InSilicoLab: A framework for domain-specific science gateways

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Golik, Tomasz Grabarczyk, Michał Trzeciak, Tomasz Twaróg,

1 InSilicoLab: A framework for domain-specific science gateways Joanna Kocot, Mariusz Sterzel, Tomasz Szepieniec, Maciej Golik, Tomasz Grabarczyk, Michał Trzeciak, Tomasz Twaróg, Piotr Wójcik ACC CYFRONET AGH, ul. Nawojki 11, Kraków, Poland

2 Challenges We are targeting researchers 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 Technical Forum

3 InSilicoLab Principles Follow the user Make tools that speak the language they speak Focus on research, not on the computation process, data retrieval, etc. Frequent feedback Single entry point Entrance to the user s research Integrated tools and data EGI Technical Forum

4 InSilicoLab Gateway Construction Focus: research Experiment Data Results Sharing Supporting tools External monitoring tools Notebooks Community features Other tools & applications EGI Technical Forum

Internals of InSilicoLab Experiment Management Data

Sharing Reuse Classification Result Management

Managed by the user Experiment Logic Execution Engine

Annotations Tagging Provenance Tracking Mediation Layer

Computational Resources Storage Resources Metadata

5 Internals of InSilicoLab Experiment Management Data Management Specification Execution Browsing Analysis Sharing Reuse Classification Result Management Preparation Storing Viewing Provenance Domain Layer Managed by the user Experiment Logic Execution Engine Automatic Parallelization Metadata Model Data Structure Annotations Tagging Provenance Tracking Mediation Layer translation from domain- to resource-specific language Computational Resources Storage Resources Metadata Repository Resource Access Layer access to e-infrastructures EGI Technical Forum

Identify the tools they use Identify data types, features, attributes Write it down as algorithms

6 How to create an InSilicoLab gateway? Step 1 Analyse the researchers work: Extract patterns in their work and all the data flows Identify the tools they use Identify data types, features, attributes Write it down as algorithms an in silico experiment logic Specify all the input data and their formats Specify the result data and their format Define data analysis EGI Technical Forum

7 How to create an InSilicoLab gateway? Step 2 Obtain an empty InSilicoLab module for your domain A stub that you will fill out with domain-specific functionality Add input forms to the interface Using InSilicoLab core library Fill the execution scripts with invocation of the domain-specific tools Add early result analysis if possible Specify the result attributes and their display EGI Technical Forum

8 How to create an InSilicoLab gateway? Step 3 (optional) Customise the portal Replace the logo Link with your request tracker or helpdesk Define authorisation method EGI Technical Forum

9 How to create an InSilicoLab gateway? Step 4 (optional) High-level integration Embed e.g. in Liferay Enables integration with other advanced tools Adds wiki pages, other community tools EGI Technical Forum

10 Case: Chemistry Domain [PRODUCTION] InSilicoLab for Chemistry Enables complex computational chemistry experiments, including phases like: Reduction of the system Quantum-chemical calculations for large sets of data Analysis and comparison of results Visualisation at every stage Recognised as an official service in PL-Grid infrastructure (within PL-Grid Plus) Required security and operational audit Embedded in PL-Grid portal (Liferay) EGI Technical Forum

11 Case: Chemistry Domain EGI Technical Forum

12 Case: Astrophysics Domain (Cherenkov Telescope Array) [PRODUCTION] Ctaportal and CTA Science Gateway Simulation of the behaviour of a telescope with different configurations Analysis and comparison of results Integration of results from many experiments Dedicated software that has to be installed on machines + hand-made scripts Large input and output files Reconstruction of the original event Integrated with CTA Science Gateway Integration with other CTA tools: DIRAC interface, Data browser, Infrastructure monitoring EGI Technical Forum

13 Case: Astrophysics Domain (Cherenkov Telescope Array) EGI Technical Forum

14 Case: Astrophysics Domain (MHD) [PRODUCTION] InSilicoLab for AstroGrid-PL Enables simulations using MHD (Magneto- Hydrodynamics) codes Developed by Astrophysics experts from outside of Cyfronet Recognised as an official service in PL-Grid infrastructure (within PL-Grid Plus) Required security and operational audit Embedded in PL-Grid portal (Liferay) EGI Technical Forum

15 Case: Astrophysics Domain (MHD) EGI Technical Forum

16 Case: Bioinformatics Domain [IN PROGRESS] InSilicoLab for Bioinformatics Will include multi-stage Gromacs experiments Combination of various tools Interaction with the user during computation is required Also developed by a domain experts team EGI Technical Forum

17 Thank you

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1 Bazaar Site Admin Toolkit (BazaarSAT) Maciej Golik, Tomasz Szepieniec ACC Cyfronet AGH CGW'12 Krakow, Poland October 22-24, 2012 Agenda 2 I) Introduction II) Some concepts III) Technical work done Introduction