Team:SYSU-Software/Design

SYSU-Software:Project

DESIGN

  • Since it is hard to find proper solutions based on cognizant circuits and chassis species when the synthetic biological systems are

  • built in complex environment, referring to basic idea of evolution, using artificial constrains as natural selection pressure and crafting a

  • new system will be a proper way to solve this problem, which provides us the source idea of CRAFT.

  • CRAFT consist of three functional parts including CRAFT Designer, CRAFT Square and Satellite.

  • CRAFT Designer serves as a design platform, generating a synthetic biological system based on users requirements towards this

  • system. Users can examine the genetic circuits, vector construction and simulating curves of this system. CRAFT Designer also provide

  • the users with standard protocols corresponding to their designs, and a channel for experiment data feedback.

  • CRAFT Square is a communication platform, serving for users to share and assistant.

  • Satellite is a distributed computing plug-in of CRAFT, undertaking nearly all calculation missions in CRAFT.

  • CRAFT DESIGNER:

  • Selection in silicon

  • In engineering, two principles, “Bottom top” and “Top down”,

  • have been frequently used when design, which mean design from

  • details to the whole and enrich details from a work frame. How-

  • ever, separately using these two principle in synthetic biology is

  • ineffective because “Bottom top” need designers have thorough

  • cognition of their target objects, while “Top down” is usually

  • overwhelmed by complex details in biological system.

  • “Living organisms have evolved to maximize their chances for

  • survival”

  • To our surprise, evolution have combined this two principles

  • perfectly, with using “Bottom up” in biology variation, generating

  • nearly all solutions for survival, and using “Top down”, when

  • facing natural selection, to delete those irrational solutions based

  • on fitness, making sure the organism have most chances for sur-

  • vival.

  • Referring to the natural evolution, CRAFT Designer was

  • emerged, and in the following, we will illustrate how CRAFT De-

  • signer was designed following evolution and what other functions

  • the users will experience.

  • Craft Customize Synthetic Biological System

  • Users can input multiple targets and set a series of restrictions on them. We also require users to select

  • where they want to set their system and what bacterium have existed in that place. Enumerating all possible

  • solution, simulating the biology variation, CRAFT Designer will generate a large amount of solution systems

  • at the back-end, and filtered with restrictions, simulating the natural selection, the most appropriate systems

  • will be remained and showed to the users.

  • Automatically Generate the Regulatory Elements

  • Based on the restrictions, every solution systems will contain a series of expression elements recom-

  • mended by CRAFT Designer, including promoter and RBS. Users can freely change these elements by drag-

  • ging the bar to change the strength of elements, and our software will estimate suitable elements to re-

  • place previous ones. Users can also examine the circuits in different strains of bacterium, and choose other

  • plasmid backbone.

  • Simulation

  • Life activity of the synthetic biological system can be shown in one chart with curves.

  • Standard Protocol

  • “Design and Redesign” is a consideration in synthetic biology based on standardization parts. Different

  • protocols also have somewhere in common, which means we can apply “Design and Redesign” in protocol

  • generation: abstract the common part of protocols as standard protocol frame and fill them with specific

  • designed system messages.

  • Standard and Scalable Experiment Feedback

  • We design a standard data frame for experiment data feedback, corresponding to previous protocol.

  • This data frame can receive experiment data in any size.

  • CRAFT Square

  • Divergent evolution in silicon

  • Gene and character will change when a specie stay in different

  • environment or ecological niche. Most of these changes occurred

  • on previous genetic basis.

  • This is how CRAFT Square was designed: a user’s system

  • might be referred by other users, which means the system have

  • entered into a new environment, and the others will modify this

  • system to fulfill their requirements, simulating the divergent evo-

  • lution.

  • We will demonstrate more details in CRAFT Square in the

  • following.

  • Share and Evaluation

  • Users can choose whether they want to share their design with others on CRAFT Square. Other

  • users can scan the shared designs and evaluate them. All evaluation will be collected and designs with

  • high score rank higher.

  • Save Duplication

  • Users can choose one design on CRAFT Square and save it. They can modify this design by changing

  • input and strength of regulatory elements, uploading data etc.. After users modifying existed synthetic bio-

  • logical systems, these systems will suit for another “environment” and keep their advantages.

  • Collaboration

  • Users can upload their design to the helping list on CRAFT Square and ask for help. Others can assis-

  • ant those who seek help with sharing computation load or finish validation experiment.

  • Satellite:

  • Responsible for Calculation

  • Since the calculation in CRAFT will occupy large

  • segment of computing resources if settle all calculation

  • missions on web server, we developed this distributed

  • computing plug-in Satellite. Users can download this

  • plug-in to their personal computer and receive

  • computing missions from CRAFT Square according to

  • the number of every design. Satellite thus provides

  • another way for commucation and collaboration between users.