Jon Fuller

Profile

I help teams design and build data science applications that scale in the cloud.

Employment

Director, Team Leader Data Products

Idorsia Pharmaceuticals Ltd | August 2021 to present

I manage a team of four scientific software engineers and data scientists. We prefer to work with Gitlab CI/CD, Infrastructure as Code (Terraform), AWS Serverless technologies (S3, Lambda, Fargate, Aurora Serverless, Athena), Java Spring Boot, Python FastAPI, and Low Code User Interfaces (Retool). We maintain and develop our Imaging platform containing nearly 100TB of images, supporting use cases in Toxicological Pathology, Pharmacology, and High-Content Screening (including Cell Painting assays). Currently we are migrating this to a cloud native architecture using AWS Lambda, ALB, EFS, S3. Together with our scientific partners we develop novel machine learning techniques to apply across the DD research value chain. Most recently this included enrichment of HTS screenings using generic HCS assays, and ChatGPT as an enhanced information retrieval tool. My role involves a mixture of technical work (~60%), coaching team/group members, and project/stakeholder management.

Scientific Software Developer

*Idorsia Pharmaceuticals Ltd | November 2019 to August 2021

Scientific Software Developer: Co-lead developer for Orbit Image Analysis software. Image Analysis Specialist: Developed deep learning based image analysis models to support Digital Pathology. Cloud Architect (AWS): Design and build an HPC environment to support NGS Analysis (AWS Batch), and deploy/manage multiple application servers (AWS Fargate).

Solution Architect

KNIME AG | April 2017 to October 2019

Multiple responsibilities within a small and growing startup. Product owner (KNIME Server). Define software requirements, manage priorities. Involved in defining strategy and technical guidance for marketing strategy. Manage the priorities and technical direction for the development team. Architecting new microservice setup, with deployment on Kubernetes (AWS EKS).

Cloud Architect

KNIME AG | April 2016 to October 2019 Cloud marketplace AMI/VM build automation and submission (AWS and Azure) using Packer and Jenkins. Linux and Windows Server builds. Templated launch of multi AMI deployments using AWS CloudFormation. Investigating KNIME software usage models with AWS and Azure services such as S3, Redshift, Athena, HDInsight, SQL Server.

Application Scientist

KNIME AG | April 2015 to October 2017

Pre-sales application support. Software demos. Suggest deployment architectures for prospective customers. Building PoCs using KNIME software. Life Science specialist.

Research Scientist

Heidelberg Institute for Theoretical Studies | October 2010 to March 2015

• Software tools to assist systems biology researchers with data mining and integration
• Homology modelling and simulation of proteins to support experimental partners
• Drug binding kinetics and mechanisms governing binding kinetics
• Molecular dynamics simulations of proteins, and phospholipid bilayers
• Brownian dynamics simulations for protein docking, and to calculate binding kinetics
• Detection and characterisation of protein-ligand binding sites

Education

PhD Bioinformatics

September 2006 to September 2010

PhD study at University of Leeds, supervised by Richard Jackson.

Thesis title: Computational approaches for drug design at the Protein-Protein interface

My PhD was primarily focussed on questions regarding the concept of how ‘druggable’ a pocket on a protein surface might be, and on performing alchemical free-energy calculations on small-molecule mimetics of a helical portion of the p53 protein that regulates apoptosis via binding to a pocket on the hDM2 protein.

My studies included a 2 month visit to work in the laboratory of Prof. Michael Shirts at the University of Virginia funded by a CCPB USPA travel award. This resulted in the publication of 2 articles describing work carried out in part in Virginia.

BA Physics, Class II Division 1

September 2003 to July 2006

Studied Physics, and included coursework in Java Programming.