AMARCORD

Contents

• Install and run
  • General Notes
  • Getting the source
  • Python parts
  • Web interface
  • Using Docker
  • Using Singularity
  • Building the documentation
  • Command line tools
• Understand
  • AMARCORD’s scope
  • Database design
  • Workflows
  • PanDDA
• Contribute
  • How to contribute
  • General notes
  • Components
• DESY specifics
  • Location on GPFS
  • Singularity Scripts
  • Starting a GUI for the SARS-CoV-2 DB on Maxwell
  • P11 live process and ingest
• Learning Resources
  • SQL
  • Frontend
  • Python
  • Continuous Integration
• Misc
  • Design Choices

Project description

AMARCORD — formerly called “The Database” at DESY — is a software originally developed at CFEL for utilizing a database to organize compound screening pipelines. It has been used to screen the Main Protease of the SARS-COV-2 virus against thousands of available compounds and offers rich introspection into the process. It has since then been used in other campaigns, and strives to be an easy-to-use and easy-to-set-up “home database” for crystallography.

Project status and timeline

Here’s a short timeline of the project so far:

• April 2020: A first prototype is developed and is successfully used in a screening campaign (the source code for this prototype is private, unfortunately). It’s still being actively used, but not actively developed anymore.

• April 2021: A second prototype is available for use at EuXFEL which is successfully used in a single beamtime (source code will be opened at some point). The database and project structure is completely rewritten for this project.

• September 2021: Keeping the database schema of the first prototype, the graphical user interface (written as a desktop application using PyQt) is switched to a modern web interface. Other modernizations are made.

• December 2021: The EuXFEL prototype of AMARCORD was used in conjunction with the CFEL TapeDrive2 to organize and automatically ingest data from the P11 beamline at DESY.

Who is developing AMARCORD?

The main developer of the project is currently Philipp Middendorf at CFEL. For questions, issues and any correspondence you can write a mail to sc@cfel.de.

Projects working with AMARCORD

• xia2pipe — Software that uses the database to trigger SLURM jobs to process and refine data. Still actively maintained (Link might be DESY-only)

Alternatives

• FragMAXapp — a web application for processing and visualisation of macromolecular crystallography data, with the focus on fragment screening campaigns

• XChemExplorer - a graphical batch data processing tool for protein crystallography