Bronze Medal

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

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

Overview of project

Present a Poster and Talk at the iGEM Jamboree.

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

Our software in Github.
Note:
Our giant software aims at operating Biobrick of device level based on synthesized DNA fragments.
But for biobrick level, the second module can also assist users to design genes, such as deletion of EcorI, XbaI, SpeI, PstI, Not I in the CDS, codon optimization and repeat smash.

Silver Medal

A. Provide a detailed, draft specification for the next version of your software tool. As our project is so large and extensible greatly, at least 5 ideas can’t be realized due to time limitation.

B. Provide a second, distinct (yet complementary) software tools project. For the third module SegmMan, we have a complementary design & synthesis method OLS chip synthesis, so that Genovo is compatible for both synthesizer and chip.

Provide a demonstration of their software either as a textual or video tutorial made available on their wiki.

Textual tutorial

Gold Medal

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.

We have software team Shenzhen_BGIC_ATCG to use the second module to design their genes. SC2.0 project also try out SegmMan module on chrVII’s segmentation.

A. Outline and detail how your software effects Human Practices in Synthetic Biology.

Share:
Web-based server for public to use Software assessment and comparison with Biostudio.
Innovation:
We interview with core leader, Dr. Patrick Yizhi Cai and talk about Genovo’s design and application.
Advertisement:
We tried to sell our team shirts to people from BGI.

B. Use SBOL in your software documentation.

We use SBOL as one of the output of first module to describe the genes in new created pathway.

A. Develop and document a new technical standard that supports one of the following:

a. Design of BioBrick Parts or Devices
Chromosome Design Standard
Design Operation Standard
b. Construction of BioBrick Parts or Devices
Assembly Strategy Standard

Safety

Question1: Are you using the iGEM Software repository at github.com/igemsoftware?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?

Answer:Yes.

Question2: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.

Answer:Yes. We store DNA sequences and circuit designs provided by users.

Question2: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?

Answer:The server is still being constructed.

Question2: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.)

Answer:

Question3:Does your software include any other security features? Please describe them here.

Answer:Yes. The software can store the data provided by users and those produced step by step, so that user won't miss their result.

Question4: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?

Answer:Yes. KEGG, partsregistry, Codon usage database, SGD, VFDB, E. coli Genome Project. We have no restriction on genes the user can choose.

Question5: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?

Answer:No.

Question6:Does your software include any other features that encourage the user to create safe designs? Please describe them here.

Answer:Yes. We develop a plugin to show the relationship between the gene or artificial logic gate gene circuit to guide user to select their target genes safely. Besides, we have reminder about biosafely selection for users.

Question7:Is your team also doing biological work in a wet lab?

Collaboration