The database of small-angle scattering data and models for biology and soft matter

Due the sanitary conditions, the workshop will be held in hybrid mode!

Organisers: Manfred Rößle, Dmitri Svergun, Dima Molodenskiy

• Registration: Closed
• Facebook
• Questions: please contact the organisers - dmolodenskiy(at)embl-hamburg.de

Small-angle scattering (SAS) of X-rays and neutrons (SAXS and SANS) is a fundamental tool to study the structural properties of materials at the nanoscale. In the biology field, the SAS biological data bank (SASBDB) designed in 2014 is available for public access at www.sasbdb.org. SASBDB is a comprehensive, free and searchable repository of SAS experimental data and models that are deposited together with the relevant experimental conditions, sample details and instrument characteristics.

Despite the broad use of SAS in soft matter no public repository of data, parameters and models was available so far. The SASBDB framework offered a possibility to also cover the soft matter applications and the recent developments in automation and extensions of SASBDB will be presented and discussed.

For biological depositions, recent improvements of the workflow and further automation of the submission and curation procedures were implemented and a cleanup of the existing SASBDB entries was conducted. For soft matter, requirements for the experimental and meta-data formats were established and possibility was offered to deposit anisotropic (two-dimensional) scattering data. Validation approaches for the experimental data, fits and structural parameters were appropriately enhanced.

These developments were performed in collaboration between the EMBL Hamburg and the Fachhochschule Lübeck, supported by the BMBF grant FKZ 16QK10A SAS_BSOFT. During the grant period (2018-2022), SASBDB grew by 1280 entries with 1700 deposited models, i.e. by 75 percent. At the workshop, the major recent advances in SASBDB for biological and soft matter depositions, standards and curation will be presented. The directions of further SASBDB maintenance and development will be discussed with the community.

SASBDB is a curated repository for small angle scattering data and models.

  The workshop is supported by BIOSAXS GmbH.

Program

Thursday, May 12, 2022

Introduction

• 10:00 - 10:30 SASBDB and soft matter extension - Manfred Rößle (TH Lübeck, DE)
• 10:30 - 11:00 Present status of SASBDB - Cy Jeffries (EMBL Hamburg, DE)
• 11:00 - 11:30 Deposition, integration, curation interface - Dima Molodenskiy (EMBL Hamburg, DE)
• 11:30 - 12:00 Automation of SASBDB tasks - Al Kikhney (Xenocs, DK)
• 12:00 - 12:30 The story of UPR modulation by CDNF - Arnab Bhattacharjee (Herantis Pharma, FIN)
• 12:30 - 14:00 Lunch break

Integration into federated archive system

• 14:00 - 14:30 Federation with wwPDB/EMDB - Sameer Velankar (EMBL EBI, UK)
• 14:30 - 14:50 Principles of model representation for intrinsically disordered proteins - Peter Tompa (University of Brussels, BE)
• 14:50 - 15:10 Protein ensemble database (PED): organisation, data storage and links - Damiano Piovesan (University of Padova, IT)
• 15:10 - 15:40 Potential extension to powder diffraction - Irene Margiolaki (University of Patras, GR)
• 15:40 - 16:40 Discussion

Friday, May 13, 2022

Soft matter extension of SASBDB

• 10:00 - 10:30 Soft matter interface/deposition - Sia Schewa (TH Lübeck, DE)
• 10:30 - 11:00 SAXS/SANS for food colloids - Elliot Gilbert (ANSTO, AUS)
• 11:00 - 11:30 Deposition for nanoparticle systems - Martin Schroer (University Duisburg-Essen, DE)
• 11:30 - 12:00 Deposition for lipid phase transitions - Thomas Gutsmann (Research Center Borstel, DE)
• 12:00 - 12:30 Concluding discussion/remarks - Dmitri Svergun (EMBL Hamburg, DE)