Team:HFUT-China/Software
BioDesigner Dolphin
OVERVIEW
There are three things that an iGEMer need in order to compete in iGEM—a novel idea, a few great teammates and a helpful software. I guess you have found an idea and a team. Now, you have found the last one—BioDesigner. BioDesigner is designed to help synthetic biologists, especially iGEMers, to retrieve for information and design gene chains.
In this year’s project, we perfected the design function inherited from HFUT-China 2016, and added a search function to it.
SEARCH
Since all of searching in the world is based on information, which is data specificlly, we collected team information data from the official website of iGEM. The raw data is of a mess and hard to be uesed for later retrieval and other usage, so we implmented data cleaning process to purify it.
With the support of our backend database, we built up the searching engine. To provide true convenience for users, the search can be conducted under cerrtain tracks by selecting a single, a group of or no tracks which lie beneath the searching box. Selecting no tracks means search under all tracks.
The results are iGEM teams which are most related to the search string. Result teams will be listed in a uniform format and the information shown is summraized to make users surf quickly. Keywords of each team’s project are also extracted using TF-IDF algorithm and exhibited.
Furthermore, we also provide most similar teams for users. If a single team is not satisfying, look at the right of the screen and the recommended teams will be clearly seen. The similarity among teams are calculated using LSI algorithm combining with the number of shared biobricks.
PROJECT
In the “Project” function, users are allowed to design and assemble the own gene chains using existing biobricks. The operations are pretty simple which can be concluded as “3D”—drag, drop and done. The biobricks are listed on the left, and by cliking on one, its information will be shown on the right. Assembling can be done by dragging biobricks and dropping it on whatever position you want it to be.
Moreover, to further inspire users’ thoughts, our system offer biobrick recommendation service by simply clicking the right button of the mouse. The recommeded results are shown on the bottom of the page. Recommendation are made using Markov models, which regards anything happens in this moment as a transition of states according to a certain probability.
GENE RELATIONSHIP
With the help of search function, users can have a clearer conception, or deeper understanding of their designs. Users can type in keywords in the searching box, then parts or compounds, some of which the users might be interested in, will be listed. The basic information, quality evaluation score and related registry page of them will also be exhibited.
For users who are interested in specific genes, to obtain more information, they do not have to scrutinize literatures in the online database on by one. Just input the name of that gene in the searching box, apart from the detailed information, users can see literatures and related diseases of that gene. We also provide corresponding links of these literatures, so users can read them on ncbi.
SYSTEM
In system recommendation page, you can get compound / gene relation graph. By typing a compound name in the left search area, you can search compounds. Each compound is followed with a add button (move the mouse over it), click on it to add it to compounds you are interested in. Click the “run” button, you can get the result graph. By clicking the gene node or compound, you can get their information.
