gems

bricklayerbelchedInternet και Εφαρμογές Web

5 Φεβ 2013 (πριν από 4 χρόνια και 9 μήνες)

136 εμφανίσεις

1

WIRTUALNE LABORATORIUM PROJEKTU PL
-
GRID A NAUKI PRZYRODNICZE

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



2

Outline


Motivation


complex scientific applications on modern
computing infrastructures


Definitions


Experiment


Virtual Laboratory


GridSpace2 as a solution


Architecture


Working with GridSpace


Applications


Computational chemistry


Bioinformatics


References, links, acknowledgments

3

Motivation


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

4

Experiment


Experiment
-

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
)


5

Architecture

of GridSpace2

(TODO: EC)


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

6

Screenshot (EC)


7

Bioinformatics applications


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 Departament of Bioinformatics and Telemedicine, Jagiellonian
University, Prof. Irena Roterman
-
Konieczna, Katarzyna Prymula


8

Chemistry application (EC)


Gaussian


CCLIB


Web UI





9

Conclusions


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


10

References


http://wl.plgrid.pl




open the Virtual Labortory in your browser


http://gs2.cyfronet.pl




learn more about GridSpaace2 technology


http://virolab.cyfronet.pl




see our earlier achievements


http://www.plgrid.pl




become a user of PL
-
Grid