PReSTO in support of Swedish structural biology

Structural biologists use Macromolecular X-ray crystallography (MX), Nuclear Magnetic Resonance (NMR) and cryo Electron Microscopy (cryo-EM) to determine 3D structures of macromolecules such as proteins, DNA and RNA. To address complex research questions structural biologists is now stretching towards cellular length scales with techniques such as cryo-EM tomography and X-ray imaging while capturing dynamics via correlative microscopy and molecular dynamics (MD) simulations. The multi-purpose and multi-technique approach to characterize how macromolecules and their assemblies interact with virus and other pathogens in space and time is known as integrated structural biology. Today structural biologists experience an increasing amount of experimental raw data being collected by modern photon counting detectors at national and international facilities. Swedish structural biology research groups using the Swedish MAX IV light source for macromolecular X-ray crystallography and the cryo-EM facilities at Science For Life laboratories are generated large amounts of raw data that require supportive and research driven computational and storage solutions.

PReSTO is available at NSC computer Tetralith, LUNARC computer Aurora and the MAX IV cluster. The NSC and LUNARC installations are available through SNIC, while the MAX IV cluster is accessible when having MX beamtime at BioMAX.

Academic PReSTO access

Swedish structural biologists can access and use PReSTO by requesting membership in compute project (SNIC 2020/5-368):

1. Download and install thinlinc client for your computer
2. Register yourself in SNIC User and Project Repository (SUPR)
3. Go to SUPR Project page
4. Search for SNIC 2020/5-368 and Request membership in that project
5. MX software may require academic online registration (e.g. Phenix), or signing of an academic license agreement on paper (e.g. CCP4). We made a set of links to license pages for MX software available in PReSTO. Once your personal academic registration and licensing is done, please contact LUNARC that will add the newcomer to the PReSTO group for MX software access at LUNARC.
6. LUNARC Aurora access: General and MAXIV specific instructions
7. NSC Tetralith access: Accept the user agreement and Request the login account at Tetralith

SME PReSTO acccess

Small and Medium sized Enterprises (SMEs) can access and use PReSTO via SMILE.

Acknowledgement to MX software authors and SNIC

We are indepted to all MX software authors that kindly share their software for academic use in an HPC environment. We list all MX software currently in PReSTO installation with links to software home page and citations. Specifically we want to mention Gérhard Bricogne and Claus Flensburg from GlobalPhasing supporting the PReSTO project since its very beginning and shared all their MX software for academic HPC use including autoPROC with Staraniso for convenient elliptical scaling of diffraction datasets. We also want to mention the developers behind XDSAPP version 2.99 (Karine Röwer, Uwe Müller and Manfred Weiss) sharing a pre-release that can process Eiger data containers directly and Graeme Winter from the DIALS development team sharing a BioMAX specific software patch for DIALS.

Beside MX software authors, the Swedish National Infrastructure for Computing (SNIC) also require acknowledgements upon publishing. Please find a SNIC acknowledgement template

Aim of this documentation

We attempt to provide get started instructions to the PReSTO environment and simply share links to excellent MX software guides and tutorials generated by MX software developers.

History of PReSTO

• 2013 PReSTO starts
  • In March 2013, the outreach activities of National Supercomputer Centre (NSC) attracts Protein Science Facility in transfering a standard Linux MX software setup into the High Performace Compute environment of NSC. PReSTO is coined.
• 2014 PReSTO menu
  • First development of the PReSTO menu.
• 2015 PReSTO get MAX IV satellite status
  • MAX IV and NSC formally decided to develop a HPC platform for MX in support of Swedish MAX IV users giving the PReSTO project the status of a MAX IV satellite.
• 2016 Easybuild installations at NSC
  • The PReSTO installation has been performed by Easybuild for rapid sharing with other Swedish HPC centers coordinated by SNIC.
• 2018 Funding from the Swedish Research Council
  • Swedish Research Council grant funding to researchers and staff from SNIC, MAX IV, Cryo-EM SciLifeLab and Swedish NMR Center to work on a collaborative software platform for Swedish structural biology
• 2020 SNIC storage project
  • We now use a complementary SNIC storage project (SNIC 2020/6-273) to support the compute project. Storage will be ramped up at NSC Tetralith reaching 20 TB and 10 M files in December 2021, while at LUNARC Aurora we have 5 TB and 2.5 M files (no ramping). However if this is too small for your project or if you plan to run molecular dynamics simulations, apply for your own compute time at NSC Tetralith or LUNARC Aurora or perhaps at Kebnekaise if interested in Cryo-EM. PReSTO project membership grant access to MX software however having your own compute time allocation is required when combining MX with compute intensive molecular dynamics or Cryo-EM calculations.
• 2021 LUNARC Aurora final year
  • Since 1 Jan 2021 LUNARC Aurora is no longer a SNIC resource, however PReSTO installation remain and can be used under a local LU project (LU 2021/2-54)