Team:SYSU-Software/Design
Synbio Hub & CORE Design:
Platform for community with useful integrations
Synbio Hub is a proof-of-principle standard bank of genetic design and crowdsourcing platform designed specifically for synthetic biology community. Collaborative construction of genetic design is made possible with the help of powerful integrations —CORE Design. By using CORE Design, you can re-use and re-design the project bank in CORE Bank, and crowdsource your design to the public in search of a better solution in the Co-development module. In the Co-development module, you can get, give and share your answers, vote for your favourite design, and designs with the highest performance (and hopefully stand the test of time) will migrate to CORE Bank for storage. CORE Design is also a powerful integration for mathematical modeling, data processing and plotting, plasmid construction, experiment scheduling and protocol management.
New methods for collaboration in Synbio: Crowdsourcing
For a long time, collaboration has been limited to two teams and does not open to the public. However, many difficult problems could have been more easily tackled with the help of collective intelligence in the Synbio community.Therefore, crowdsourcing might help. Henk van Ess once defiend crowdsourcing.
Obviously, in Synbio crowdsourcing helps uncouple difficult genetic designs into easier one, and via collaborative construction of these simpler ones, one can assemble a complete circuits.
So how would crowdsourcing help the practices in Synbio? How does Co-development employ the theory of crowdsourcing to help in genetic design?
1. Communication leads to great collaboration.
Most of us have experience in Q & A (Question and answer) platform. It is a good way for communication between experts and non-technical individuals. Hence, in CORE we adopt this user-friendly way as blueprints. Users can ask questions, answer them, remark and comment on the genetic designs, and so on. iGEMers can use this platform to communicate, and the connections between iGEM teams around the world is closer still.
2. Crowdsourcing and collaborative construction of genetic design.
Co-development is NOT JUST a Q & A platform. It is a well-designed platform for synthetic biologists. According to the principle of modular design, a complex network design can be separated into several relatively independent modules. So if you have problems designing one modules of a complex network, you can outsource this module to other iGEMers or synthetic biologists, seek help and tackle problems together. You can also give your answer — the design, together with many other synthetic biologists in the community.
3. Rate the design.
We encourage everyone to share their answers — the designs. For one particular question, there might be more than one answer; how can we identify which one is better? The rating system in CORE might help you. This time, the rating system depends on the grade given by every user. You can vote for your favourite (and also the most reliable) design and CORE uses the radar map to map out the average ratings by different users.
CORE bases crowdsourcing on the user-friendly Q & A platform, and is well-designed for synthetic biologists in that it provides users a platform for collaborative construction of genetic designs, and share, rate and visualize the performance of the designs.
Standardized “Synbio Hub” Bank: “Open Source” Synbio
GitHub is a successful repository for open source software. It contains several features: hosting projects, integrated issue tracking, collaborative review and easy management. These features are also applicable to Synbio and in iGEM. For instance, there were so many great projects from 2004 to 2014 in iGEM. These projects were documented in the team wiki, with different formats and styles. Information on these is scattered in the wiki, making them difficult to use and re-use.
So, how can these features apply to Synbio? There are two important components in GitHub: the bank, and the collaborative code review and management.
The most important one is the bank: in general it is for open source projects, and invites everyone to share, use and modify the codes. This features help make software development more collaborative.
CORE employs the idea of “repository” from “GitHub”, and adjusts this idea to the standardized bank of genetic design of teams. This idea is implemented as CORE Bank, a bank for genetic designs.
1. Standardized documentation of genetic design.
In CORE Bank, every single documentation of genetic design contains four parts: Description, Modeling, References and User Reviews. These four parts constitutes the standard documentation of genetic design.
2. SBOLv made sharing easier.
Every genetic design is represented using SBOLv standard; it is a standard that supports the specification and exchange of genetic design information in synthetic biology. With SBOLv in CORE, design sharing is made easier.
3. Safer exchanging and sharing of genetic design.
In the bank, there might be genetic designs with unknown safety problems. These safety problems might be new to CORE, and are hard to identify. Hence, we crowdsource the task of evaluating safety level of a genetic design to the community; users can vote for five aspects of the performance of a circuits, and one of the aspect is “Safety”.
4. Machine learning algorithms help choose design that stands the test of time.
In Co-development, every user can vote for their favourite design based on five aspects as mentioned.
Machine learning algorithms will help. Machine learning uses supervised algorithms to learn the
weights of different aspects for genetic design that can be moved into CORE Bank and that cannot
be. After that, when new designs are created and a substantial number of users have voted for the
circuits on the five aspects, CORE will use the weights learn from previous designs to decide
which one can be moved into Bank. For more details, please see “Documentation/Back-end”.
CORE Bank aims at documenting every design in a standardized way and through bank of the projects helps the design, re-design and re-use of projects. So get inspirations on this bank!
Genetic Design and Wet-lab Assistance
Roberta Kwok has pointed out that in Synbio, five challenges remain: 1) many of the parts are undefined; 2) the circuitry is unpredictable; 3) the complexity is unwieldy; 4) many parts are incompatible; 5) variability crashes the system. Synbio is the application of engineering principles on biology, and by strictly using these engineering principles one can fulfill the powerful potentials of synthetic biology in genetic design.
1. Abstraction and Design Hierarchy.
Synthetic biology has abstracted biological systems into four levels: DNA, parts, devices and systems (Drew, 2005). By designing complex systems following up the four levels, one might easily design biological components of higher-level based on the lower-level ones. In CORE, we abstracted the genetic design of previous years into basic units — parts. Through the use of these parts, we assembled many genetic devices like AND Gates. (Sprinzak & Elowitz, 2005). The devices are the basis of genetic design in CORE.
2. Design based on biological devices.
It is a common sense that starting from the scratch is (nearly) always the most laborious ones. If we already have a genetic design and want to modify, and we want to use another parts of higher performance, what should we do? In CORE, we can design circuits based on the previous project! For instance, starting from the projects with motility function and a biosensor, we can make a design that make bacteria gather aroundcertain stimulation.
3. Uncoupling of genetic design.
If we have difficulties designing a complex network, you can just use CORE Design to design only the easiest parts, and then crowdsource the other parts to the public. The theory of modular design helps us uncoupling a complex circuit and does their separate jobs.
4. Standardization:
Compatible to standard assembly methods and assembly standard (RFC 10) in the Plasmid module. Use of SBOL (v) standard helps information parsing and exchanging.
1. Data processing and mathematical modeling:
Modeling module support synthetic biology by generating a simulative plot of expression in a circuit thus provides a reference for biologists. Data processing module makes it easier to visualize the data and allows users to skip quickly between data and design.
2. Plasmid viewer:
The Plasmid module can support synthetic biology by support the use of biological parts in construction of plasmid, and support the use of standard preffix and suffix in biological parts.
3. Experiment scheduling and protocol managements:
This module lists protocols and schedules in a clear way, which help users better understand what to do and make better use of their time. Protocols and schedules can also be editted in order to meet different requirements.