Team:USTC-Software/Achieve/Medal

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.

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 (remember, the iGEM judges will be looking for substantial team-based software projects).read more

Silver Medal

Provide a detailed, draft specification for the next version of your software toolread more

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

Add

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.read more

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.read more

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

Our software effects Human Practice in Synthetic Biology in some ways:

Safety: Thought most synthetic biological experiments will be safe, there still some dangerous attempt about inputting disease gene into bacteria. Our software could figure out the gene’s effects in advanced to experiment. So it makes the synthetic biological experiments more safety to some extent.

Sharing: Not only open all of our codes on github, our team also created an integrate API of our source code which detailed introduce the structure and function of all the code. So we really hope everyone sharing and developing our software everywhere!

Innovation: Just as we said, our software is the first one which focuses on the forward and reverse analysis of the effect of input gene. We also create a brand new algorithm and idea to figure out the change of GRN after new gene’s coming.

Or

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

The gene information could be output in SBOL when clicking the button “SBOL it!”. The file whose name is same as the name of gene containing in. For example: This is a file named “gutM.xml”

Plus

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

design of BioBrick Parts or Devices

construction of BioBrick Parts or Devices

characterization of BioBrick Parts or Devices

the analysis, modeling, and simulation of BioBrick Parts or Devices

Actually, our software could model all parts in Biobrick Parts. So we choose two parts containing promoter and protein gene of LuxR which are used more than 1000 times.

Biobrick Part 1: BBa_R0062   Promoter (luxR & HSL regulated -- lux pR)
Biobrick Part 2: BBa_C0062   luxR repressor/activator, (no LVA?)

Our software analyze the stability of the GRN after importing. Because those parts are multiple transcriptional regulator, the score of the stability is only two stars which means that after LuxR’s import the expression of each gene changed a lot.

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

Or

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