Team:UESTC-software/Medal requirements
Medal Requirements
Bronze
UESTC-Software team had been signed up for the collegiate track of the iGEM competition as a "software" team. Certainly we had a great summer for our joint efforts and will attend the Giant Jamboree.
2. Meet all deliverables on the Requirements page (section 3), except those that specifically mention parts.Our team had completed the deliverables in time, including team wiki, poster, presentation, project attribution, safety forms and judging forms.
3. 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.This is it! Click Our Attributions Page(), and you can find individual attributions of each one who has made contribution to our project ,including members, mentors and other supporters.
4. Document at least one new substantial contribution to the iGEM community that showcases a project made with BioBricks. This contribution should be equivalent in difficulty to making and submitting a BioBrick part.This summer we created the software, Bio101, which focused on DNA storage. Having verified all Biobricks, we affirmed that the generated sequence wouldn’t be same as any composition of Biobricks, especially those labeled as dangerous, which proved the randomness and innocuousness of our project.More details will be shown on Project Page().
Sliver
We tested the speed, efficiency, stability of our system, including the ratio of the DNA sequences file size and original file size, the transforming speed, GC content and the number of homopolymers and Restriction Enzyme cutting sites. Additionally, we do wet lab and successfully restore our file.More details will be shown on Validation and Testing Page().
2. Convince the judges you have helped any registered iGEM team from high school, a different track, another university, or another institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem..This year, we interacted with 4 other iGEM teams in a variety of activities! Our key contributions to the research of other teams were following.
- (1) Collaboration with the team UESTC-China, we helped them build a tool for analyzing large amount of experiment data.
- (2) Contribution to the constant of iGEM Southwest China Union (iSCU).
- (3) Organizing a meeting with TMMU and NJU.More details will be shown on Collaborations Page().
This year, in addition to addressing DNA information storage system, we wanted to explore other issues, specifically between the scientific community and the general public. Therefore, we had done hundreds of interviews with citizens before we designed software Bio101, software Bio1024 and the game Bio2048, the three projects. We set following three questions:QUESTION 1: How much do you know about Biology? QUESTION 2: What is your attitude towards Synthetic Biology? QUESTION 3: What advantages do you want DNA storage to have?
We found universal phenomenon that many people thought that biology, especially synthetic biology is too far to touch for themselves, which became the central problem combining our project and society we aimed to solve. We tried to achieve it from three aspects that included collaborations, edutainment and DNA storage popularization.SOLUTION 1: Bio2048, popularization and feedback of edutainmentSOLUTION 2: Collaboration, the online and offline publicity and discussionSOLUTION 3: Bio101, to be scientists tomorrow. More details will be shown on Human Practice Page().
GOLD
This summer, we had done hundreds of interviews with citizens before we designed software Bio101, software Bio1024 and the game Bio2048, the three projects. Human practice, which is necessary for a birth of a project, means that every design and change should relate to humanity and make more and more practice. We addressed the above problem we found with 3 ambitious projects, which partly formed our design:
(1) We created the software, Bio101, based which we held the activity, “to be scientist tomorrow”. During the activity, students in Grades 6 and 7 with their parents took part in our lecture and interactions, which promoted their interests in knowing DNA storage and other biological knowledge.
(2) We created a new game called Bio2048, which encourages people to learn more about biology through an entertaining way. Not only did we put it onto the Tencent Application of Treasure for ordinary people to download and play, but also combined it with the education of biology, arousing student interests of study.
(3) We contributed to the continuation of iGEM Southwest China Union as the founders of it, which highlights undergraduate research in synbio in Southwest China. As a part of that union, we organized an iGEM Meeting as well as science presentations and social activities with 4 other schools and groups.More details will be shown on Human Practice Page().
2. Improve the function OR characterization of an existing iGEM project (that your team did not originally create) and display your achievement on your wiki.During learning and consulting process, we discovered that CUHK putted forward a similar project about DNA information storage system in 2010 iGEM competition. Their system aims to store text information into DNA. We recognize their results, but there are some problems we will pose directed against their system:
(1) Cannot transform arbitrary file format, only text.
(2) There are too many homopolymers (i.e., repeated consecutive bases or repeated bases fragment, such as TAAAAAC or TACTTACTTACT) in the DNA sequences. This will lead to catastrophic error during the synthesizing or storing progress.
(3) Not provide an appropriate error correction component in system. If a small area of DNA sequences goes wrong, its influence is deadly for the whole system.
Based on the above problems, this system is immature. In order to circumvent these defects, add more functions and own better performance, we do this:
(1) Regard to a computer file, the system read its binary information first. Then, do other operation to it. In this way, the system can transform any file formats.
(2) We use differential coding to ensure that there is no homopolymer in DNA sequences. We use appropriate compression coding to ensure the bases appearing in DNA sequences are almost random and guarantee lower content of G, C nucleotide
(3) Our system reads of length 100 bps shifted by 25 bps so as to ensure four-fold coverage of the sequences. It means that even though one of the sequences goes wrong, it will not influence other three sequences, and we can get the information from its redundancy sequence.
(4) Add a header and a footer to the sequences, which contains address code and check code. It will help identity the location of a sequence in the file and help us know whether the sequence goes wrong during the synthesizing or storing progress.More details will be shown on Project Page().
3. Demonstrate a functional proof of concept of your project (biological materials may not be taken outside the lab ).You can use our software in various ways:(1) Starting from source code — GitHub: ()
(2) Install on the hard disk without having to start from source code: you can also download the install package of Bio101 in the GitHub repository, and install CORE on Windows, Mac OS X and Linux.
(3) Using Bio101 online! ()Also, we have developed a detailed API document. For more details, please see documentation page(). We will demonstrate our software at iGEM Giant Jamboree in the software demo suite.
4. Bring your prototype or other work to the Giant Jamboree and demonstrate it to iGEMers and judges in your track showcase (biological materials may not be taken outside the lab).We will show our project in Giant Jamboree!
CATALOGUE