Francis Crick Institute: Python Training

Francis Crick Institute: Python Training

The Francis Crick Institute


Biomedical Research

The Challenge

The Francis Crick Institute host a number of biomedical experts and statisticians undertaking cutting edge research to help improve treatment, diagnosis and prevention of human disease. Facilitating data intensive research often necessitates programming skills.

To help achieve their goals, the Institute asked us to provide training in Python programming to groups of research staff. Their aims range from undertaking traditional statistical analysis to writing code to help conduct experiments. One of the challenges here was to tailor the training program to their domain, making the content engaging and relevant to experts in genetics and biomedicine.

The Project

We continue to deliver a regular training program for researchers at the Institute. A pathway of sessions ranging from introduction to the language, through programming concepts, data analysis and modelling and visualisation have been put together with bespoke content focusing on topics such as RNA sequencing. Through each iteration, we work with the team at the Francis Crick to refine and further tailor the training program, resulting in a unique offering built just for them.

To keep participants engaged we developed a range of materials, training booklets, presentations and Jupyter notebooks to guide them through their learning journey. Training sessions are lead by an instructor through live coding demonstration and discussion. The sessions are fully interactive throughout, encouraging participants to work together and writing code from the off.

A virtual training environment is provisioned for training courses, giving access to Jupyter and training resources in the cloud. This serves as a useful centrepoint for resources and provides a fail-safe should there be any installation and setup issues on individuals’ laptops prior to a session.

Our Results

This is an on-going delivery with the Francis Crick Institute. Feedback is always positive and we continue to expand upon the training roster specifically tailored to their work. We have successfully delivered training to hundreds of researchers who are now using Python to further their research.

So far we have delivered training at a range of levels to more than 100 researchers during over 30 courses.

Relevant Case Studies

DiAGRAM: A Shiny app for the National Archives

The National Archives

Jumping Rivers created a feature rich, bespoke Shiny dashboard through a series of development and user testing sprints. Custom widgets were created using React, to give a tailored application. Using a combination of continuous integration and deployment, the dashboard was deployed directly to via GitHub.

Read more about The National Archives
Scottish Government: Fair Work Data Explorer - Shiny App

Fair Work Data Explorer

Jumping Rivers created a data pipeline and visualisation dashboard for public and policy maker consumption. The aim was to increase transparency and encourage positive change to the workplace environment. The application allows exploration of key performance indicators stratified by a host of protected characteristics.

Read more about Scottish Government
Banking Firm: Code Review & R Package Development

Banking Firm

The client came to Jumping Rivers having already written the code for their problem in VBA. They were trying to evaluate four measurements for agreements with their clients. However, VBA is limited in speed. Jumping Rivers were required to build a bespoke R package to replace and quicken the code.

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TRACS International: Dashboard Development for Monte Carlo Simulation

TRACS International

At the end of 2017, TRACS International contacted Jumping Rivers. TRACS International estimates the volumes of oil and gas in subsurface reservoirs. Their work involves combining a set of inputs for each reservoir layer (such as area, thickness, and up to five other inputs) – and then multiplying these inputs together.

Read more about TRACS International
Electrics Company: Applying Machine Learning Tools to Highlight Anomalous Data

Electrics Company

Over the last two years, we have been working with a cutting edge electronics company to build advanced algorithms using R and Python. Since they are at the research & design stage of the development process, their data structure is unique and challenging.

Read more about Electrics Company
Environment Agency: Development & Deployment of 'Water Body Explorer' Shiny App

The Environment Agency

After winning a Water Hub Hackathon, Jumping Rivers were contracted to create a platform for the client using R Shiny, published on Posit Connect. The platform aggregates raw data from many third party sources both internal and external to the EA, through bespoke APIs, commercial databases, and asset management systems.

Read more about Environment Agency
Financial Institution: Bespoke Report Generation using R Markdown

Financial Institution

The client wanted to assess the viability of R and R Markdown as a reporting tool for creating complex, bespoke documents. We recreated sample reports for them in R Markdown, showcasing that all of their specifications could be met, and provided them with example code and training.

Read more about A Financial Institution
Fujifilm: Shiny Dashboard Creation for Experimental Risk Assessments

Experimental Risk Assessments

Jumping Rivers built a tool for creation of experimental risk assessments via a centralised web application. The dashboard allows for collaborative working during the data entry and assessment formulation, report generation and tracks versions along iterations of the process.

Read more about Fujifilm
NHS Scotland: R Training

NHS Scotland

In the spring of 2018, NHS Scotland expressed a need to move from their existing software, SPSS and SAS, to using R. The difficulty they faced was that there are over two hundred data scientists in NHS Scotland, which made training everyone in the new software a logistical challenge.

Read more about NHS Scotland
Northumbrian Water: Interruption to Supply Risk Mapping using Spatial R Package

NWL Risk Mapping

In spring of 2020 Northumbrian Water engaged with Jumping Rivers to build a modelling solution to better understand risks to the consumer within their network in order to provide a better service.

Read more about Northumbrian Water