Our Vision Apply intelligent models and algorithms, achieve the - - PowerPoint PPT Presentation

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Our Vision Apply intelligent models and algorithms, achieve the - - PowerPoint PPT Presentation

Oct 06, 2022 434 likes •837 views

Our Vision Apply intelligent models and algorithms, achieve the complex system design. Integrate various data and define standard parts, therefore direct wet lab experiment. Workflow CAST Designer Cross platform :windows, Linux,

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Apply intelligent models and algorithms, achieve the complex system design. Integrate various data and define standard parts, therefore direct wet lab experiment.

Our Vision

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Workflow

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流程图 CAST Designer

Cross platform :windows, Linux, ios Easy deposited

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Workflow

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Regulation Network

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Regulation Network to Gene Circuit

Gene 1 Repressor Gene 2

Regulation Network Gene Circuit

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Parameters & Control Panel

promoter RBS

Plasmid backbone Repressor/ activator

inducer

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Parts & Dynamic Parameters

Gene Circuit

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Gene Circuit

One gene,

  • ne panel

Parts update with dynamic parameters’ alteration Real-time simulation

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A Demo Video

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Workflow

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  • 1. Deterministic, stochastic and time delay simulations
  • 2. Remove the uninterested curve
  • 3. Based on powerful models and algorithms

Simulation

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Challenges in Modeling

Challenge Ⅰ： Complex of synthetic circuits Challenge Ⅲ : The fluctuations of the circuits Challenge Ⅳ: Inconsistent parameters for simulation Challenge Ⅱ ：Evaluation of regulator strength

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Challenge Ⅰ：Complex of Synthetic Circuits

Solutions: improved ordinary differential equations (ODEs)

1.Combine regulatory and metabolic ODEs as well as Hill Equations 2.Multi-level modeling

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promoters constitutive inducible

One operon Positive (activator) inducer co-repressor Negative (repressor) inducer co-repressor Two operons

repressor + activator repressor + repressor activator + activator

Level 3: Co-regulators Level 2: Transcription factors Level 1: No regulations

Transcription: Promoters

Regulation and Metabolic Networks

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Translation: CDSs, RBSs and terminators

𝒆[𝐐𝐬𝐩𝐮𝐟𝐣𝐨] 𝒆𝒖 = 𝐔𝐅 × 𝐔𝐟𝐬𝐅 × 𝒏𝑺𝑶𝑩 − 𝑬𝒇𝒉𝑸𝒔𝒑[𝑸𝒔𝒑𝒖𝒇𝒋𝒐]

Metabolic networks: enzymatic reactions

𝑒[𝑄] 𝑒𝑢 = 𝑊 𝑛𝑏𝑦 [𝑇] 𝐿𝑛+[𝑇]

𝒆[𝒒𝒔𝒑𝒖𝒇𝒋𝒐] 𝒆𝒖 = 𝑾𝒏𝒃𝒚[𝑻] (𝑳𝒏+[𝑻])(𝟐 + 𝑱 𝑳𝑱) 𝒆[𝒒𝒔𝒑𝒖𝒇𝒋𝒐] 𝒆𝒖 = 𝑾𝐧𝐛𝐲[𝑻] 𝑳𝒏 𝟐 + 𝑱 𝑳𝑱 + [𝑻]

Regulation and Metabolic Networks

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Challenge Ⅱ: Evaluation of regulator strength

Cascades Cyclic circuits

New Iteration Algorithms

Interface

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Challenge Ⅲ: The fluctuations of the circuits

𝒆𝒏𝑺𝑶𝑩(𝒖) 𝒆𝒖 = 𝜷𝟏 ∙ 𝒏𝐒𝐎𝐁 𝐮 +

𝒍=𝟐 𝒏

𝜷𝒍 ∙ 𝒏𝑺𝑶𝑩(𝒖 − 𝝊𝒍)

Solutions: stochastic and time delay simulations

Time Concentration

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Challenge Ⅳ: Inconsistent Parameters for Simulation

Solutions: develop the data standardization process Output: PoPS and RIPS

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Workflow

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Satisfied Simulation Result

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Plasmid

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Protocol

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Protocol

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Protocol

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Wet-lab Validation

design protocol experiment

We successfully validated our model with wet-lab experiment

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Experiment VS. Simulation

We successfully validated our model with wet-lab experiment

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Conclusion & Human Practice

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Distinctive Features

  • Automatic Design
  • Construct new software system to convert primary idea

into complex gene circuit.

  • Innovative models and algorithms
  • New Iteration Algorithms
  • Improved simulation models for multi-level regulation

and metabolic network.

  • Wet lab experiments
  • Successfully validate our model with a self practice wet

lab experiment.

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Human Practice

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TEDx Salon

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TEDx Salon

We spread the iGEM idea with Sun Yat-sen University students.

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Medal Request

Bronze Medal Register the team, have a great summer, and have fun attending the Regional Jamboree and World Championship Jamboree. Create and share a description of the team's project via the iGEM wiki. Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree. Develop and make available via the The Registry of Software Tools an open source software tool that supports synthetic biology based on BioBrick standard biological parts (remember, the iGEM judges will be looking for substantial team-based software projects). Silver Medal Provide a detailed, draft specification for the next version of your software tool Provide a second, distinct (yet complementary) software tools project. In addition the team must: Provide a demonstration of their software either as a textual or video tutorial made available

  • n their wiki. This tutorial should explain all the features of the tool as well as provide sample

input and output as appropriate. Gold Medal To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:

  • 1. Have another team utilize the software developed by your team. You must clearly show

how your software was used and the results that were obtained.

  • 2b. In place of requirement two, a team may instead use SBOL in your software

documentation.

  • 3a. Develop and document a new technical standard that supports one of the following:

The analysis, modeling, and simulation of BioBrick Parts or Devices The sharing of BioBrick Parts or Devices, either via physical DNA or as information via the internet.

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Best Human Practices Advance Best New Standard

Special Award

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Acknowledgment

Sponsors