• 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.