Pumas Boot Camp - 2020
This is the first public release of a pharmacometric learning repository from India that was built from ground up using Pumas (Pharmaceutical Modeling and Simulation) platform. This repository is open to contributions and will grow over time.
This repository contains the 50 exercises from Pharmacokinetic and Pharmacodynamic Data Analysis: Concepts and Applications by Gabrielson and Weiner. We thank the authors of the textbook for permitting us to publish our learnings via an open forum. The repository is open to contributions and will grow over time.
We are a group of sixteen pharmacometric enthusiasts comprising students, research scholars, and academicians working in different universities and research institutes across India. We are extremely proud to be associated with the first Pumas Boot camp (PBC), the end product of which is this release of 50 end-to-end reproducible examples of Pharmacokinetic (PK) models written in Pumas. This is a significant achievement given that most of us were just getting started in the fundamentals of PK and started the PBC with little to no background experience in coding. The fact that we achieved this in a 100% virtual setting showcases the possibilities ahead, both in terms of conducting such activities and learning from experts. Last, but not least, as a community, especially in academia and research institutes in India, education on such advanced topics and the tools to perform such analytics were historically not accessible. The availability of an advanced modeling and simulation tool, Pumas has changed that as it allows us to explore and learn in a modern, fast, and innovative tool.
We strongly believe that this will be the impetus for a more widespread growth of modeling and simulation science in India, which has historically been subdued by the lack of expert education and accessible tools.
Where is the repository and how to access it
The repository and the examples are being developed as part of Society of Pharmacometrics and Health Analytics (SOPHAS) and can be accessed here.
However, if you would like to browse through the repository examples, they can be easily accessed via the Pumas Tutorials website at tutorials.pumas.ai
The Workshops that lead to the Boot camp
In February 2020, there were a series of 5 workshops held by the Society of Study of Xenobiotics (SSX India) in Mumbai, Hyderabad, Bangalore, Pilani, and Noida that were conducted by Dr. Vijay Ivaturi from the University of Maryland School of Pharmacy and Dr. Surulivel Rajan from Manipal College of Pharmaceutical Sciences. The goal of these workshops was to provide a basic understanding of the science of modeling and simulation and provide hands-on experience in Pumas, a new age modeling and simulation platform written in Julia Language.
Sixteen of us across the workshops reached out to Vijay and expressed interest to learn and explore further. This interest sparked the idea of conducting this PBC. The sixteen of us represented different levels of background experience in coding and modeling and simulation.
The PBC was structured to enable deep learning of the simulation tools
The Pumas Boot camp kicked off on March 16th, 2020, and was designed to be an 8-12 week intensive learning experience with set intermediate deliverables. The primary objective of the event was to learn and understand the 53 Pharmacokinetic modelling exercises presented in Gabrielson and Weiner’s Pharmacokinetic and Pharmacodynamic Data Analysis: Concepts and Applications, 5th ed. textbook and reproduce the models in the book using Pumas.
The format of the event was to have 4 teams and 12 weeks to complete modeling 53 exercises. A slack channel was created for all members to communicate in real-time and regular meetings and didactic activities were held via zoom. Every week, each team received a set of exercises for which they had to learn the science, understand the model, and then develop the corresponding Pumas code to reproduce the results in that exercise.
The lectures and exercises were focused on the following
Pharmacokinetics concepts: For each exercise, a deep-dive discussion was held to understand the basic pharmacokinetic principles and the questions being asked in the exercise. Such discussions happened within each team, but the meetings were open for others to join. This allowed all members to learn from each other.
Project Management tools: The importance of a solid project management workflow was stressed upon us initially and a version control system was chosen. We were introduced to Git and it’s tools for project management. Github is a website that allows you to store your code on the web and collaboratively work with multiple individuals.
Julia as a language: A “no compromises” programming language for data scientists, Julia combines the ease of a dynamic language with the speed of a compiled language. We were taught to code in Julia using JuliaPro
Pumas framework: Pumas is a Julia-based comprehensive platform for pharmaceutical modeling and simulation and this software served to be our workspace for constructing all the 53 PK models.
Forums to ask questions: “The art and science of asking questions is the source of all knowledge”. As new users to Julia and Pumas, we used various online resources and discussion forums in addition to our internal slack channel. These include the Pumas discussion forum, the Julia discussion forum, and multiple other resources that are listed at the end.
Documentation and Good practices: We, the user group, began to document our efforts and not only use the resolutions to their issues on time but also retain that knowledge for later use.
