Chris Morris presents West-Life, a world-wide e-infrastructure for structural biology | OSFair2017 Workshop Workshop title: Open Science as a service: tools for research communities Workshop overview: The aim of this workshop is to work with research communities especially interested/relevant to open science publishing paradigms: publishing of literature, datasets, methods, and experiments for reproducibility and transparent assessment of science. This will be an interactive session with communities presenting their requirements and current tooling to identify overlaps, better and cost-effective solutions. When: DAY 2 - PARALLEL SESSION 3

1. West-Life:
World-wide E-infrastructure for
structural biology
Chris Morris, STFC

2. Outlook
• Structural biology aims to understand the molecular
basis of life
• Experimental centres
– Synchrotrons (MX), 47 in world
– Electron microscopes (EM), rapid growth
– Nuclear Magnetic Resonance (NMR) instruments, ~200 in Europe
– A long tail of other techniques
• Researchers in every university
– And in pharmaceutical companies
– Around 25,000 structural experiments per year

3. Scientific Process
• Identify a protein of interest (“target”)
• Make recombinant DNA (“construct”)
• Express in E.Coli or other tractable culture
• Purify
• Can crystallize? MX
• Can’t crystallize? EM, NMR etc
• Determine structure using software tools
– Automatic for simpler MX structures
– Months of guided computation for some EM structures
• Publish…
Sample
Prep.

4. Scholarly communication practices
• Literature
– Life Sciences papers are often open
access
• Datasets:
– Final structure is deposited in Protein
Data Bank
– Intermediate data too
• Software suites and services
– CCP4, Phenix, weNMR
– Rapid developments for EM
PDB new entries / year
(log scale)

5. Scholarly communication desiderata
• Archiving experimental data
– Some progress, but 100M for MX, 1TB for EM
– XFEL a firehose
– full access for reviewers
• Full provenance, structure to sample
– Reproducibility of sample prep is poor
• Reproducibility of processing
– PDB-REDO reprocesses with latest algorithms
• Automatic acquisition of metadata
– Scientists don’t like housekeeping

6. For more detail…
The Life Cycle of Structural Biology Data
https://www.rd-alliance.org/group/structural-biology-
ig/outcomes/life-cycle-structural-biology-data
Corresponding author: Chris Morris
Contributors: Claudia Alen, Lucia Banci, Alexandre Bonvin, Pablo Conesa, Alfonso
Duarte, John Helliwell, Rob Hooft, Brian Matthews, Antonio Rosato, Sameer Velankar,
Geerten Vuister, John Westbrook, Martyn Winn