * 2020-07-29 2022-02-03 X Development Llc Kinematic modeling of biochemical pathways
CN112562782B (en) * 2020-12-16 2024-02-09 中国科学院深圳先进技术研究院 Construction method of synthetic gene loop model
US11797274B2 (en) * 2021-06-22 2023-10-24 Altered State Machine Limited Interoperable composite data units for use in distributed computing execution environments

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2342664A1 (en) * 2008-09-03 2011-07-13 Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. Computer implemented model of biological networks
EP2465946B1 (en) * 2009-06-08 2016-10-05 Korea Research Institute of Bioscience and Biotechnology Method for screening and quantifying various enzyme activities using a genetic enzyme screening system
US9697460B2 (en) * 2009-11-30 2017-07-04 Trustees Of Boston University Biological analog-to-digital and digital-to-analog converters
EP2577535A4 (en) * 2010-06-02 2014-10-22 Univ Texas Methods and systems for simulations of complex biological networks using gene expression indexing in computational models
WO2014015196A2 (en) * 2012-07-18 2014-01-23 The Board Of Trustees Of The Leland Stanford Junior University Techniques for predicting phenotype from genotype based on a whole cell computational model
JP6419082B2 (en) * 2012-12-13 2018-11-07 マサチューセッツ インスティテュート オブ テクノロジー Recombinase-based logic / memory system
US20140180660A1 (en) * 2012-12-14 2014-06-26 Life Technologies Holdings Pte Limited Methods and systems for in silico design

Also Published As

Publication number Publication date
EP3161697A4 (en) 2018-03-14
US20170147742A1 (en) 2017-05-25
CN106663146A (en) 2017-05-10
EP3161697A1 (en) 2017-05-03
WO2015199614A1 (en) 2015-12-30

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