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

Our Vision

Workflow

流程图

CAST Designer

Cross platform :windows, Linux, iosEasy deposited

Workflow

Regulation Network

Regulation Network to Gene Circuit

Gene 1 Repressor Gene 2

Regulation Network

Gene Circuit

Parameters & Control Panel

promoter

RBS

Plasmid backbone

Repressor/activator

inducer

Parts & Dynamic Parameters

Gene Circuit

Gene Circuit

One gene, one panel

Parts update with dynamic parameters’ alteration

Real-time simulation

A Demo Video

Workflow

1. Deterministic, stochastic and time delay simulations2. Remove the uninterested curve3. Based on powerful models and algorithms

Simulation

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

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

pro

mo

ters

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

Translation: CDSs, RBSs and terminators

𝒅[𝐏𝐫𝐨𝐭𝐞𝐢𝐧]

𝒅𝒕= 𝐓𝐄 × 𝐓𝐞𝐫𝐄 × 𝒎𝑹𝑵𝑨 −𝑫𝒆𝒈𝑷𝒓𝒐[𝑷𝒓𝒐𝒕𝒆𝒊𝒏]

Metabolic networks: enzymatic reactions

𝑑[𝑃]

𝑑𝑡= 𝑉𝑚𝑎𝑥

[𝑆]

𝐾𝑚+[𝑆]

𝒅[𝒑𝒓𝒐𝒕𝒆𝒊𝒏]

𝒅𝒕=

𝑽𝒎𝒂𝒙[𝑺]

(𝑲𝒎+[𝑺])(𝟏 +𝑰𝑲𝑰)

𝒅[𝒑𝒓𝒐𝒕𝒆𝒊𝒏]

𝒅𝒕=

𝑽𝐦𝐚𝐱[𝑺]

𝑲𝒎 𝟏 +𝑰𝑲𝑰+ [𝑺]

Regulation and

Metabolic Networks

Challenge Ⅱ: Evaluation of regulator strength

Cascades

Cyclic circuits

New Iteration Algorithms

Interface

Challenge Ⅲ: The fluctuations of the circuits

𝒅𝒎𝑹𝑵𝑨(𝒕)

𝒅𝒕= 𝜶𝟎 ∙ 𝒎𝐑𝐍𝐀 𝐭 +

𝒌=𝟏

𝒎

𝜶𝒌 ∙ 𝒎𝑹𝑵𝑨(𝒕 − 𝝉𝒌)

Solutions: stochastic and time delay simulations

Time

Co

nce

ntr

atio

n

Challenge Ⅳ: Inconsistent Parameters for Simulation

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

Workflow

Satisfied Simulation Result

Plasmid

Protocol

Protocol

Protocol

Wet-lab Validation

design protocol experiment

We successfully validated our model with wet-lab experiment

Experiment VS. Simulation

We successfully validated our model with wet-lab experiment

Conclusion & Human Practice

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.

Human Practice

TEDx Salon

TEDx Salon

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

Medal RequestBronze MedalRegister 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 toolProvide 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

on their wiki. This tutorial should explain all the features of the tool as well as provide sample input and output as appropriate.Gold MedalTo 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 DevicesThe sharing of BioBrick Parts or Devices, either via physical DNA or as information via the internet.

Best Human Practices Advance

Best New Standard

Special Award

Acknowledgment

Sponsors