Team:SYSU-Software/Medal
Medals
Bronze
Your team must convince the judges you have achieved the following 6 goals:
√ 1. Register for iGEM, have a great summer, and attend the Giant Jamboree.
√ 2. Complete the Judging form.
√ 3. Create and share a Description of the team's project using the iGEM wiki, and document the team's parts (if any) using the Registry of Standard Biological Parts.
For a description of our project, please click “Project/Description”. As a software team, we have no new parts for submission to the Registry.
√ 2. Complete the Judging form.
√ 3. Create and share a Description of the team's project using the iGEM wiki, and document the team's parts (if any) using the Registry of Standard Biological Parts.
For a description of our project, please click “Project/Description”. As a software team, we have no new parts for submission to the Registry.
√ 4. Present a poster and a talk at the iGEM Jamboree. See the 2015 poster guidelines for more information.
√ 5. Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.
Attribution: https://2015.igem.org/Team:SYSU-Software/Attributions
√ 5. Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.
Attribution: https://2015.igem.org/Team:SYSU-Software/Attributions
√ 6. Develop and make available, via the iGEM GitHub page, an open source software that supports Synthetic Biology based on Standard Parts or interacts with the Registry. (For questions about the iGEM Github page, contact software [at] igem [dot] org.)
The GitHub page: https://github.com/igemsoftware/SYSU-Software-2015
Our project, CORE, supports Synthetic Biology because, for one thing, it can promotes communication, collaborations and co-development of genetic design in the synthetic biology community; for another, the CORE Design module made use of biological parts and devices to construct genetic circuits. For more details, click here!
The GitHub page: https://github.com/igemsoftware/SYSU-Software-2015
Our project, CORE, supports Synthetic Biology because, for one thing, it can promotes communication, collaborations and co-development of genetic design in the synthetic biology community; for another, the CORE Design module made use of biological parts and devices to construct genetic circuits. For more details, click here!
Silver
In addition to the Bronze Medal requirements, your team must convince the judges you have achieved the following 3 goals:
√ 1. Provide a comprehensive, well-designed User Guide for your software and upload it to your wiki. Be creative! (An instructional video may work as well.)
We provide a tutorial (User Guide) of CORE in the software as well as in wiki. To see the user guide in wiki, please click "Project/Tutorials"!
We provide a tutorial (User Guide) of CORE in the software as well as in wiki. To see the user guide in wiki, please click "Project/Tutorials"!
√ 2. Develop a well-documented library or API for other developers (rather than "only" a stand-alone app for end users.)
We have provided the API documents. Please click "Project/Techniques" to read more!
We have provided the API documents. Please click "Project/Techniques" to read more!
√ 3. Demonstrate that you followed best practices 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, and documentation of releases and changes between releases.
We have employed various techniques to ensure the quality of the software, and make the developing process as smooth as possible. These techniques include continuous integration, automatic unit testing, automatic documentation generation, bug tracking facilities and changes between releases. For more details, please click "Project/Techniques".
We also did user studies (in a small range of people covering wet-lab and dry-lab backgrounds) during and after the developmental cycle of CORE. For more details, please click "Project/Validation".
We have employed various techniques to ensure the quality of the software, and make the developing process as smooth as possible. These techniques include continuous integration, automatic unit testing, automatic documentation generation, bug tracking facilities and changes between releases. For more details, please click "Project/Techniques".
We also did user studies (in a small range of people covering wet-lab and dry-lab backgrounds) during and after the developmental cycle of CORE. For more details, please click "Project/Validation".
Gold
In addition to the Bronze and Silver Medal requirements, your team must convince the judges you have achieved at least two of the following goals:
√ 1. iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. We refer to these activities as Human Practices in iGEM. Demonstrate how your team has identified, investigated and addressed one or more of these issues in the context of your project. (See the Human Practices Hub for more information.)
Our Human Practices includes four parts: Scientific and Societal Thinking, Project Assessment, Public Engagement and Integrated into Project.
We brainstormed what potential impacts our project will have on scientific problems (like, scientific communication and collaboration, transparency and reproducibility, safety, security, etc.) and societal questions (like, intellectual property rights, ethics, regulation, etc.) before we began our project. Through various kinds of practices (like, survey, consulting professors, attending lectures, discussions, etc.), we gained more insights into our project and our responsibilities, and were aware of these potential impacts when planning the project.
With the potential impacts on scientific problems and societal questions in mind, when designing the project we integrated many fine details into the software. We tried hard to make more positive contributions to scientific and societal practices, and reduce and even eliminate the potential negative impacts. When the project was (nearly) complete we did project assessment and public testing, and got many feedbacks from the experts and the public, which helped us improve the project.
