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VIRTUAL LABORATORY AND ITS APPLICATION IN
GENOMICS
Luiza Handschuh Karol Marcinkowski University
of Medical Sciences, Department of
Haematology Institute of Bioorganic Chemistry
PAS, Center of Excellence for Nucleic Acid-based
Technologies INGRID 2008, Lacco Ameno,
11.04.2008
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Virtual Laboratory - definition and advanteges

• The Virtual Laboratory is a distributed
  workgroup environment, with the main task of
  providing a remote access to the various kind of
  rare and expensive scientific laboratory
  equipment and computational resources
  (http//vlab.psnc.pl/)
• A specific representative of the RIS (Remote
  Instrumentation Systems)
• Based on grid environment, already implemented in
  the VLab System by Poznan Supercomputing and
  Networking Center (PSNC)
• Independent on physical location of the
  instruments
• Designed to cooperate with many other grid
  systems
• Devoted to experimental and computational tasks
  supporting the postprocessing phase of experiment
• Experiments made in other laboratories and their
  results can be shared enabling the workgroup

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Modular architecture of the Virtual Laboratory
system
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• Preparing a sample and/or input data
• (e.g. parameters)
• Measurement/computation
• Data processing and visualization
• Data storage and management

Experiment execution in the Virtual Laboratory
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Workflow management

• Dynamic Measurement Scenario (DMS) design
• Analysis of application
• Connection diagram construction
• Description of additional dependecies
• Generation of
• applications and
• links description
• Generation of the
• measurement
• scenario
• description

an example workflow In Scenario Submission
Application in NMR studies
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Data storage and management
Digital Library a crucial component in most
typical RIS VL systems, a module responsible
for data storage and management (DSM)

• unique digital collection
• possibility of software extention
• cooperation with the library integrated systems,
  e.g. catalogue databases
• possiblity of searching and browsing
• widespread access (via Internet)

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Biological introduction
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Functional genomics how the genom works?
PROTEIN
RNA
DNA
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Genomics answers the fundamental biological
questions
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Microarray experiment
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Application of functional genomics tools for
establishing complex model of tumor
transformation.Studies on molecular mechanisms
of acute myeloid leukemia pathogenesis as a
part of a huge project announced by Polish
Ministry of Science and Informatization in
2005 Application of functional genomics and
bioinformatics for creation and characterisation
of models describing biological processes of
great importance in medicine and agriculture
(PBZ-MNiI-2/1/2005) Institute of Bioorganic
Chemistry PAS, Poznan Karol Marcinkowski
University of Medical Sciences, Department of
Haematology Poznan Supercomputing and Networking
Center Poznan University of Technology
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Research model acute myeloid leukemia AML M1
FAB type
Haematopoesis scheme
AML M1 is almost homogenous cell population
(myeloblasts consist 90 of the whole bone
marrow cell pool) Molecular determinants of this
AML type are still not well described.
Blasts from patient with FAB M1 AML (Cancer
Medicine, 5th edition)
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Schematic description of research
IMPLICATED INSTITUTES
UMS
- Karol Marcinkowski
University of Medical Sciences
IBCH
- Institute of Bioorganic
AML patients / healthy bone marrow donors
Chemistry PAS
UMS
PCNS
- Poznan Supercomputing
CD 34 cells isolation from

and Networking Center

blood and bone marrow samples
UT

• Poznan University
• of Technology

CD 34

miRNA analysis
Transcriptome analysis
Standard clinical
IBCH
IBCH
IBCH
using DNA
Proteome analysis
UMS
using DNA microarrays
diagnosis
UT
UT
UT
microarrays
-
morphology based blood and bone marrow cell
analysis
- microarray probe selection
- DNA microarray printing
- total protein extraction
- microarray printing
(commercial probes)
- 2-dimensional electrophoresis
- RNA isolation and labeling
- miRNA isolation
- gel scanning and analysis

• immunophenotyping,
• molecular biology tests

- hybridisation
- miRNA i labeling
- protein identification
- cytogenetics
- scanning and analysis
- hybridisation
using mass spectrometry
- scanning and analysis
IBCH
IBCH
UMS
IBCH
UT
UT
UT
UT
Normalisation
PCNS
and bioinformatic analysis
Elaboration of new AML diagnostic
Genomics virtual
UT
PCNS
of obtained data
IBCH
tools based on DNA microarrays
laboratory establishement
UT
UMS
protein 2DE analysis results
Elaboration of a
Hospitals
Biological model of leukemic transformation
IBCH
PCNS
country-wide data base
Research institutes
UT
UT
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Microarray construction
Microarray of our own design 924
oligonucleotide probes (DNA fragments, 50-70 nt)
complementary to the genes involved in AML
pathogenesis and control ones
AROS (70 nt)
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Example of preprocessed microarray images
HL60
19sz
The same slide No.19
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First step of computational work data collection

• Grid adjustment
• Quantitative analysis - pixels counting for each
  spot and background (mean and median)

Signal intensity 1- 216 (65535)
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Fragment of gpr file with microarray raw data,
generated by Scanarray Express
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Virtual Genomics Laboratory automation of
microarray data analysis
I. Raw data normalization
II. Normalized data analysis
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High level analysis of microarray data -
examples Left 55 genes at least 4-fold
overexpressed in the tested samples comparing
to the healthy control Samples No. 20, 22 27
represent patients after treatment Wright Ge
nes differentiating samples with various types
of leukemia
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Experiment execution in the Virtual Laboratory
of Genomics
In future equipement should be directly available
for scientists/doctors who work in other
laboratories/institutes in Poland via Internet
Now only the multistep analysis of the
microarray data can be automated the same
universal strategy will be applied in every case
in order to obtain satisfactory gene expression
results
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Outlook of Virtual Laboratory of Genomics
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The authors of publication
Marcin Lawenda, Norbert Meyer, Maciej Stroinski,
Jan Weglarz Poznan Supercomputing and
Networking Center Luiza Handschuh, Piotr
Stepniak, Marek Figlerowicz (director of the
project) Institute of Bioorganic Chemistry PAS
Others participants of the project Maciej
Kazmierczak,Mieczyslaw Komarnicki, Krzysztof
Lewandowski Karol Marcinkowski University of
Medical Sciences, Departament of
Haematology Piotr Formanowicz, Jacek Blazewicz
Poznan University of Technology, Institute of
Informatics
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