Team:SJTU-Software/Requirement/Medal

1. Bronze

The following 4 goals must be achieved:

1. Register the team, have a great summer, and have fun attending the Jamboree in Boston.
We have registered a team named “SJTU – Software” in April. All of our team members have worked together and developed “Easy BBK” for the whole summer. Nine of our team members and one of our instructors will attend the Giant Jamboree in Boston this year at the beginning of November.

2. Create and share a description of the team's project via the iGEM wiki.
The address of our wiki is https://2014.igem.org/Team:SJTU-Software/Overview. The introduction, user tutorial and insight into our project is shared here.

3. Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.
We will talk and present a poster at the World Championship Jamboree.

4. Develop and make available via The Registry of Software Tools, an open source software tool that supports Synthetic Biology based on Standard Parts.
User could download Easy BBK here. https://2014.igem.org/Team:SJTU-Software/Project/Download

2. 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.
The assessment model in “Easy BBK” are based on the information of standard Parts collected from Registry. In the model, we have taken into consideration 13 attributes of the biobricks and have modified the weight of those attributes to rank the standard Parts in a reliable manner.
Additionally, the components in the “design” part of “Easy BBK” are based on the legend available on Registry. Although a little modification have been made on each component, they are easier to be identified by users.

2. Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)
User Guide is available on this link: https://2014.igem.org/Team:SJTU-Software/Project/Tutorial

3. Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc).
Detailed API documentation are automatically built from source code documentation using doxygen. Download of this documentation is available through this link:xxxxxxxxxxxxxxxxxxxxxxxxxx.

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.
Documentation of automated unit testing, test coverage are built using EclEmma and are available through this link:xxxxxxxxxxxxxxxxxxxxxxxxxxxx . Bug tracking facilities, documentation of releases and changes between releases are available on Github.

3.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.
To find out whether Easy BBK is a user-friendly software which can help people with search biobricks of good quality and present their bio-systems. We have contacted 9 members of SJTU-bioX-Shanghai and members of SUSTC-Shenzhen to conduct user studies. More detailed information of user studies are available here: https://2014.igem.org/Team:SJTU-Software/Project/UserStudy.

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

1. Make your software interact / interface with the Registry.
Users can access the main page of the biobrick from “Search”. Additionally, biobricks can be uploaded to Registry. User guide is available through this page: https://2014.igem.org/Team:SJTU-Software/Project/Tutorial.

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.
The assessment model is further developed from the attributes used to assess the biobricks used by 2012 UT-Tokyo-Software. Description of their attributes are available through this link: https://2012.igem.org/Team:UT-Tokyo-Software/Project/BioBrickSearch. Description of attributes used to assess the biobricks are available through this link: https://2014.igem.org/Team:SJTU-Software/Database/AssessmentModel.

3. Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)
A well documented API documentation was automatically built from source code documentation using doxygen. Download of this documentation is available through this link:xxxxxxxxxxxxxxxxxx.

4. 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.
We have encountered two safety problems during the development of our software.
The first one is the safety of our server. We have once accidentally upload user name and password of the server to GitHub without notice. Then we have changed the password to get access to the server. Later, we planned not to upload the file which contained the user name and password of server, but we will still compile the file in the executable file. Other users and developers won’t get access to this.
The second one is with the username and password of the users who want to upload biobricks to Registry. We process this in a special way so that the username and password will not be saved locally or anywhere.