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 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 modeled 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, after the first prototype was done, we decided to try it out ourselves and began to enter data.

Our first prototype

With the testing of the 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

With 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 case studies are presented below:

Protein Data Bank

Users provide the data along with references and experimental results. Authors should consider their entry as a representation of their scholarly work.
Annotation staff does not judge the quality of the data but bring out potential errors to the attention of the author. Then, the PDB curation staff corresponds and collaborates with the author to ensure representation of their data within the PDB entry.
The main challenge ahead for PDB curators deals with the increasing volume and complexity of the data The solution lies in close collaboration between the groups involved; the authors, database staff, and users of the PDB.

Wikipedia

An article that we read is just the current draft; every time it is changed, they keep both the new version and a copy of the old version. This allows them to compare different versions or restore older ones as needed. There are only a few bad people who abuse this privilege by vandalizing or propagandizing. Hence, it is almost accurate.
Many people act as editors. If they see an error on a page they are reading, they correct it. If they can make a small addition that is helpful, they will do it on the spot. Writers, editors, and admins work together to solve almost all of the problems that you would expect to arise in an open platform like Wikipedia Several hundred visitors who have been contributing to Wikipedia for a period of time are granted administrator privileges. These privileges give them the right to do things like deleting and un-deleting pages, blocking and unblocking IP addresses, etc.
Additionally, once user accounts are more than a certain number of days old and have made more than a certain number of edits, they automatically become autoconfirmed, allowing the direct creation of articles, the ability to move pages, to edit semi-protected pages, and to upload files.

Google Maps

Local Guides in Google Maps, a gamified program for getting its users to update data in Maps and upload photos of local venues, compels people outside the company to be a part of it. Different points for the impact of the data submitted induce more and more people to actively participate and upgrade themselves.
After the data being submitted, Maps will show notifications to users near the location saying that 'someone suggested new info'. Users can either verify that information, only after which it will be published to maps.
Based on the reviews and comments by the people on the edits and data uploaded, Google forwards them to that user and asks to confirm the accuracy of the data. Edits won't appear unless made some positive changes.

YouTube

Each media company or a copyright owner such as Warner Bros, etc. publish original music or videos on YouTube and submit a part of their each content called Digital watermarking which YouTube calls it as content ID. Content ID consists of audio and video matching tools that match each and every video uploaded to the site against video and audio content along with Title/Description/Tags for Affiliate/CPA/Google Ad-Sense platforms, provided by content owners (i.e. networks, record labels, film studios, etc.).
Rights holders who claim their content with Content ID generally more than double the number of views against which we run ads, doubling their potential revenue. And we’re seeing media companies make the most of this revenue opportunity – in the last quarter alone, claims to make money from videos increased 200%.
Allows people to like, comment, share the video and subscribe the channel. YouTube provides many viral marketing advantages, from easily embedding videos on websites to sharing them on social media.

BRENDA

The BRENDA Database is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases.
Each entry is connected to a reference and the source organism.
Users can propose new enzyme by filling all the information along with all the required references of published papers or can complain against the accuracy of an existing data.
In order to assess the kind of connection or dependency the relationship was classified into four categories:
1. Causal Interaction’ of a disease caused by a malfunction of the enzyme;
2. ‘Ongoing Research’ when the disease–enzyme relationship is suspected but research is still under way;
3. ‘Diagnostic Usage’ when the enzyme is part of the diagnostic course of action like the measurement of its activity, the test for its presence or the assay of its functional characteristic parameters; and
4. ‘Therapeutic Application’ when the enzyme is applied as a therapeutic agent or considered as a drug target. The results of the procedure are evaluated with respect to precision, recall, accuracy, and specificity in a 5-fold cross-validation process.

Team:IIT-Madras/HP/Silver