Experiment Workbench - The DIstributed Computing Environments ...

quaggahooliganInternet και Εφαρμογές Web

5 Φεβ 2013 (πριν από 4 χρόνια και 8 μήνες)

113 εμφανίσεις

1



The PL
-
Grid Virtual Laboratory in the Life
Sciences Domain

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

Institute of Computer Science AGH

ACC Cyfronet AGH



2

Outline


Motivation


complex scientific applications on
modern computing infrastructures


In
-
silico e
xperiment
s and
Virtual Laboratory


GridSpace2 as a solution


Architecture


Working with GridSpace


Examples of a
pplications


Computational chemistry


Bioinformatics


Conclusions

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 (
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


5

Working 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

6

Experiment Workbench

7

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


8

Analysis of water solutions of aminoacids


Involving multiple steps realized with many

tools, langauges 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
Departament of
Chemistry
, Jagiellonian University,
Dr. Mariusz Sterzel,
Klemens Noga




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