Polska Infrastruktura Informatycznego Wspomagania Nauki Polska Infrastruktura Informatycznego Wspomagania Nauki w Europejskiej Przestrzeni Badawczejw Europejskiej Przestrzeni Badawczej

Institute of Computer Science AGHInstitute of Computer Science AGHACC Cyfronet AGHACC Cyfronet AGH

The PL-Grid Virtual Laboratory The PL-Grid Virtual Laboratory in the Life Sciences Domainin the Life Sciences Domain

Maciej Malawski, Maciej Malawski, Eryk CiepielaEryk Ciepiela, Tomasz Gubała, , Tomasz Gubała, Piotr Nowakowski, Daniel Harężlak, Marek Kasztelnik, Piotr Nowakowski, Daniel Harężlak, Marek Kasztelnik, Joanna Kocot, Tomasz Bartyński, and Marian BubakJoanna Kocot, Tomasz Bartyński, and Marian Bubak

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OutlineOutline Motivation – complex scientific applications on

modern computing infrastructures In-silico experiments and Virtual Laboratory GridSpace2 as a solution

─ Architecture─ Working with GridSpace

Examples of applications─ Computational chemistry─ Bioinformatics

Conclusions

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MotivationMotivation Complex scientific applications on

modern computing infrastructures─ Clusters, Grids, Clouds

Diverse software packages─ Applications (Gaussian, NAMD,…)─ Web Services─ Scripts: Perl, Python, Ruby

Different users─ Chemists, biologists─ Programmers─ End users

Various data types─ Files, databases, URLs

Exploratory programming─ Unstructured, dynamic, prototyping

Collaboration─ Teams, communities

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ExperimentExperiment Experiment (in-silico)- a process that combines

together data with a set of activities (programs, services) that act on that data in order to produce experiment results─ Experiment plan – a specific type of software─ Experiment run – a specific execution of the experiment

Complex workflow going beyond manual simple and repeatable execution of installed programs

Combines steps realized on a range of software environments, platforms, tools, languages etc.

Developed, shared and reused collaboratively amongst ad-hoc researching teams

Composed of collaboratively owned libraries and services used (called gems) and experiment parts (called snippets)

Virtual Laboratory – environment for development, execution and sharing of experiments

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Working with GridSpace2Working with GridSpace2 Easy access using Web

browser Experiment Workbench

─ Constructing experiment plans from code snippets

─ Interactively run experiments Experiment Execution

Environment─ Multiple interpreters─ Access to libraries,

programs and services (gems)

Access to computing infrastructure─ Cluster, grid, cloud

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Binding sites in proteinsBinding sites in proteins Comparison of Services for Predicting

Ligand Binding Sites─ Multiple services available on the Web─ Conversions between data formats─ Visualization scripts (Jmol, Gnuplot)─ Single access based on experiments

developed in Virtual Laboratory Calculation of hydrophobicity profiles

─ Multiple scales, parameters, input data─ Computed using PL-Grid resources –

easy access to Zeus cluster at Cyfronet─ Management of experiment results:

~ 1 Million output files─ Using semantic integration framework for

metadata management

Collaboration with Department of Bioinformatics and Telemedicine, Jagiellonian University, Prof. Irena Roterman-Konieczna, Katarzyna Prymula

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Analysis of water solutions of aminoacidsAnalysis of water solutions of aminoacids Involving multiple steps realized

with many tools, languages and libraries used for─ Packmol – molecular dynamics

simulations of packing molecules in a defined regions of space

─ Jmol – visualization of solution─ Gaussian – computing a spectrum of

the solution─ Python/CCLIB – extracting spectrum

info─ jqPlot – displaying plot

Collaboration with computational chemists of ACC Cyfronet AGH and Department of Chemistry, Jagiellonian University, Dr. Mariusz Sterzel, Klemens Noga

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ConclusionsConclusions Complex scientific applications need dedicated tools

and approaches. In-silico experiments are supported by Virtual

Laboratory powered by GridSpace2 technology. Applications:

─ Bioinformatics─ Computational chemistry─ More are welcome!

Virtual laboratory is open for PL-Grid users.

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ReferencesReferences http://wl.plgrid.pl

– open the Virtual Laboratory in your browser

http://gs2.cyfronet.pl – learn more about GridSpace2 technology

http://virolab.cyfronet.pl – see our earlier achievements

http://www.plgrid.pl – become a user of PL-Grid