Access to experimental data is the key factor for improvements of scientific reproducibility

Integrated Resource for Reproducibility in Macromolecular Crystallography

Part of the US National Committee for Crystallography workshop series on
Exploring Structural Database Use in Crystallography

The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) includes a repository system and website designed to make the raw data of protein crystallography more widely available. Its focus is on identifying, cataloging and providing the metadata related to datasets, which could be used to reprocess the original diffraction data. The intent behind this project is to make the resulting three dimensional structures more reproducible and easier to modify and improve as processing methods advance.

 Date: Apr 7, 2022 11:00AM - 2:00PM ET

Register here: Click


Speakers:

Introduction:
Stephen Burley - Director of RCSB Protein Data Bank (PDB)

John Helliwell (University of Manchester):
 IRRMC – proteindiffraction.org a growing repository of diffraction experiments used to determine protein structures in the PDB.
David Cooper (University of Virginia):
 IRRMC tools for "wrangling" data from protein diffraction experiments.
Dariusz Brzezinski (Technical University of Poznan):
 Detecting anomalies in X-ray diffraction images using convolutional neural networks
Brinda Vallat (Protein Data Bank):
 New system for archiving integrative structures
Wladek Minor (University of Virginia):
 Scientific reproducibility and access to unprocessed experimental data

Session title: Access to experimental data is crucial for scientific reproducibility

Learning Objectives

  1. Participants will learn about the proteindiffraction.org repository of diffraction experiments used to determine structures that are din the protein data bank

  2. Learn about the IRRMC tools used for working with data from the archive

  3. Learn about progress in using neural networks to find anomalies in diffraction images and malfunctions of experimental systems

  4. Learn about wwPDB plans for archival of integrative structures, whose models rely on combining information from multiple techniques and sources. The experimental data supporting the models may come from techniques such as X-ray crystallography (X-ray), nuclear magnetic resonance (NMR) spectroscopy, three-dimensional electron microscopy (3DEM), small-angle solution scattering (SAS), chemical cross-linking mass spectrometry (CX-MS), Förster resonance energy transfer (FRET), electron paramagnetic resonance spectroscopy (EPR), hydrogen-deuterium exchange mass spectrometry (HDX-MS), and other biophysical and proteomics methods.

  5. Learn how access to unprocessed experimental data impacts scientific reproducibility.