1.
Why we need PIDs for Structural
Biology
Marcus Povey
EOSC Symposium, Budapest
November 2019

2.
Instruct-ERIC
• Instruct-ERIC helps facilitate access to
cutting edge research infrastructure
within the domain of Structural Biology
• We have centres all around Europe
• 13 member countries, with 2 observers
• Funded through direct member country
contribution at the ministerial level

3.
Instruct on the ESFRI Roadmap

4.
Our Mission
• ACCESS – Facilitating access to cutting
edge research infrastructure and
methods
• FACILITY – Helping research
infrastructures manage their equipment,
and representing their interests
• COMMUNITY – Contributing to the wider
scientific community as a whole, and
helping researchers, projects and
infrastructures work better together
• DATA – Improving access to research data,
and facilitating Open Access
• ARIA Cloud!
DATA
FACILITY
ACCESS
COMMUNITY

5.
Structural Biologists
use Microscopes
• 12 Samples (grids) in a loader
• Each grid can potentially have multiple
structures that are of interest (projects
with 96 well grids are underway)
• Outputs ~1-3TB of HD Video per day

6.
Electron Microscopy
Researcher submits a
proposal for access
Researcher produces a
sample locally
Sample is loaded
onto a grid
Grid goes into Electron
Microscope
Micrographs go into
pre-processor
Particle picking, auto
& manual processing
Datasets are
analysed by 10s of
software packages
3D structure
determined
Structure deposited
into PDB/EM-DB
Researcher submits a
publication to journal

7.
There are a lot of
things to track…
• Number of sample grids
• Potentially multiplied by samples on
a grid
• Multiplied by grids in a microscope
• Multiplied by frames of video
• Multiplied by number of microscopes per
facility
• … multiplied by the number of facilities.

8.
... But wait, there’s
more!
• We need to know the data processing
workflows used
• We need to identify samples and
associated metadata
• We need to know a given machine’s
configuration
• Software and software versions used to
process and analyse data
• Researchers involved in project
• Funding applications (proposals)

9.
Structural Biologists
also use
Synchrotrons…
• Similarly large data volumes
• Similarly complex machine configurations
• Similarly complex data processing
workflow to produce results

10.
Crystallography
Researcher submits a
proposal for access
Researcher produces a
sample locally
Sample added to
crystal plate
Crystal plate imaged
regularly
Crystals loaded onto
pins
Crystals shot with X-
Rays at synchrotron
Diffraction pattern
auto-analysis and re-
running
3D structure
determined
Structure deposited
into PDB
Researcher submits a
publication to journal

11.
Why Identify? –
Improving workflows
• Different samples need to prepared in
different ways
• Not all experiments are successful
• Do-overs are expensive!

12.
Why Identify? - FAIR
• Want to be FAIR! (improve findability,
interoperability and reproducibility of
data sets)
• Commitment to Open Access
• But… Data sets are too large to practically
move about
• Machine configurations are often only
available on the machine itself
• Software gets modified
• How do we make this findable, accessible
and reusable?

13.
Some Problems to Consider
• Will require minting of large quantities of PIDs
• … In near real time
• Metadata schema around existing PIDs seem focussed around
publications
• ... But we’d need to extend (and make it machine readable)
• … ditto how best to link / graph data together
• Some facilities have rolled their own solutions, how to cooperate?

14.
@ARIA_access
aria@instruct-eric.eu
Thanks!