Team:SJTU-Software/Description

Development

We, the students from Shanghai Jiao Tong University, have a long tradition of taking part in the iGEM competition. Until 2014, we only had wet lab team for our school. But in 2014, our seniors organized the first software team of SJTU. Thanks to the experience shared by last year’s software team, we have a much more mature software team this year.
Before we considering the project of this year, we firstly conducted carefully investigation on projects of former software teams. During the process, we found a common problem that the former project only got maintenance for the year when the team took the competition. Under this condition, several years later, we cannot contact the people who were responsible for the software then and some of the software are excellent. In order to prevent this problem from happening to our project, we consulted the members of last year’s software team after we determined our main idea. Consequentially, we absorbed the most important results of easyBBK in our software. First of all, as an outstanding software, easyBBK has a highlight in the search function. So we added the search function on our push system (which helps users to construct and design devices. Moreover, we made the scoring system of easyBBK to be more flexible by allowing users to choose the weight of different parts and filter the score range.
Meanwhile, we use the usage count of every existing biobricks to determine the difference of their performances. After standardizing the format of biological data, we can have better and more concrete standards like the expression level to evaluate the property of biobricks. In the end, we hope SJTU software teams can continue to inherit and develop the work of former teams. This would meet the requirements of iGEM competition better.
When we have collaborations with other igem teams, we find that most of teams use new parts to build their devices. Due to the new parts don't have enough feedbacks and uesd times which are the core grading standards in our algorithm, our software is hard to evaluate those kind of bricks with a high score. However, when we use blastn to compare the new parts' sequence with the existing parts' sequence in the database, we find that most of the new parts' sequence have high similarity with the old part in the database. Some parts even have same sequence as old parts in the database. And we also find that there are many parts with the same sequence in the database. So we want to add the blastn function to our website. When the researchers upload a part to the database, we can compare its sequence with the parts in the database. If there are some parts with same sequence as the new one in the database, we can inform the researchers this information and refuse the upload.
The blastn function can also help the users to find out which biobricks in the database is similar to their own biobrick. By checking these biobricks' information, users may get more help and enlightenment in their reseaches. What's more, blastn function can help our algorithm to evaluate the devices that cantain the new parts, which have been explained in our collaborations with other igem teams.
Our web-based tool BASE can search, evaluate and visualize biobricks at part, device levels. But at system level, the regulation relationship between devices have not been added to the scoring system. There are few data can be found to measure the regulation relationship between devices, so the collected information is not enough to build and perfect our scoring algorithm. I believe this will be a big improvement of our project if this function is added.