Gold Medal

To earn a Gold Medal, in addition to the Silver Medal requirements, a team must:

1.Have another team utilized the software developed by your team. You must clearly show how your software was used and the results that were obtained?

XMU-China used our software to kee their experimental records and put them on their wiki.

2a. Outline and detail how your software effects Human Practices in Synthetic Biology. Such topics include: safety, security, ethics, or ownership, sharing, and innovation.

Link to Safety Questions 

Link to E' NOTE effects on Human Practices

OR

2b. In place of requirement two, a team may instead use SBOL in your software documentation.

The sequences, written by SBOL, can be input into Brick Worker to be optimized.

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
5. the sharing of BioBrick Parts or Devices, either via physical DNA or as information via the internet.

Brick Worker fulfils first 4 tasks with BioBrick Parts.

E' NOTE can share lab journals and other information within a team or a group via the Internet.

OR

3b. Build upon existing software from a previous iGEM competition found on the The Registry of Software Tools

Brick Worker expands the evaluation range of SUSCT-Shenzhen-B, by which we can optimize all kinds of BioBricks.

   Silver Medal

To earn a Silver Medal, in addition to the Bronze Medal requirements, a team must do ONE of the following:

1. Provide a detailed, draft specification for the next version of your software tool

Tutorial of Brick Worker

Tutorial of E' NOTE

2. Provide a second, distinct (yet complementary) software tools project.

We design two softwares called Brick Worker and E' NOTE.

In addition the team must:

1. 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.

Tutorial of Brick Worker

Tutorial of E' NOTE

   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 Registry of Software Toolsan 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).

Our code can be found on the Registry of Software Tools

Basic Safety Question for iGEM 2013

1. List and describe all new or modified coding regions you will be using in your project. (If you use parts from the 2013 iGEM Distribution without modifying them, you do not need to list those parts.)

2. Highest Risk Group Listed

1

3. Please describe the chassis organism(s) you will be using for this project. If you will be using more than one chassis organism, provide information on each of them:

4. Do the biological materials used in your lab work pose any of the following risks? Please describe.

a. Risks to the safety and health of team members or others working in the lab?

No. According to the Final Risk Assessment of the U.S. Environmental Protection Agency (EPA) (1997), E. coli K-12 are not likely to pose any risk to human or animal health, to plants or to other microorganisms. In addition, we will use gloves and eye protected glasses during the experiments.

b. Risks to the safety and health of the general public, if released by design or by accident?

No. E. coli K-12 are not likely to pose any risk to human or animal health, to plants or to other microorganisms. Although strains we use in our lab work have antibiotic genes, but they can still be killed by other common antibiotics. We only use E. coli and we will have disinfection after the experiment.

c. Risks to the environment, if released by design or by accident?

No. Since E. coli K-12 are ubiquitous in the environment, they won't endanger any regular species in the environment.We only use E. coli and we will have disinfection after the experiment.

d. Risks to security through malicious misuse by individuals, groups, or countries?

No. We only have the directional optimization of promoters and use GFP to characterize them. GFP won't do any harm to the safety and health of the public and the environment.

5. If your project moved from a small- scale lab study to become widely used as a commercial/industrial product, what new risks might arise? (Consider the different categories of risks that are listed in parts a - d of the previous question.) Also, what risks might arise if the knowledge you generate or the met hods you develop became widely available? (Note: This is meant to be a somewhat open - ended discussion question.)

Using site-specific mutagenesis of genes might bring in safety problems, so strict treatment of waste is required in commercial production. Besides, the methods we use are widely used in the lab, and they won't cause any disadvantages if used properly.

6. Does your project include any design features to address safety risks? (For example: kill switches, auxotrophic chassis, etc.) Note that including such features is not mandatory to participate in iGEM, but many groups choose to include them.

No.

7. What safety training have you received (or plan to receive in the future)? Provide a brief description, and a link to your institution's safety training requirements, if available.

