T7 – Exploring programmatic access to Protein sequence, function and structure with UniProt and PDBe


Date: Saturday September 8, 2018

Time: 9:00 – 17:00

Venue: Stavros Niarchos Foundation Cultural Center

Room: B_Computer Room & Maker Space




Andrew Nightingale, EMBL-EBI, Wellcome Genome Campus Cambridge, UK

Mihaly Varadi, EMBL-EBI, Wellcome Genome Campus, Cambridge, UK



Integrating publicly available biological data from multiple data sources (including your own) can be critical to analyse data and infer patterns that may not otherwise be obvious. Learn how to discover and integrate biological information as well as visualisation components from protein resources at the European Bioinformatics Institute (EMBL-EBI), with a focus on UniProt and PDBe. Learn about accessing data such as gene-protein relationships, protein sequences, protein structures and function. Explore our dedicated API services (such as the Proteins API and PDBe API) to access this data programmatically, while also learning how to integrate freely available visualisation components, such as PDBe’s LiteMol viewer and UniProt’s ProtVista to visualise both public data as well as your own.


Target audience

This tutorial is intended for participants interested in programmatic access and visualisation of protein related data. Attendees should have a background in biology or computational biology, with knowledge of protein biology and some experience of scripting (in any language).


Tutorial website

All material related to the tutorial will be available from the tutorial’s Github page.


Provisional schedule

9am Introduction to open protein data from EMBL-EBI and applications
10am Guided hands-on exploration
10:30am Coffee break
11am Introduction to UniProt and PDBe programmatic access services and APIs
12pm Guided hands-on exploration
12:30pm Lunch
1:30pm Introduction to UniProt and PDBe open access visualisation components
2:30pm Guided hands-on exploration
3pm Coffee break
3:30pm Group workshop


The Group workshop at the end of the day will be an opportunity for you to work on solving data analysis problems. If you have your own topic that you wish to submit, so you or a small group can develop code to solve, then submit as an issue to the workshop Github. These will be added as data analysis problems.


5pm Close


Requirements and materials

We recommend that participants bring their laptops with an installation of Python v3.6 or higher and Jupyter Notebook. If you would like to use Java or another language instead of Python during the hands-on sessions, that’s fine too.