Use the tech wisely: As we still grapple with the impact of COVID-19, the role of technology became even more critical in these unprecedented times. Technology products and services were indispensable to supporting us to work remotely and achieve the goal of the boot camp.
Material that educates: We not only learned, but have also started to transfer what we learned so far, to the next generation user group of Pumas, through blogs, videos, and notes.
We faced our Challenges through teamwork and Collaboration
Anything you do for the first time is going to raise a great deal of skepticism about whether something like this will work? The organisers did a great job of convincing people across different locations, the list started with some 8-10 people initially and gradually expanded to about 16 as the event gained momentum. For example, we had the opportunity to introduce ourselves more than twice in 6 weeks, because someone new would join every other week.
The biggest challenge was securing venues in different places. Oh sorry, securing 100% internet connectivity all day long, especially during team meetings. Well, we indeed missed those tea breaks and the hot piping samosas which we would get in whole day events like this boot camp. The advantage of any virtual whole day event like this, there was no worry about important logistics needs like food, drinks, and in some places security staff, etc.
Being able to connect from home at one’s one comfort, technology did an excellent job of addressing these challenges and moving forward seamlessly.
Virtual Platforms kept the Boot camp running seamlessly
“Collaboration equals innovation” as they say, amidst the global pandemic COVID-19, we leveraged technologies to virtually collaborate, communicate, and pursue this boot camp. Thanks to the online meeting platforms such as Zoom, Webex and Google Meets that allowed us to flawlessly connect from home and allowed us to achieve the deliverable. This boot camp included researchers/students and faculty across India and a helping hand from the US.
Our Next Big Steps will be Collaborating with Global Experts
At the outset, it was super fun to work with researchers, on hot topics in pharmacometrics and successfully achieve the goals of the boot camp. Yes! Check out the repository on GitHub that has 50 pharmacokinetic models from Gabrielson's book out there for you!
Oh, we have an announcement, don’t miss out on the blog post coming up soon on how we took the next leap in the field by collaborating with global experts, and conducted INTEGRATE PHX 2020. It’s bigger in scale, we had global experts in pharmacometrics, programming, The Julia developer team on board, and the majority of the early-stage researchers/students who participated at PBC 2020 participated through a reliable cloud platform from across the globe.
‘PUMAS is My New Addiction’
Usually, people have some sort of addiction in their lifetime, I do not know how I got Pumas and coding as my addiction, but believe me the way Dr. Ivaturi has walked us through the workshop, I made up my mind that this is the science I am looking for. Coming from a Drug Regulatory field where there is always a set of guidelines, I found a new “Me” when I started working on various pharmacokinetics exercises in Gabrielson & Weiner book. I had so much of “FITOOR (-Passion)” for this work that in case if I am not able to do it in a daytime (due to my work-from-home job), I would work almost for the whole night. My husband was like: I am feeling jealous that you love coding/PK exercise more than me now :)!!! Few important Lessons: NEVER EVER UNDERESTIMATE the importance of “()” (parenthesis) and “.”(dot) in Pumas. As wrong parenthesis in Differential Equation (Dynamics Block) can lead to a complete change of the meaning of drug movement in different compartments … Trust me, BEST ADDICTION EVER – much better than “ALCOHOL & NETFLIX” :) ----- From Arti R. Thakkar
The Pharmacometrics Bootcamp Team
In no particular order, “Kudos to us”.
Dr. Surulivelrajan Mallaysamy, Dr. Arti R Thakkar, Anand Patil, Aishwarya Ravi, Saikumar Matcha, Architha Aithal, Parsshava Mehta, Arun Prasath, Monika Dauluri, Devika Unnithan, Nikita Ramwani, Ramya Mahadevan, Rishav Kumar, Priya Sharma, Shyam Sundar Ramesh, Nvisha Sharma, Vijay Ivaturi
Acknowledgments:
We acknowledge and thank Dr. Dan Weiner for permitting us to use the case examples from their textbook. This book is an excellent reference for anyone who wants to learn the essential concepts of PK-PD modeling and we are happy to have used this book for pharmacometrics learning and practice
Dr.Thanga Mariappan, President, SSX India Chapter for being instrumental in organizing pharmacometrics workshops using Pumas tool across India
Dr.Vijay Ivaturi, University of Maryland School of Pharmacy for supporting our initiative and helping us all along with his inputs and guidance and also being the brain behind the Pumas tool and allowing students and academicians to use the tool without any restrictions.