Team:SYSU-Software/Contribution
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Team:SYSU-Software/Contribution
Overview
In order to understand the primary need of synthetic biologists, we sent out questionnaires to researchers (see HP page) and received an amount of feedback that optogenetics researchers are troubled by selecting appropriate photoreceptor protein and linking it with target protein, and they desire for a platform to rebuild target proteins into opto-controllable elements. Considering their needs, we designed Phoebus, which is hoped to be a complete consistent for synthetic biologist.
Database
At present, there is no online natural linker database based on the latest protein structure and updated in real time. Therefore, according to the data of NCBI and CDD, we subtract the conserved domain sequence from the full-length sequence of a single protein to get linker, which is put in the database SLinker. In order to make the SLinker database more complete, reported artificial linkers are added to it.
Finally, we get a database Slinker, each linker records primary sequence, sequence length, three-dimensional structure, solution accessibility, and related conservative domain information. Users can determine the length range, solvent accessibility, terminal amino acid type and other requirements to obtain their desired linker sequence and display it.
Figure 1 | SLinker database
Human Practices
We communicated with a wide range of stakeholders through questionnaires and meetings, understanding their needs and adjusting our software to them.
In order to enhance the collaboration between software teams and experiment teams, we participated in the ccic (Conference of China iGEMers Community) and some other conferences, received valuable advice from the judges and peers. Through the communication with other software teams, we make sure that our projects are complementary to each other, focusing on different layers of synthetic biology. For those teams who focus on metabolism, we provide a novel and efficient platform to design and pre-arrange their experiment. Besides, we establish Phoebus Community for users to communicate about our project and extended ideas of synthetic biology in our software.
Figure 2 | Phoebus community
We believed that this kind of collaborations should be further promoted. With the cooperation of teams and researchers, we will be able to accelerate the development of synthetic biology.
Standardization
To build an automated element design platform, we standardize the process of designing opto-controllable:
To achieve our goal, we collected some widely used and reported optogenetic switches to build a database, constructing SLinker mentioned above, and use structure prediction and evaluation algorithm to make the 3D model of opto-elements to fit users’ demands. Thus, our project provides examples for other researchers to carry out such designs, and they can use our standardized software or follow our procedure to conduct their own researches.
Education
We host a seminar and a street promotion for students who are not quite familiar with synthetic biology nor iGEM. Vivid explanations and interesting examples are used to arose their interest towards synthetic biology and help them to have a certain idea of iGEM, which may encourage them to pursue the path of synthetic biology and participate in iGEM (see Education page).
Inspiration
Our project solved one part of the grand synthetic biology problem "regulate the biochemical process directly" by automatically performing the standard work flow of opto-controllable elements design. Phoebus can strongly inspire other teams because they can introduce our method to their own project to make better progress in gene expression regulation and other researches. It can also further approach the improvement of efficiency for bio-elements design and construction. We think it will have a good development prospect in the future.
Open Source
After the competition, we will open our project for all researchers to add their achievement to it or update the software according to their target. Open source makes researchers in various fields closer to our project, by which they can use our functions more freely, contributing to the construction of prosperous open community.