Team:SYSU-Software/require

Bronze Medal
1. Register the team, have a great summer, and have fun attending the Jamboree.
2. Create and share a description of the team's project via the iGEM wiki.
3. Present a Poster and Talk at the iGEM Jamboree.
4. 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
To earn a Silver Medal, in addition to the Bronze Medal requirements, a team must do ONE of the following
We have done both.
1. Provide a detailed, draft specification for the next version of your software tool.
We plan to improve our software tool in several aspects presented below: First, the regulation network of E.coli would be introduced and simulated by our next version of software so that interaction between artificial genes and host metabolism could be considered during creature design. Second, Biobrick designer for riboswitch and riboregulator would be added, moreover, regulators’ dynamic characteristics would be predicted by our software and directly used in circuit design. Third, we would construct interface to programmable laboratory instruments so that the experimental process would be more automated and standardization.
2. Provide a second, distinct (yet complementary) software tools project.
We have provided a lovely flash game to introduce basic concept of synthetic biology and it is located on our wiki page.
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.
A(presented on wiki)

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.
Using our database functions, Team SYSU-China's biobrick designs are shared among team members and output as SBOL format file which can be delivered through Internet during their experiment.
2a. Outline and detail how your software effects Human Practices in Synthetic Biology. Such topics include: safety, security, ethics, or ownership, sharing, and innovation.
OR
2b. In place of requirement two, a team may instead use SBOL in your software documentation.
All the Biobricks data from our software’s database could be expressed in SBOL format.

PLUS
3a. Develop and document a new technical standard that supports one of the following:
1. design of BioBrick Parts or Devices
2. construction of BioBrick Parts or Devices
3. characterization of BioBrick Parts or Devices
4. the analysis, modeling, and simulation of BioBrick Parts or Devices
We have developed a simulation system that every regulatory element is given several standard dynamic parameters. Thus most gene expression process can be simulated with our system. Furthermore, newly found element can be also definited with these parameters to be simulated. 5. the sharing of BioBrick Parts or Devices, either via physical DNA or as information via the internet.
We are providing the improved SBOL format for Biobrick sharing. We combined several standard dynamic information for different type of Biobricks with other tradition information and hopefully it would lead to a new era of quantitative design.
OR
3b. Build upon existing software from a previous iGEM competition found on the The Registry of Software Tools

Special Award
1.Best Human Practices Advance: Will the world be a safe place if we make biology easy to engineer? How do the lessons of the past inform the discussion going forward? Think beyond just convincing people that “synthetic biology is good.” Find a new way to help human civilization consider, guide, and address the impacts of ongoing advances in biotechnology.

We not only constructed an online game for spreading basic concepts of synthetic biology, but also held a TEDxSYSU project to introduce the origin and development about synthetic biology.
2.Best Model: Mathematical models and computer simulations provide a great way to describe the functioning and operation of BioBrick Parts and Devices.

To fulfil the concept of quantitative design, we introduced a brand new model to simulate Biobricks’ function and operation. Details are shown on our wikipage.

3.Best New Standard: Standards help to make sharing biological parts easier. For example, the BioBrick DNA assembly standard makes it easier to construct parts from pre-existing parts created by the entire BioBrick community. What other sorts of standards can you create? How about a standard system for measuring promoter activity, a standard method for reporting compatible/ incompatible parts, a standard to help describe and control post-translational modifications (such as phosphorylation), or chassis-specific standards (for instance, a system for describing and sharing transgenic yeast)?
We are providing the improved SBOL format for Biobrick sharing. We combined several standard dynamic information for different type of Biobricks with other tradition information. Moreover, we apply JSON format instead of XML to interact with web application more easily and be transmitted faster.