Medals

Bronze

The following 4 goals must be achieved:

1.Register the team, have a great summer, and have fun attending the Jamboree in Boston.

Early this year we have registered the team and in summer our team did our best to collect data in literature and the Registry to build our database.

2.Create and share a description of the team's project via the iGEM wiki.

We already gave a brief but overall introduction to our team’s project in the iGEM wiki. In addition we have always been checking and improving our wiki.

3.Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.

Yes. Our Wiki designer also designed beautiful posters for this wonderful academic journey.

4.Develop and make available via The Registry of Software Tools, an open source software tool that supports Synthetic Biology based on Standard Parts.

Yes. We developed our software via The Registry of Software Tools.

Silver

In addition to the Bronze Medal requirements, the following 4 goals must be achieved:

1.Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.

Based on frameworks, FLAME utilizes standard parts on Registry to construct theoretically reliable circuits and/or systems. In addition, although many biological parts and devices have been standardized by synthetic biologists and iGEMers, there are still not enough characterized and standardized circuits or systems that can be used in a plug-and-play fashion to facilitate construction of larger networks. So we propose that circuits and/or systems could be characterized and standardized in a way similar to parts and devices, and the Simulation module may help users accomplish this task.

2.Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)

Our User Guides are informative and detailed. We make it as straightforward and interesting as possible in order to help users quickly master FLAME. We also recorded a video as an introduction to FLAME.

3.Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, hetc).

Yes. We have already provided the API documents.

4.Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage , bug tracking facilities, documentation of releases and changes between releases.

Yes, for example, bug tracking facilities of our software can be seen in the Github (https://github.com/igemsoftware/SYSU-Software_2014), where documentation of releases and changes between releases are there. More information about realistic test cases is on "Validation" page.

Gold

In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved:

1.Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.

Experiments and data from papers have been done to test and verify the algorithms adopted by our software. In addition, efficiency as well as accuracy was validated in a variety of ways. For more details please see "PROJECT-Validation" page.

And the second goal can be any one of the following:

1.Make your software interact / interface with the Registry.

In FLAME, construction of circuits and/or systems is based on standard biobricks on the Registry. Furthermore, users can search for their needed biobricks from Registry in FLAME.

2.Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks.

For one thing, we learned from CAST (developed by our team in 2013) and tried our best to improve the latest software, FLAME. For example, FLAME uses new models, which are still based on ordinary differential equations (like CAST) but can work more efficiently because new models rely less on complicated computation.

For another, we propose that we could characterize and standardize a circuit or system with methods already adopted by synthetic biologists to characterize and standardize a biological part or device, which could probably be viewed as improvements of existing synthetic biology frameworks. Simulation module in FLAME provides important clues on the performance of a circuit or system.

For more details, please see "Overview" and "Design".

3.Develop a well-documented library or API for other developers (rather than “only” a stand-alone app for end users.)

Yes. We have developed a detailed API document.

4.Support and use the SBOL and / or SBOLv standard.

Still in progress at the time wiki freezes.

5.iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. Describe an approach that your team used to address at least one of these questions. Evaluate your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.

Based on the principles of sustainability, we established a platform inside our software where researchers can search related biobricks and papers and furthermore share them with others. We also encourage users to upload their results after using our software, as can be easily found in history list or user profile, so that every biological circuit design can be an inspiration for other users and help concentrate their attention on more creative work. Moreover, with the help of simulation in our software, researchers are informed ahead of real experiments of possible results and cautions and thus avoid unnecessary experiments and wastes.

As for the issue of safety, construction of genetic circuits and/or systems is based on a limited but sufficient number of biological parts (such as LacI and/or TetR ). These biological parts have been adopted by synthetic biologists and iGEMers for years, and their safety has been evaluated. It is relatively safe to use these biological parts to design and build circuits and/or systems. In addition, FLAME is based on frameworks. Frameworks originate from synthetic circuits (such as toggle switch) reported in literature, after years of evaluation and improvements by synthetic biologists, there should be little safety concerns. In sum, we will improve our software further regarding sustainability, safety and environmental protection and help serve iGEM community.