Human Practices: https://2015.igem.org/Team:SYSU-Software/Practices
√ 2. Address a problem that you would like to co-develop with a wetlab team. This should be a collaboration where the wetlab team posts a problem they are having and your team addresses the issue by creating an online software solution.
Wet-lab team NJU-China wants a tool that can track the movements of the mice in the cage while recording the positions of the mice in the form of coordinates. We developed this tool and this tool can be downloaded here!
Collaborations: https://2015.igem.org/Team:SYSU-Software/Collaborations
√ 3. Re-use and further develop a previous iGEM software project (or parts thereof) and demonstrate how future teams can continue this trend through good code documentation, use of open source materials and creation of great instructional materials.
For the software itself, we re-used and refined some useful functions in FLAME, project of 2014 SYSU-Software. Following are what we did.
Our Human Practices includes four parts: Scientific and Societal Thinking, Project Assessment, Public Engagement and Integrated into Project.
We brainstormed what potential impacts our project will have on scientific problems (like, scientific communication and collaboration, transparency and reproducibility, safety, security, etc.) and societal questions (like, intellectual property rights, ethics, regulation, etc.) before we began our project. Through various kinds of practices (like, survey, consulting professors, attending lectures, discussions, etc.), we gained more insights into our project and our responsibilities, and were aware of these potential impacts when planning the project.
With the potential impacts on scientific problems and societal questions in mind, when designing the project we integrated many fine details into the software. We tried hard to make more positive contributions to scientific and societal practices, and reduce and even eliminate the potential negative impacts. When the project was (nearly) complete we did project assessment and public testing, and got many feedbacks from the experts and the public, which helped us improve the project.
Human Practices: https://2015.igem.org/Team:SYSU-Software/Practices
√ 2. Address a problem that you would like to co-develop with a wetlab team. This should be a collaboration where the wetlab team posts a problem they are having and your team addresses the issue by creating an online software solution.
Wet-lab team NJU-China wants a tool that can track the movements of the mice in the cage while recording the positions of the mice in the form of coordinates. We developed this tool and this tool can be downloaded here!
Collaborations: https://2015.igem.org/Team:SYSU-Software/Collaborations
√ 3. Re-use and further develop a previous iGEM software project (or parts thereof) and demonstrate how future teams can continue this trend through good code documentation, use of open source materials and creation of great instructional materials.
For the software itself, we re-used and refined some useful functions in FLAME, project of 2014 SYSU-Software. Following are what we did.
1. In FLAME, radar map was used to demonstrate the ratings of different aspects for a defined genetic circuit. We found that radar map is a good way to representing ratings, so we reuse it to representing the ratings of different aspects for a genetic design. However, we made a big change to this settings; CORE allows every user to rate these aspects of a design (while in FLAME, user cannot rate the circuit), then computes the average and shows the result via this radar map.
2. In FLAME, there are many useful devices (represented as “frameworks”). These frequently used devices (AND gates, OR gates, NOT gates, etc.) are re-used by CORE, and in CORE users can directly use this device to engineer their circuits. Further, we enable users with more flexibility; we allow users to edit (delete, add, or change) the parts in these devices. (In FLAME, users cannot edit the parts in the “frameworks”.)
For the biological parts, we abstracted the logical relations between every part in the genetic design of previous iGEM team projects. These parts can be re-used by users to re-engineer the projects of previous teams.
√ 4. Demonstrate your software at the iGEM Giant Jamboree in the software demo suite. You should show a functional prototype that teams can use in following years. (Contact software AT iGEM DOT org for information about the software demo suite.)
You can use our software in various ways:
Starting from source code — GitHub: https://github.com/igemsoftware/SYSU-Software-2015
Install on the hard disk without having to start from source code: you can also download the install package of CORE in the GitHub repository, and install CORE on Windows, Mac OS X and Linux
Using CORE online! http://core.sysusoftware.info
√ 4. Demonstrate your software at the iGEM Giant Jamboree in the software demo suite. You should show a functional prototype that teams can use in following years. (Contact software AT iGEM DOT org for information about the software demo suite.)
You can use our software in various ways:
Starting from source code — GitHub: https://github.com/igemsoftware/SYSU-Software-2015
Install on the hard disk without having to start from source code: you can also download the install package of CORE in the GitHub repository, and install CORE on Windows, Mac OS X and Linux
Using CORE online! http://core.sysusoftware.info