InSilicoLab : from Generic Solutions to Application-Specific Science Gateway Joanna Kocot , Mariusz Sterzel, Tomasz Szepieniec, Maciej Golik, Tomasz Grabarczyk, Tomasz Twaróg, Piotr Wójcik ACC CYFRONET AGH, ul. Nawojki 11, 30- 059 Kraków, Poland
The Idea of InSilicoLab • Workspace gathering all that a researcher needs for their in silico experiments › Enabling performing large-scale, long- lasting data- and computation-intensive experiments › Facilitating categorisation and description of data Enabling searches and browsing EGI Community Forum 2013
For Whom? • Reaserchers from different domains of science › Whose experiments are composed of different activities – creating non-trivial workflows › Who need control over the flow of their data and organizing it › Who want to collaborate within a group or with other groups EGI Community Forum 2013
For Whom? • Computational Chemistry › Simulation of the solute-solvent system at the Molecular Dynamics level › Reduction of the system Selection of the solute with its solvation shell Selection of relevant frames › Performing quantum-chemical calculations for large sets of data › Analysis and comparison of results › Visualisation at every stage EGI Community Forum 2013
How to create a useful system? • Analysing the researchers work: › Specific group › Ways of working › Common problems • We intend to aid in solving SPECIFIC problems • We cannot support solving ANY scientific problem › We assume it cannot be done in a universal and comprehensive way EGI Community Forum 2013
For Computational Chemistry EGI Community Forum 2013
For Whom? • Cherenkov Telescope Array › Simulation of the behaviour of a telescope with different configurations, including, e.g.: Camera configuration Trigger – filtering › Analysis and comparison of results Integration of results from many experiments › Reconstruction of the original event › Dedicated software that has to be installed on machines + hand-made scripts › Large input and output files EGI Community Forum 2013
How to reuse the existing solution and stay useful? • Using the same model • Reusing common parts • Creating a specific tool, but: › Having the general model in mind, › Thinking how the new solutions could be used to improve others EGI Community Forum 2013
For Cherenkov Telescope Array EGI Community Forum 2013
InSilicolab Features • Environment for running experiments on computer infrastructure › Parallelization of tasks › Application- and domain-specific interface • Data management › Automatic attachment of metadata › Possibility to tag and annotate data objects › Results of one experiment can directly serve as input to another › Tracking of the data objects origin EGI Community Forum 2013
InSilicoLab Architecture Experiment Management Data Management Domain Analysis Preparation Specification Layer Sharing Storing Execution Managed by Reuse Viewing the user Browsing Classification Provenance Result Management Mediation Experiment Automatic Data Provenance Logic Parallelization Structure Tracking Layer translation from domain- to Execution Metadata Annotations resource-specific Engine Model Tagging language Resource Computational Metadata Access Resources Repository Layer Storage access to Resources e-infrastructures EGI Community Forum 2013
How to start in a new domain? Discover a pattern in the researchers work • › A joint effort of the developers and the researchers teams • Put it down as experiment logic › Implement input and results management › Specify metadata descriptions • Adjust interface › Input specification › Result display › If neccessary: new data types management This can be done also by people who are not InSilicoLab developers EGI Community Forum 2013
Validation MHD code created at Centre for Astronomy, • Nicolaus Copernicus University in Toruń, Poland › http://piernik.astri.umk.pl/ Integration with the InSilicoLab framework was • performed by the Piernik application developer › Only aided by the InSilicoLab team First prototype created in less than one month • • Production deployment planned for September EGI Community Forum 2013
Validation EGI Community Forum 2013
Summary InSilicoLab is an abstract model of creating • specific portals/science gateways • Available to researchers performing in silico experiments in many domains of science Operational in three different instances: • › Computational Chemistry › Cherenkov Telescope Array › Piernik for AstroGrid-PL (Beta) Open for new collaborations • › Planned: Biochemistry portal EGI Community Forum 2013
Thank you! http://insilicolab.cyfronet.pl insilicolab@cyfronet.pl
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