The iGEM-er’s Guide to the Chassis(es)

For many teams, being unfamiliar with a host organism is a setback for choosing to work with it, though the host organism may be well suited for the project.

To help out teams deal with new host organisms, we have compiled a manual called the "The iGEM-er’s Guide to the Chassis(es)". We provide a detailed explanation of of all things teams would have to consider, right from procuring the strain, to designing biobrick parts, the difficulties they'd face and how to overcome them. The manual can be found here

Suggestions to iGEM HQ

As an incentive to work with new organisms, we presented a proposal to iGEM Foundation to create a “Best New Chassis award” as one of the special prizes in the upcoming editions of the competition. The award was to be given to an iGEM team that adds a satisfactory biobrick part collection (with promoters, backbone plasmid, codon optimized reporters, etc.) that will enable users to work with a host organism for which biobrick parts did not previously exist. We believed this prize can act as a great motivation and a catalyst to encourage more people to work with newer organisms and develop synthetic biology protocols, parts, and tools for them. The prize can be modelled similar to the Special Prize, Best Advancement in Plant Synthetic Biology; where iGEM rewards a team for doing interesting work with a plant chassis.

We could not convince the iGEM Foundation to implement it this year due to time constraints, but we hope to propose the award early next year.

Iterative testing and redesign

We believed that entering data on our database could be a tedious and confusing process and we wanted to make this process as user-friendly as possible. Hence, we after the first prototype was done, we decided try it out ourselves and began to enter data.

Our first prototype

With the testing of first prototype by ourselves, we realized that the what data was to be entered in what field was not clear. Our instructors also gave us the same feedback. Hence, the user interface was completely overhauled, to include a help section on the left and data fields on the right. The second prototype is shown below.

Second prototype with a major UI overhaul

The testing by entering data ourselves continued and we got more insights on the design. One of our team members accidentally closed the 'add page' while filling up data, as he had multiple tabs open on his browser and was trying to close all unwanted tabs. All the data he had entered so far was lost. Hence, we added a confirmation before the tab is closed. This is shown below:

The confirmation before close

Case studies on the functioning of other databases

We several conversations with stakeholders and experienced data curators in bioinformatics, we realized that data curation and management is a major issue. Hence, we conducted case studies on the functioning of some popular and well-known databases, to come up with a roadmap for the operation of our database.

The databases we studied include the Protein Data Bank, Wikipedia, Google Maps, YouTube and BRENDA. The case studies and our derived roadmap are presented on our Integrated Human Practices Page

Team:IIT-Madras/HP/Silver

The iGEM-er’s Guide to the Chassis(es)

Suggestions to iGEM HQ

Iterative testing and redesign

Case studies on the functioning of other databases