Yes,every member of our laboratory received biosafety training including standard laboratory operation and WHO Biosafety Manual training before the experiments. All members learnt about the "C3H3"which is well known in the college of chemistry and chemical engineering. http://210.34.15.138/rule/10384_2_c_18.pdf

8. Under what biosafety provisions will / do you work?

a. Please provide a link to your institution biosafety guidelines .

http://210.34.15.138/rule/10384_2_c_18.pdf

b. Does your institution have an Institutional Biosafety Committee, or an equivalent group? If yes, have you discussed your project with them? Describe any concerns they raised with your project, and any changes you made to your project plan based on their review.

No, we haven't discussed our project with an Institutional Biosafety Committee, but we discussed the safety problem with our instructors and confirmed that this project is safe enough if experimental rules are strictly observed.

c. Does your country has national biosafety regulations or guidelines? If so, please provide a link to these regulations or guidelines if possible.

http://english.biosafety.gov.cn/Center/200511/t20051101_13462.html

d. According to the WHO Biosafety Manual, what is the BioSafety Level rating of your lab? (Check the summary table on page 3, and the fuller description that starts on page 9.) If your lab does not fit neatly into a category 1, 2, 3, or 4, please describe its safety features [see 2013.igem.org/Safety for help].

Level 1.

e. What is the Risk Group of your chassis organism(s), as you stated in question 1? If it does not match the BSL rating of your laboratory, please explain what additional safety measures you are taking.

Risk group 1.

Faculty Advisor Name:

Fang Baishan

Faculty Advisor Signature:

iGEM Software Division Coding Practices Questionnaire

1. Are you using the iGEM Software repository at github.com/igem software? If you have instead stored your code elsewhere, please explain where and why you have put it there. If your code is not in the iGEM repository, are you using any version control system such as Git, CVS, or SVN?

E' Note is a web software using SVN and Brick Worker is biobrick evaluation software which will use the iGEM Software repository at github.com/igemsoftware.

2.User Data

a. Does your software store any private data supplied by the user? (For example: the user's name and email address, passwords, DNA sequences, circuit designs, etc.) If yes, please describe what kind of data is stored. If no, skip the rest of this question and move on to question 3.

Yes, E' Note stores users' name, email address, passwords and experimental data that they submit. And Brick Worker doesn't store any private data.

b. What is the URL or IP address where the user's private data is stored? Where is the physical computer or hard drive that contains the user's private data?

E' Note's URL is http://sae.sina.com.cn/ that store the user's private data. It is the SinaAppEngine which is a Cloud platform made by sina corporation that contains the user's private data.

c. Please describe any encryption, password protection, etc. that you use to protect the user's data. (It is not mandatory to have such protections, but if you do, describe them.)

Because we rent the SinaAppEngine to make E' Note's application active, the user's private data is wholly stored in its cloud storage which will be protected by a group of safety professionals.

3. Does your software include any other security features? Please describes them here.

No, E' Note is in virtue of SinaAppEngine to make the most powerful protection and Brick Worker is to evaluate and analyze the biobrick sequences and does not include any storage of the user's data.

4. Does your software let the user create a design by choosing parts/genes from a list/database, such as the Registry? If so, which lists/databases are included? Is there any restriction on which parts/ genes the user can choose?

Yes. For Brick Worker, in the primer design part, we allow the user to choose transcription factors and add transcription factor binding sites (TFBS) to the primer sequences, and the TFBS data is derived from RegulonDB.

5. Does your software allow users to write new data into any public lists or databases? If so, do you check the new data for errors before allowing it to be written?

No.

6. Does your software include any other features that encourage the user to create safe designs? Please describe them here.

Yes. Our Brick Worker help user to locate the essential part of promoter and RBS so the user can design mutation in these sites to improve the quality of the biobricks and in the protein coding sequences optimization part our software automatically optimize the protein coding sequences to a higher expression level.