Team:UESTC-Software/Description
Background
Nowadays, synthetic biology urgently needs a computer-aided software for gene pathway design, which is what we
called gene pathway CAD. From 2014 to 2018, many teams were devoted to achieving this goal but hardly made
breakthroughs.
Synthetic biology is an interdisciplinary subject that combines biology with engineering. One
of the most powerful software in engineering is AutoCAD. This is a computer-aided design (CAD) software that
architects, engineers, and construction professionals rely on to create precise 2D and 3D drawings. The
standard component library includes industry-specific features and intelligent objects which is the core of
this software.
In 2018, UESTC-Software found that iGEM still lacked joint analysis and retrieval with traditional databases
(GenBank, UniProt, QuickGO, etc.), hindering the exploration and use of iGEM Registry. Some iGEMers also
pointed out that the retrieval and interface in iGEM Registry were unintelligent and did need to be improved.
Therefore, we launched BioMaster 1.0, a new comprehensive biobrick database based on iGEM Registry, which
integrated UniProt, QuickGO, EPD, etc., to provide a more effective searching method for parts.
Inspiration
Our inspiration partly comes from the analysis of previous software projects of iGEM teams. In the early stage,
we brainstormed with our PI and advisors. Since 2014, as many as 14 teams have been involved in
database-related projects. Most of them were related to the design of genetic pathways or focused on search
engines in the biological field. However, many projects were functionally similar with each other and difficult
to promote. Therefore, we wanted to make something different.
When we integrated the feedback of iGEM judges and usage survey of BioMaster 1.0, it can be concluded that the
quantity and quality of reference databases, experience of search, art utilization, accuracy of mapping
relationship between databases were still of great significance to synthetic biologists. In addition, iGEM
Registry itself has a lot of errors during data collation, such as wrong feature annotations, which can
interfere with the search and use of parts. Although iGEM strives to improve parts year by year, the existing
data still requires a viable screening and display approach.
So we decided to build a more standardized and complete database ——BioMaster 2.0. It was designed to retain the
popular features of version 1.0 and meet the software teams' needs in development and cooperation.
Our Project
BioMaster integrated UniProt, QuickGO, KEGG, BRENDA, ExplorEnz, STRING, BioGRID, EPD and PromEC databases
centered on iGEM Registry to provide more comprehensive biobrick information. Based on the version 1.0,
BioMaster 2.0 has significantly stridden in three aspects: data integrity, searching accuracy and user
friendliness.
1. By adding KEGG, BRENDA and other enzyme-related databases, we have doubled the quantity of
primary reference databases.
2. Considering the feature of sequence annotation, a novel filtering strategy was adopted to
improve the mapping accuracy between databases.
3. In addition, we redesigned the website architecture and database structure. A weight
algorithm was also established for searching results recommendation.
All endeavors make BioMaster 2.0 a more integrated and user-friendly database, which provides
synthetic biologists with stable data updating and search services in the long term.
For now, BioMaster 2.0 has improved well-received features in version 1.0 and plans to get
further: to provide data support services to other software teams in the future. Currently, we've offered
searching and data supporting services to two pathway design teams (USTC, Tongji), which received positive
feedback.
How to Use It
For individual users, BioMaster provides a quick and varied query service.
They can search keywords or database numbers such as "cellulose degradation". BioMaster 2.0 will screen out all
relevant iGEM components, including description, sequence, providers, functions, structures, annotations,
interactions, experimental background, and references of protein and genes. In
addition, it allows to directly jump to major databases through the links.
For research teams, BioMaster provides data support services. Users can download all data in our database. We
also developed a web program with docker, and thus BioMaster can be easily migrated.
We are committed to providing better data supporting service for other software teams.
Professional teams are also capable of using URL to obtain rich data about biobrick. The data provided is authorized,
so users don't have to worry about infringement.
Our project：http://www.biomaster-uestc.cn
Our judging release: Click Here