Team IIT-Madras

Design

An easy access platform with a database of various host organisms and a collection of tools to work with them.

The blueprint of an organism

To create the database of host organisms, we first started by defining a template/blueprint of the data that needs to be collected about each organism. Our proposed blueprint consists of the following:

Scientific name (genus, species and strain) and taxonomy
Biosafety level
A description of what makes the host special for synthetic biology applications
Genotype
Growth characteristics
Culture sources for obtaining the organism
Maintenance protocols
Transformation protocols
Other protocols
Biobrick parts for this organism
Vectors for the organism
Metabolic models
Genome sequence

Building the database

A database site design consists of two essential components: a backend that is responsible for storing data on the server and serve the data when requested, and a front-end that is responsible for creating a visual interface between the back-end and the user.

Back-end

Our backend is powered by Flask, a framework for Python. All the data about different organisms are stored as .json (JavaScript Object Notation) files on the server.

Front-end

The front-end was done using HTML, CSS and JavaScript.

User Experience Design

Home page

When the user hits on the home page, (s)he can either search for organisms, browse through the index or choose to contribute data for an organism that are not yet in the database.

Add/edit page

The add new organism page and edit organism data page have a similar design, carefully designed to provide the user with the description of the data that is expected to be entered.

View page

The details about each organism can be viewed on the view page. The page is designed for easy navigation to different sections of the entry. This page also contains a link to edit the entry

Chassis tools

We decided to make ChassiDex the one-stop solution for dealing with your host. Hence, we intended to integrate some chassis tools which can be used on the different chassis within the database. These are tools that are vital to molecular biology work on the chassis and such an assembly of tools at one place eases the process of working with them.

Codon optimization tool

We have designed and integrated a highly interactive tool for codon optimization. The optimized sequence can be manually edited to remove restriction sites or reduce GC content, using a drop-down menu that shows codons that can be used to replace the current codon without changing the amino acid.

Future work

We plan to similarly integrate more such chassis tools such as those for genome analysis and metabolic simulations.

Team:IIT-Madras/Design