Circuit Topology - A versatile platform for biomolecular topology analysis

The Product

Our client - Leiden Academic Centre for Drug Research (LACDR) - had developed a novel framework for the analysis of proteins and DNA/RNA molecules called 'Circuit Topology'. For this, they made code in Python that could perform the analysis, but using it requires notable understanding of both the code and, in general, coding in Python. For analyzing and interacting with proteins (and other molecules) the number one go-to software is PyMOL, which does not require extensive coding knowledge. As such, our project aimed to make the client's Circuit Topology analysis code more accessible by implementing it as a GUI plugin for PyMOL.

The product is a plugin .zip file that, once imported in PyMOL, can be opened as an additional GUI with buttons and features that are integrated with both the client's code and PyMOL's own API. The impact that a complete GUI plugin has is two-fold: 1) the client's code becomes much easier and more efficient to use, and interacts with PyMOL and proteins in new ways, significantly improving the client's workflow when working with proteins; 2) the client's underlying code becomes much more accessible to the wider scientific community, growing the Circuit Topology theory's impact on science.

Link to demo of our product on Google Drive (file too large to upload): View Demo

The Customer

Our client is the Leiden Academic Centre for Drug Research (LACDR). They are a research institute that has published numerous papers on the Circuit Topology theory that they first developed and published in 2014. In 2022, the client published a paper covering the code implementation of the Circuit Topology theory in Python. Our clients were often understandably busy so getting in contact with them outside of client meetings could sometimes be challenging. We held biweekly meetings with the client during which we always held demos to generate feedback on the current working version of the product.

  • "We were successfully able to implement the code as a plugin in PyMOL with little to no bugs remaining by the end of the project."
  • "We conducted weekly meetings in order to achieve a consistent product and maintain our sprint direction."
  • "Our meetings with clients were productive despite confusion that sometimes arose due to unclear requirements."
  • "We familiarized ourselves with the basics of Circuit Topology in order to better understand the clients' code and requirements."
The Team

Our team followed the agile Scrum framework, with clearly assigned roles: Matīss was the Scrum Master and contact person, Ella served as Product Owner focusing on plugin installation and documentation. Adam, Tomas and Alex worked on plugin development, particularly with multiple file analysis and tunable hyperparameters, as well as cross-platform compatibility. Ella worked on automatic plugin installation, while Matīss worked on developing significant GUI features, such as molecule coloring/visualization and multi-chain analysis. Tomas and Adam handled extensive testing across branches, and Leila developed CT Folding Score, its appropriate unit tests, and helped define and manage our workflow with clear definitions of done and ready.

We divided work based on expertise and evolving needs. For example, Ella quickly picked up on implementing automatic plugin installation, and, consequently, was most knowledgeable on its intricacies. As such, she continued to be responsible for this part of the plugin throughout the course of the project. Collaboration happened through regular sprint meetings, updated Scrum boards, product development sessions (2x a week) and proactive peer support, especially when tasks like GUI integration or plugin installation became unexpectedly complex.

The biggest challenge we overcame was managing scope and expectations. Initially, we were overly ambitious about our weekly goals and the size of the project, but we quickly adapted by refining our planning, leading to a smoother and more efficient Scrum process.

We are most proud of the fact that our plugin is already being actively used by researchers at LACDR, fulfilling our client's vision for a robust and accessible scientific tool. We are also extremely proud that the client is satisfied with the product enough that they want to bring it to the attention of the wider scientific community.

The Technologies