Team:SYSU-Software/HP/Gold
GOLD
During the Human Practice activities, we have found much more aspects that our software can improve
to fit for a wider range of users, much easier and safer in use. We integrated our Human Practice activ-
ities with software in two aspects.
Safety Design
After consulting to the professor and discussing with freshmen, we found ourselves fail to take chemicals and chas-
sis into consideration.
Chemicals Safety
Not only the professor, but the freshmen figured that since the operation in our software was simple and nearly all
reactions in over 7000 chassis species had been collected, some users might use our software to derive the circuit syn-
thesizing dangerous chemicals or their precursors, such as drugs. Theoretically, this situation is very likely to happen.
Some users might face other kinds of safety problems when their original targets are harmless, but the selected cir-
cuit will produce deleterious intermediate products. However, users are unlikely to know what exactly produce except
his targets in circuits when experiment because details are hidden behind the user interface.
To solve the problems above, we tried to add a recognition system in our software and set a ban list from China
State Administration of Work Safety, formulated following Globally Harmonized System of Classification and Labeling
of Chemicals (GHS), and selected 148 chemicals labeled with toxic as our ban list. Every chemical in this list has an
unique CAS number, same as those in our software, and our system can work through these pairs.
Chassis Species Safety
Our advisors also reminded us that chassis species in our software will cover the organisms in Risk Group 3 and 4,
so we should delete the these data in our software, ensuring that the results will only give the users species in Risk
Group 1 or 2.
To solve this problem, we made a list of species in Risk Group 3 and 4, originally coming from Appendix B in NIH
Guidelines (April 2016), and then we deleted the chassis species belonging to the list.
Parts Safety
Our results combine CDS sequences with promoters and RBSs meeting the requirements from users, which come
from iGEM Registry, and form complete circuits. Although unlike the CDSs, promoters and RBSs won’t express pro
teins that might have potential safety problems to the environment or organisms, we are not sure if some of them are
also labeled with red flags. Considering this, we search the whole database for promoters and RBSs in Registry and find
that all promoter and RBS parts are freed of Red Flags, thus we can use nearly all promoter and RBSs parts if they are
still available.
Model Design
Our previous ideas finally suggested that we can’t find existed data for all function realization in our software, espe-
cially promoters and RBSs strength. Nearly all promoter and RBS parts in iGEM Registry are without strength, thus we
can’t determine which part we should use. Thus we developed a model from previous work to calculate the strength
of these parts through their sequences.
Apart from the main project, we also wonder if we can use our model to calculate the strength of promoters of
RBSs in Registry. So we downloaded all sequence data from Registry and use our model calculating their strength,
making a data frame.
We would develop this model into a small tool so that every team can use it to calculate the strength of their con-
structed promoters or RBSs.
