Team:SYSU-Software/Assessment
Risk Assessment
Software facilitates genetic design, but also poses great challenges to traditional biosafety programs and awarenesses. In order to ensure the safety of CORE, we did several risk assessments after our project was nearly complete.
The guideline here for us to do the risk assessment is White List for 2015. The White List roughly contains two parts: Whole Organisms (including viral genomes), and Parts.
(1) Testing whether parts originating from Risk Group 3 or 4 organisms exist in the database.
Most parts with known origins in the database of CORE are of Escherichia coli K-12 origin (Unfortunately, in Registry most of the parts from E. coli does not explicitly tell us whether they came from E. coli strain K-12 or other strains, but in Registry these parts have NO red flags.) Other parts with known origins came from either Risk Group 1 or Risk Group 2 organisms.
(2) Testing whether parts with Red Flags exist in the database. Some parts in the Registry have Red Flags; that is, they might in some way be risky to the experimenters and/or the environment. For a complete list of parts with Red Flags, please click here. To test whether there are any risky parts in the database of CORE, we search the complete list of parts with Red Flags against the database. Here is the result.
2. Biosafety assessment helped by others.
Results of Searching Parts with Red Flags against the Database
When we were talking with Prof. He on topics of biosafety and biosecurity, we also invited him to do risk assessment of our software, CORE.
Feasibility Assessment
Feasibility assessment of CORE consists of three parts: feasibility for safe design and feasibility for design sharing.
(1) Safer design is approachable with the help of CORE.
Safer design in iGEM and synthetic biology is necessary, but this should not cause too much inconvenience to the users. So we have our software assessed by some experts on safety in the campus.
We first asked Prof. Jianhua Yang, instructor of our team, to help discover any inconvenience in our software with regard to biosafety. As far as he was convened, he insisted that software should contain enough warning and notifications so that users with limited experience can be reminded that they should always be a responsible synthetic biologists. So we added a warning in the CORE Design module. When users click the “Download” button to download their design for further processing or information parsing between other CORE users, they will be alerted that they should be responsible for the safety problem in the circuit design. We also included this warning in the “Save” function.
Prof. Yang also asked us a question:
"Whether the software is able to discover the potential risks of the new part or the genetic circuit with this new part?”
This question remains a challenge to us, and we devise algorithms to help find dangerous parts if these parts already exist in Registry. However, for a part with unknown function or even totally new to the biologists, what should we do? So we make use of the power of “Crowdsourcing”, and let every user of CORE evaluate how safe the part, the device, and also the circuit is.
After we made the improvements mentioned above, the safety evaluation system in CORE is more feasible to the users: it can do its utmost to help users design safe circuits, while not cause too much inconvenience to the users.
(2) Genetic design sharing is more accessible in CORE.
In the past, when we wanted to share our design with others, we had to use some kind of software (say, Photoshop) to draft the circuit design, then used this draft to share our ideas with others. There were two problems in this kind of practices. First, design from one team is hardly understandable to the other teams if we do not use standardized representation style to show our design; second, these designs are hard to modify because they have already saved as pictures (although with the help of Photoshop we can make modifications, but it seems awkward). So CORE can help us with this kind of sharing practices.
To tackle the first problem, we embedded into CORE the CORE Design module. This module serves two functions. The first function is that users can use CORE Design to easily design circuits using SBOLv standard, a standard aiming at promoting communication in synthetic biology. The second function is that CORE Design can make design more easy with the help of ODE. With standardised representation of genetic circuits (through the use of SBOLv standard), genetic design can be more easily understood by others.
To tackle the second problem, we devised data structures to help parse genetic design between the three modules. To see more details, please see “Project/Design” and “Project/Documentation” page.
All in all, with the help of CORE, design sharing can be made easier and more accessible.
End-user considerations
End-user considerations are most important to a software team. Before we completed the project, we did a survey to find out who will be our potential users, and we found out that potential users of CORE would be experimental synthetic biologists (who would be interested in the function of the software instead of the implementation of it.), and developers (who would be interested in how to extend the software to make new ones.)
So we specifically designed CORE to meet these two kinds of users.
(1) For synthetic biologists, they prefer a software with least requirements and more convenience.
Most of our users are synthetic biologists, and they seldom care about how to install the server. They may prefer a software with setup instructions, and even the software can do all the setup procedure for the users. So, to facilitate users to make use of CORE and design genetic circuit,as well as to further give expression to the potential of "Crowdsourcing", it is highly recommended that users click on http://core.sysusoftware.info/, and use CORE online!
(2) For advanced users or developers, we enable CORE with powerful potential for extension.
We have provided the Source Code in GitHub. Please click https://github.com/igemsoftware/SYSU-Software-2015/. CORE is designed to be extended. For more technical support materials, please see “Project/Techniques”.