Team:UESTC-Software/Demonstrate
Overview
We demonstrated and promoted the BioMaster 2.0 to iGEMers in Giant Jamboree. A short guide
video was recorded to prove the efficiency of BioMaster, and you can also experience it directly from www.biomaster-uestc.cn. In the early testing of BioMaster, there were
many sincere feedbacks from synthetic biologists and iGEM teams. We also got contacts with official iGEM
Registry about technical details on copyright issues. To ensure the safety and legitimacy of data, we consulted
lawyers on intellectual property issues. Currently, BioMaster 2.0 is open to the public, providing downloads of
databases and docker images.
Demonstrate Video & Animations
Database Demonstrate Video
Database Demonstrate Animations
EC Number Prediction Function
Promoter Prediction Function
Uploading Files and Using Keys
Web BLAST & ID Mapping Tools
SBOL-design Tool
Click "Add New Member" to add new feature part.
Drag and drop the placed feature part to adjust the position.
Double-click any part to replace it.
Drag the part into the “trash" zone to delete it.
Click "Add module part" to add module parts.
We designed memory function so that when you click ”Cache”, you can just click "Load" to
restore your design whatever you do.
Download the edited total part locally in PNG, FASTA and GenBank formats.
Resources
Use BioMaster 2.0 through
www.biomaster-uestc.cn
Gain access to the data through download page of BioMaster
Get the code and docker version for BioMaster 2.0 on UESTC-Software GitHub
Vist our repositories for BioMaster 2.0 through UESTC-Software Docker Hub
Our judging release: Click Here
Feedback
There are many iGEM teams which tested BioMaster and gave sincere feedback, such as 2019-CSU-CHINA,
2019-SJTU-Software, 2019-Tongji-Software, 2019-SCU-China and so on. Meanwhile, we invited some previous iGEMers
and professions to use it. They gave affirmation to our database and also gave us some advice to improve it in order to serve synthetic biology better.
“The UI surface is really nice and user-friendly ! I love both web pages and
brochures, including wikis. It is worth learning for us. As the BioMaster has a lot of functions, I suggest
you
to make a brief description of each function to improve users' experience.”
------SJTU-Software
“You all did a great job! It indeed provides us many useful statistics so that
we can refer to it. But you can do it better. Regarding the aspects of corresponding between UniProt and
STRING, the gene name was used to correspond two databases, which may result in the corresponding species
being not the same as the search. Actually you can label the species in the interaction diagram to
provide references for the related interactions. As for the screening and forecasting section, accuracy is
absolutely very important. You need to test the results to ensure that the accuracy is at a high level.”
------Tongji-Software
“BioMaster2.0 is useful and it helps users to improve their efficiency when
they’re searching for biobricks.
UESTC-Software developed a method to broaden annotations in iGEM-Registry by using BLAST tools according to
the original sequences. Ambiguous annotations created in the past are corrected now! For whom has never
learnt about bioinformatics, acquiring a large amount of information in the same website is cheerful.
‘Search’ module permits users typing more search fields. It can also help someone who
can't afford a VPN
account to get access to a ’mirror’ of iGEM-Search.
Personally speaking, I like ‘Synbiohub’ most. Considering that traditional plasmid
graphics software, such as
SnapGene and SimVector, does not allow to design or display two or more plasmids in one file, we need a
brand-new software to satisfy the desire. Moreover, I noticed that you designed a ‘Comment’ module on
the page of the search result. It reminds me that BioMaster has the potential to be a public forum which
provides a platform for iGEMers to discuss about the details of particular system. If you put ‘Comment’
and ‘Synbiohub’ together, we can create an interactive platform of academic exchange like Researchgate.net.
In conclusion, Synbiohub makes us design or understand artificial genetic loop faster and better.”
------CSU-CHINA
“BioMaster is a good project, the SBOL visualization tool is very interesting. The
database shows lots of additional information for a part, it’s good but a little messy. You should concern
about adding more preset parameters in BLAST. And there do have some bugs in the early version, you need to
test
it more carefully.”
------SCU-CHINA
Safety
Safety with BioMaster 2.0
BioMaster 2.0 is a biobrick database centered on iGEM Registry. It focuses
on database integration as well as
some practical functions such as EC number prediction, SBOL visual design, cross ID search and so on. The data
in the
BioMaster2.0 comes from databases with security certifications and declarations.
Our prediction function is only meant to provide users with a prediction result for their reference.
