Software

ChassiDex

While iGEM teams and the synthetic biology community has mostly focussed on developing DNA parts called ‘BioBricks’ for use in biological systems, the parts have to be ultimately used in an organism called host or sometimes even ‘chassis’. For most projects, researchers try to stick with using a few familiar model organisms such as Escherichia coli for the host system requirements. Lack of experience is often a reason to avoid unfamiliar yet apt organisms for the project at hand. To explain this with an analogy, imagine Taxi-hailing apps being available only for desktop computers because the developers do not know how to develop applications that run on mobile phones. Hence, in the 2017 edition of iGEM, Team IIT Madras worked on developing a database of host organisms called ChassiDex that aimed to curate different organisms along with all the information about them that is relevant in the context of synthetic biology. The idea of having such a database was very well received by the synthetic biology community that attended the iGEM Giant Jamboree in 2017. We have continued working on the project and revamping it with suggestions received, with the hope to improve this project and create a team to manage the database. The website for the database is available at Chassidex.org.
Additionally, We also developed some independent tools to help make life easier for synthetic biologists. These include CUTE,a codon table generator and ComicSyns,a font for synthetic biologists.
Code on GitHub

Chassidex Main Page

Sample Organism: A. Baylyi
Our Organism of interest for the year

CUTE: Codon Usage TablE generator

Codon Usage Tables. Every host organism has its own codon bias: the biased usage of particular codons when two or more codons in the genetic code stand for the same amino acid. While expressing a protein heterologously in a host organism, the DNA sequence is optimized to match the codon bias of the host, while keeping the protein sequence constant. This process is known as codon optimization and is done to increase expression in the chosen host organism. With ChassiDex, we aimed to make working with novel hosts easier for biologists, and also realized the role of codon optimization in doing so. While trying to synthesize GFP reporter for Acinetobacter baylyi, IDT told us they do not have a good quality codon usage table which they could use for A. baylyi. The only one they had access to was the one from Kazusa^[1]: a database of codon tables that was generated in 2007 using the genome and coding sequence data available at that time. For A. baylyi, only two coding sequences were available and considered for generating the table, and this wasn’t statistically significant. However, a large number of coding sequences have been identified from the sequenced genome of A. baylyi now and we decided to build a software tool to generate the codon table ourselves. We have integrated this tool with ChassiDex, hoping to help out synthetic biologists who find themselves in a similar situation as ourselves. The tool is hosted at CUTE ChassiDex and has the following features designed for the end user who is not a geek in programming:

Completely Graphical User Interface (GUI), no coding or command line knowledge is required to use the tool.
Runs in the web browser and hence across all Operating Systems (Windows/MacOS/Linux)
No download/installation required.The tool can be used by simply visiting the website. Even on the website, no login or registration is required to use the tool.
It is written in JavaScript and the entire program is front-end, which means we do not have to manage server-side code. This reduces operating costs for us.

Future improvements:

We used this tool to generate a codon usage table for Acinetobacter baylyi, which was used by IDT to codon optimize our GFP reporter protein.
We also found this codon optimized version of GFP to show a higher expression in A. baylyi compared to the unoptimized one.

Code on GitHub

A Codon Bias Table generated for a FASTA Sequence taken from NCBI

ComicSyns

Draw SynBio circuits with ease! ComicSyns is an icon font that lets you draw SynBio circuit symbols by simply typing in characters on your keyboard! The symbols are adapted from SBOL Visual^[2]

Code on GitHub

ComicSyns Main Page

Link to our GitHub organisation

References

Nakamura, Y., Gojobori, T., & Ikemura, T. (2000). Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Research, 28(1), 292.