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Architecture

This page provides information about the 'EGI Applications Platform', hereafter referred to as the Platform.

The Platform is designed to support the long tail of science. The long-tail of science refers to the individual researchers and small laboratories who - opposed to large, expensive collaborations - do not have access to dedicated computational resources and online services to manage and analyse large amount of data. The Platform allows individual researchers and small research teams to reuse, develop and share compute and data-intensive applications and simulations on large, distributed networks of computers in a user friendly way.

What can you access in the Platform ?

The Platform is accessible through this User Registration Portal (URP) and offers grid, cloud and application services from across the EGI community for individual researchers and small research teams.

The Platform offers the following type of resources:

• Applications that are made available ‘as services’ through the science gateways.
• Science gateways that provide graphical web environments for building and executing applications in the platform.
• Cloud sites suited for both compute/data intensive jobs and hosting of scientific services
• High-throughput computing sites for running compute/data-intensive jobs
• Storage resources for storing job input and output data, and for setting up data catalogues

Available resources

Current available resources, in terms of Scientific Applications and Science Gateways & Portals, grouped by categories.

Scientific Applications

Computer Science & Mathematics

• The R Project for Statistical Computing (v3.2.2) is a language and environment for statistical computing and graphics.
  • The application is accessible through the Catania Science Gateway. The user manual is available here.
• GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments.
  • The application is accessible through the EC3 portal.

Cultural Heritage

• The Semantic Search Engine (SSE) is a framework conceived to demonstrate the potential of information coupled with semantic web technologies to address the issues of data discovery and correlation.
  • The application is accessible through the Catania Science Gateway. The user manual is available here.

Life Sciences

• Chispter is a user-friendly analysis software for high-throughput data. It contains over 300 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.
  • The application is accessible through the Catania Science Gateway. The user manual is available here.
• ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences.
  • The application is accessible through the Catania Science Gateway. The user manual is available here.
• Galaxy is an open, web-based platform for data intensive biomedical research.
  • The application is accessible through the EC3 portal. Instructions on how to use Galaxy workflows with EC3 are available here.
• AutoDock Vina is an open-source software for doing molecular docking.
  • The application is available through the WS-PGRADE/gUSE portal. The user guide to run the AutoDock Vina application is available here
• NAMD is a parallel molecular dynamics code designed for high-performance simulation of large bio-molecular systems.
  • The application is available through the EC3 portal.

Others

• Hello World is simple grid-based application that demonstrates the use of remote resources by printing the hostname where the job is executed.
  • The application is accessible through the Catania Science Gateway. The user manual is available here.
• Apache Tomcat is an open source implementation of the Java Servlet, JavaServer Pages, Java Expression Language and Java WebSocket technologies. The Java Servlet, JavaServer Pages, Java Expression Language and Java WebSocket specifications are developed under the Java Community Process.
  • The application is accessible through the EC3 portal.
• Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
  • The application is accessible through the EC3 portal.
• Docker is an open-source project that automates the deployment of Linux applications inside software containers.
  • The application is accessible through the EC3 portal.
• Hadoop is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.
  • The application is accessible through the EC3 portal.
• Berkeley Lab Checkpoint/Restart
  • The application is accessible through the EC3 portal.
• Marathon a production-grade container orchestration platform for Mesosphere's Data Center/Operating System (DC/OS) and Apache Mesos.
  • The application is accessible through the EC3 portal.
• Chronos is a distributed and fault-tolerant scheduler that runs on top of Apache Mesos that can be used for job orchestration.
  • The application is accessible through the EC3 portal.

Science Gateways & Portals

• The Catania Science Gateway (CSG) is a new generation of Science Gateway based on standard that changes the way e-Infrastructures are used. The gateway incorporates several scientific applications and offers these "as services" for the user. The CSG provides users with an intuitive web interface to execute applications on the grid resources of the platform. The CSG take cares of starting the job in one of the available resources of the platform, of transferring the needed files (e.g. executable, input files, etc.) and downloading the output(s) in behalf of the users. CSG is open source and released under the Apache 2.0 license.
  • The implementation of the CSG tailored for supporting the users of the long tail is available here

• The WS-PGRADE Portal (Web Services Parallel Grid Runtime and Developer Environment Portal) is the Liferay-based web portal (WS-PGRADE web application) of gUSE, wich also includes a graphical portal service. WS-PGRADE is a Web portal hosted in a standard portal framework, using the client APIs of gUSE services to turn user requests into sequences of gUSE specific Web service calls. WS-PGRADE is integrated with the cloud resources of the platform, and provides a 'job wizard' interface for the user. Through the wizard one can define with a few clicks a computational job that WS-PGRADE will execute on the cloud resources. The environment takes care of instantiation of Virtual Machine image for the job, for sending input data for the job, and for the retrieval of job outputs.
  • The implementation of the WS-PGRADE/gUSE tailored for supporting the users of the long tail is available here

• Elastic Cloud Computing Cluster (EC3) is a tool to create elastic virtual clusters on top of Infrastructure as a Service (IaaS) providers. EC3 uses 'recipes' to deploy TORQUE (optionally with MAUI) and SLURM clusters that can be self-managed with CLUES: it starts with a single-node cluster and working nodes will be dynamically deployed and provisioned to fit increasing load (number of jobs at the LRMS). Working nodes will be undeployed when they are idle. EC3 is integrated with the cloud resources of the platform, and provides a 'job wizard' interface for the user. Through the wizard one can define with a few clicks a computational job that WS-PGRADE will execute on the cloud resources. The environment takes care of instantiation of Virtual Machine image for the job, for sending input data for the job, and for the retrieval of job outputs.
  • The implementation of the EC3 portal tailored for supporting the users of the long tail is available here

Who can access the Platform ?

The Platform is open for any researcher who needs a simple and user-friendly access to compute, storage and applications services in order to carry out data/compute intensive science and innovation. You need to be affiliated with, or at least have a partner (for example a referee), at a European research institution to qualify for access. The Platform is designed to meet the needs of individual researchers and small research groups who have limited or no experience with distributed and cloud computing.

Access requires acceptance of Acceptable Use Policy (AUP) and Conditions of Use of the 'EGI Access Platform'

How can you access the Platform ?

1. Login to the User Registration Portal (URP) with an EGI CheckIn account.
2. Provide information about your affiliation to a research institute.
3. Request resources: indicate approximately how much computing and storage capacity, and when will you need.
4. After your request is approved, login to any of the science gateway portals to use pre-deployed scientific applications or to build and execute your custom compute & data intensive applications.

Presentations about the Platform

• Overview of the EGI Platform for serving the long tail (EGI Community Forum, November 2015): [1]
• Poster and animated slides from Demo at EGI Community Forum, November 2015 (Winner of best demo prize): [2]
• Slideset about the concept of the EGI long-tail of science platform (from Nov. 2014): [3]
• Slideset about the authentication and authorization model adopted (from Nov. 2015): [4]
• Slideset about the staus report of the platform at the EGI Conference 2016: [5]
• Slideset about the staus report of the EGI platform at the DI4R Conference 2016: [6]

Contact

Would you like to access an application, Science Gateways/Portals or resource in the platform that is not yet integrated ? Request it in email at long-tail-user-requests@mailman.egi.eu!

HelpDesk

For generic questions or inquiries, please contact the Platform support team at applications-platform-support@mailman.egi.eu.

For gateway-specific support please contact:

• Catania Science Gateway (CSG): sg-licence@ct.infn.it
• WS-PGRAGE/gUSE portal: portalwide@lpds.sztaki.hu
• EC3 portal: micafer1@upv.es