West-life services and tools for structural biology

Transcription

1 West-life services and tools for structural biology Tomáš Kulhánek STFC Daresbury Laboratory Catalin Condurache STFC Rutherford Appleton Laboratory CernVM Workshop, CERN,

2 West-Life West-Life is a H2020 Virtual Research Environment project that aims to provide the application level services specific to uses cases in structural biology, covering all experimental techniques (e.g. Xray, cryo-em, NMR, SAXS), enabling structural biologists to get the benefit of the generic services developed by EUDAT and the EGI. 10 partners, STFC (UK), Instruct, NKI (NL), LUNA (FR), UU (NL), CIRMMP (IT), INFN (IT), EMBL, MU (CZ), CSIC (ES)

3 Members of the Fore tribe of Papua New Guinea

4 Kuru disease Fore people were being struck down by a fatal debilitating disease. The victims initially lost their ability to walk Followed by inability to swallow or chew. This led to weight loss and death Caused death of 2% of Fore people per year.

5 Structural biology Study the structure of proteins

6 Protein structure determination X-ray crystallography

7 Cryo electron microscopy Transmission electron microscopy Sample is vitrified in liquid ethane Images noisy 2D projections Class averages are constructed for each orientation Ultimately results in 3D density maps

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9 Nuclear Magnetic Resonance

10 Protein structure Protein Database PDB ( Uniprot (uniprot.org) - resource of protein sequence and functional information

11 West-Life Integrate existing software tools and methods - X-Ray crystallography (CCP4), NMR (CCPN, WeNMR), Cryo-EM (CCPEM, Scipion), SAXS, SANS, Mass Spectrometry, Virtual Folder data management support, aggregation of scattered data storage providers and public databases (PDB,Uniprot) Repository exemplar implementation of data management for small facilities Virtual Machines with preinstalled software of major software tools for different techniques

12 Instruct

13 Virtual Folder configure connection to data provider, B2DROP (provided by EUDAT default 20 GB space - single, uses WEBDAV) Dropbox (multiple, proprietary API, 2GB default, up to 1TB commercial), Filesystem (multiple, local scratch disk space, mounted facility storage, USB) WEBDAV (standard interface, any storage provider, e.g. B2DROP, Pcloud, ) Simple data browser and viewer Common interface to data WEBDAV API

14 Virtual Folder access to scattered data

15 Integration with web based tools

16 Scipion PowerFit workflow

17 Virtual Machine Based on CervnVM 4 Software for structural biology distributed via CernVM FS Virtual Folder mounted as directory in file system

18 Virtual Machine Virtual machine Customized VM with software and tools installed and connected to virtual folder to support integrative structural biologist. Image size 18 MB!, first boot downloads additional 100MB, optimal for cluster/cloud deployment with caching CernVM 4.0, bootloader to Scientific Linux 7.3(RHEL) Software and tools distributed by CernVM-FS, read-only file system /cvmfs/west-life.egi.eu SCIPION, West-life related tools /cvmfs/facilities.gridpp.ac.uk CCP4 Suite /cvmfs/wenmr.egi.eu

19 Prions are infectious proteins. Prions reproduce by recruiting normal cellular prion protein (PrP C ) and stimulating its conversion to the disease-causing (scrapie) isoform (PrP Sc ). Prion aggregates are extremely stable and accumulate in infected tissue, causing tissue damage and cell death. Prion hypothesis

20 Prion hypothesis Prions are believed to cause Kuru disease, Bovine Spongiform Encephalopathy, Creutzfeldt-Jakob disease Long incubation period primary method of infection in animals is through ingestion Fore tribe, funeral feast was banned in late 1950 Decrease of Kuru disease

21 Summary West-Life project: support integrative structural biology approach Use of CernVM and CernVM-FS VM are deployed in heterogenous environment, may not have access to proxy Issues with institutional firewalls limiting access only to ports 80 and 443 Prion hypothesis: structure of prion proteins and it s link to Kuru disease (4yx2,4n9o)