Services for the European Open Science Cloud

Training material

E.g., 11/13/2019
E.g., 11/13/2019
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This section provides a list of training materials being used during the EOSC-hub training events.

DisVis web server Tutorial

DisVis is a software developed in our lab to visualise and quantify the information content of distance restraints between macromolecular complexes. It is open-source and available for download from our Github repository. To facilitate its use, we have developed a web portal for it.

This tutorial demonstrates the use of the DisVis web server. The server makes use of either local resources on our cluster, using the multi-core version of the software, or GPGPU-accelerated grid resources of the EGI to speed up the calculations. It only requires a web browser to work and benefits from the latest developments in the software based on a stable and tested workflow. Next to providing an automated workflow around DisVis, the web server also summarises the DisVis output highlighting relevant information and providing a first overview of the interaction space between the two molecules with images autogenerated in UCSF Chimera.

The case we will be investigating is the interaction between two proteins of the 26S proteasome of S. pombe, PRE5 (UniProtKB: O14250) and PUP2 (UniProtKB: Q9UT97). For this complex seven experimentally determined cross-links (4 ADH & 3 ZL) are available (Leitner et al., 2014). We added two false positive restraints - it is your task to try to identify these! For this, we use DisVis to try to filter out these false positive restraints while assessing the true interaction space between the two chains. We will then use the interaction analysis feature of DisVis that allows for a more complete analysis of the residues putatively involved in the interaction between the two molecules. To do so, we will extract all accessible residues of the two partners, and give the list of residues to DisVis using its interaction analysis feature. Finally, we will show how the restraints can be provided to HADDOCK in order to model the 3D interaction between the 2 partners.

HADDOCK2.4 basic protein-protein docking tutorial

This tutorial will demonstrate the use of HADDOCK for predicting the structure of a protein-protein complex from NMR chemical shift perturbation (CSP) data. Namely, we will dock two E. coli proteins involved in glucose transport: the glucose-specific enzyme IIA (E2A) and the histidine-containing phosphocarrier protein (HPr).

The structures in the free form have been determined using X-ray crystallography (E2A) (PDB ID 1F3G) and NMR spectroscopy (HPr) (PDB ID 1HDN). The structure of the native complex has also been determined with NMR (PDB ID 1GGR).

These NMR experiments have also provided us with an array of data on the interaction itself (chemical shift perturbations, intermolecular NOEs, residual dipolar couplings, and simulated diffusion anisotropy data), which will be useful for the docking. For this tutorial, we will only make use of inteface residues identified from NMR chemical shift perturbation data as described in Wang et al, EMBO J (2000).

2019 ISR School

Training materials used during the 2019 International Incoherent Scatter Radar (ISR) School 

How to apply bioinformatics to metallo-proteins

Table of Contents

• Sequence patterns and protein domains
• MetalPDB and related tools
• Structural Databases
• Structure refinement and protein dynamics

OPENCoastS platform video tutorial

This video tutorial shows how to use this simple service to create coastal forecast systems.
Access at: https://opencoasts.ncg.ingrid.pt/

OPENCoastS user manual

OPENCoastS is an online service (https://opencoasts.ncg.ingrid.pt/) that assembles on-demand circulation forecast systems for selected coastal areas and keeps them running operationally for a period defined by the user. This service generates daily forecasts of water levels and vertically averaged velocities over the region of interest for 48 hours, based on numerical simulations of all relevant physical processes. Presently, all forecasts are made with the model SCHISM (http://ccrm.vims.edu/schismweb/) and are supported by the computational resources from INCD - Infraestrutura Nacional de Computação Distríbuida (https://www.incd.pt), a node of the EGI - European Grid Infrastructure (https://www.egi.eu). Access to the service is granted through a registration procedure, and is obtained after acceptance of the registration by the OPENCoastS user support. OPENCoastS is jointly developed and maintained by LNEC - Laboratório Nacional de Engenharia Civil (LNEC - http://www.lnec.pt), LIP - Laboratório de Instrumentação e Física Experimental de Partículas (LIP - https://www.lip.pt), CNRS-LIENS - Centre National De La Recherche Scientifique - LIttoral ENvironnement et Sociétés (CNRS-LIENS - https://lienss.univ-larochelle.fr) and Universidad de Cantabria (UC - https://web.unican.es).

Federated AAI for EIDA Services

EIDA is the European Integrated Data Archive insftrastructure within ORFEUS to provide access to seismic waveform data and related metadata in European archives. EIDA has been stablised in 2013.  EPOS-ORFEUS Competence Center works on new federated seismologiical services for EIDA. The presentation slides introduced the new Authentication and Authorization for EIDA developed by the CC. The two presentations were given in EGU 2019 conference, April 10th 2019, Vienna, and in EPOS Seismology Meeting, May 7th 2019, Potsdam, respectively.

A user documentaion is also avaialbe at: https://geofon.gfz-potsdam.de/eas/EIDAAuthenticationService.pdf

Transparent data movement from EGI to EUDAT

The main goal of the EOSC-hub project is to synergize the services and infrastructures from major European providers including EGI and EUDAT, enabling researchers to freedom of choice of the services, data and infrastructure necessary for their work.  Users from many communities have reported interest in being able to use resources provisioned by these 2 infrastructures simultaneously in a transparent fashion, i.e.:

  • using single sign on mechanisms between infrastructures
  • being able to transparently transfer data between infrastructures

EOSC-hub WP6 has been endeavoring to enable transparent data access between the infrastructures. The main data management components in EGI and EUDAT are respectively, EGI-DataHub based on Onedata platform and B2SAFE/B2STAGE based on iRODS. Currently no transparent mechanisms allowing users to move data between these infrastructures exists, the only options are manual transfers using such tools as GridFTP.

These two demo videos present the managment of data transfer across EGI, EUDAT, INDIGO data and compute services. 

The first demo video shows the how data can be transparently moved from EGI to EUDAT. It divided into 4 sections:

  • Registration of B2STAGE storage in EGI-DataHub
  • Creation of dsata space in EGI-DataHub supported by the B2STAGE storage
  • Upload of some data to the data space
  • Data access from GUI and command line

The second demo video presents import of existing data from EUDAT to EGI. The demo is divided into the following 4 sections:

  • Registration of B2STAGE storage in EGI-DataHub
  • Creation of data space in EGI-DataHub supported by the B2STAGE storage from which existing data is imported to EGI-DataHub
  • Access of data from B2STAGE using EGI-DataHub user interface
  • Automatic discovery of new data added on the B2STAGE storage

ELIXIR AAI Training

This set of training materials introduce ELIXIR AAI service for user authentication and authorisation. The service is developed by the ELIXIR Compence Center. The training is delivered during the ECCB 2019 conference

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