Interested in quickly setting up and running in silico simulations of synthetic biological systems? Having trouble understanding the biological modeling language and tools jargon? This basic guide will go through some of the most commonly used tools and languages used for modeling and simulations of biological circuits and systems. It will also point out links and articles for more advanced development.
In this blog post, I start by talking about SBML - the universal standard language for writing biological models. Building on SBML, I talk about how to read, write, and simulate SBML models quickly using various GUI and scripting open source tools. The focus in this guide will be on Python based simulations and analysis tools.
What’s the domain of attraction of a two protein synthetic toggle switch equilibrium point? How stable is a toggle switch with disturbances and leaky expression? Answers for these and similar other questions in this blog post.
All real systems have nonlinear dynamics but unfortunately it is hard to work with these nonlinear dynamics to get meaningful and strong results that would help us in the design/engineering of these systems. Hence, linearization is often used in modeling and analysis of complex real world systems. As you can imagine, this would be a very conservative and limited approach. In this post, I talk about how we can leverage techniques from nonlinear analysis to study a common biological system - the toggle switch.
i-Bike was a student project that I worked on from 2015 to 2017. In 2015, for a student hardware competition at IIT Kharagpur, I came up with an idea of building an autonomous bike. Along with another student, Subhamoy Mahajan, we came up with a design plan and formed a team of 10 other students. Together we led this team to make this a reality – and the end product was something that does not exist anywhere in the world – something completely unique and innovative.
i-Bike is a bike that a user can hail like a taxi using their mobile phone app - the bike drives itself autonomously to the user! But that’s not all, the key innovation with i-Bike is that once the user receives the bike, they can “convert” the bike back to a normal bike within seconds and then ride this bike just like a normal bike to their destination. Finally, the user may leave this bike anywhere and the bike autonomously parks itself. All autonomous navigation is highly robust (for a bike, which is inherently unstable) since the balancing is achieved using passive control mechanisms. i-Bike could potentially revolutinize the micro-mobility industry and the last-mile transportation.
We enjoyed a lot of success with the i-Bike as a student project - winning multiple engineering design competitions, collaborating with major industry players in the automotive industry, and plenty of media attention at the time. Subsequently, we filed an Indian patent for the tech.