Transcript SPBSU ORGANIZATION OF THE INFORMATIONAL

"St.Petersburg State University - scientific and communication
links in St.Petersburg region and some future plans of GRID
applications"
V.Bychkov, G.Feofilov, Yu.Galyuck, A.Zarochensev, V.I.Zolotarev
St.Petersburg State University, Russia
Reporter: G.Feofilov
Contents:
1. SPbSU and SPbSU Communication Center
2. Links and research
3. Some plans of GRID applications
20.10.2004
The 1st Nordic Grid Neighborhood Workshop, Linkoping, Sweden
St.Petersburg state university today
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See http://www.spbu.ru/e/
20 faculties
11 scientific institutes
Academical School
Over 25 000 students
Over 2000 postgraduate students
About 5000 lecturers and researchers
Education Faculties:
Natural Sciences
Faculty of Applied Mathematics
Faculty of Biology & Soil Science
Faculty of Chemistry
Faculty of Geology
Faculty of Geography & Geo-Ecology
Faculty of Mathematics & Mechanics
Faculty of Medicine
Faculty of Physics
Education Faculties :
Humanities
Faculty of Economy
Faculty of History
Faculty of International Relations
Faculty of Journalism
Faculty of Law
School of Management
Faculty of Oriental Studies
Faculty of Philology
Chair of Russian for Foreigners
Faculty of Philosophy
Faculty of Psychology
Faculty of Sociology
Department of Sports and Physical Culture
Reseach Institutes:
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Astronomy
Biology
Complex Social Researches
Computing Mathematics & Control Processes
Chemistry
The Earth's Crust
Geography
Information Technologies
Mathematics & Mechanics
Physics (V.Fock Institute for Physics)
Physiology
Radiophysics
SPbSUniversity Communication Center
Some scientific and communication links
of St.Petersburg State University
• PNPI (Gatchina),
• Institute for High Performance Computing
(St.Petersburg) – see a report by V.Korkhov
at the present workshop
• JINR(Dubna),
• CERN(Geneve)
• ALICE collaboration at CERN since 1992
Some topics of research at the SPbSU
high productivity complex in 2003:
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Research Institute for Laser Physics (St.Peterburg): “Model Simulations
of non-paraxial auto-focusing laser radiation and formation of super
narrow space solitons(the “ Optical needles”)”.
ITEPHI SPII RAS (St.Peterburg): :” Optimization of electromagnetic
fields configurations of complex corpuscular-optical systems and
search for extreme of multi parameter function (10 and parameters)”
PNPI, Gatchina : “High precision calculations of electron structure and
properties of heavy atoms and molecules with heavy ions”,
SPb Institute for Informatics and Automatization: “Model simulations
and control of the geophysical environment”
Institute for High Molecular Compounds (St.Peterburg): : “Computer
simulations of polymer systems with anisotropic interactions between
elements” Physics and Technical Institute named after A.F.Ioffe (St.Peterburg):,
“Microscopic theory of dielectric and segneto-electric properties of
crystals”
S.I.Vavilov’s Optical Institute (St.Peterburg): “ Model simulations for the
optical system light protection”
2004:
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Petersburg Nuclear Physics Institute (Gatchina): “Distributed analysis and
HEP data storage for PNPI” (GRID technologies for HEP, - for ATLAS)
Physics and Technical Institute A.M.Ioffe and Institute for Informatics, RAS
(St.Peterburg): : ‘Microscopic theory of physical properties of segnetoelectrics and similar materials”, and “ New electron phase transitions in
structures based on the fullerens”
I.P.Pavlov SPb Institute for Physiology, RAS:”Quantum-chemistry
calculations of biologically active substances”
SPb Institute for Machines Problems: “Study of polymer units with
anisotropic interactions between the nodes”
SPbSU: “Study for Enhancement of Reliability for Distributed Monte Carlo
Simulations”
SPbSU: “Parallel implementations of Parton String Model event generator”
SPbSU: “Search for quark-gluon string fusion phenomenon in relativistic
nucleus-nucleus collisions”
Principles:
• Cooperation and joint research are
welcome
• Free usage of computer power is
provided for scientific applications and
research
What is important for the future?
• practical tasks: middleware development
and gaining of experience
• practical tasks: the LHC ALICE data
analysis - more computing power is
required for ALICE for the future data
analysis
• practical tasks: involvement of students of
other specializations (not only
physicists) into the GRID applications
Near plans for SPbSU!:
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Data Challenge for ALICE (to continue using 8 computers cluster)
transition to gLite
creation of a NordGrid cluster in St.Petersburg State University
Physical Programme preparations for ALICE:
(calculations based on the Monte Carlo event generators in parallel mode,
Long Range correlations search in NA49 and NA57 at SPS data and ALICE
Physical Programme)
Participation of the students of the SPbSU/ALICE group in applications of
NordGrid for computing (?)
Some other possible applications in GRID - (chemistry? biology? etc…?.
Experience of St.Petersburg State University with the IBM and further
developments
Some of these tasks could be very
efficiently solved in cooperation with
the NordGrid
PROBLEMS
Questions:
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Physics and science in Russia?
A NATIONAL CATASTROPHE
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WHAT IS TO BE DONE?
…. We have to work…
Practical applications of our knowledge
gained in HEP to the medicine
This may/should! include GRID
technologies for:
• digital mammograms
• patients medical data storage,
transfer, security, easy access for the
doctor (see the HealthGRID)
• early cancer screening programs
ISTC Project#2887 “Preparations of Technical
Proposals for development of the North-West
Regional Centre for Hadron Therapy and
Diagnostics in St.Petersburg”
– submitted in Aug.2003 by a group of 7 St.Petersburg institutions,
-- was supposed to be considered by the ISTC: in March 2004/July 2004/October 2004?
Three major goals:
• the choice of the medical accelerator
• the concept of the precise diagnostic
equipment complex and
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the practical demonstration of the
latest information technologies
(GRID) for digital mammography
and for early cancer detection
Some Medical links:
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ESTRO-ENLIGHT and European Hadron Therapy Centers
CERN (PIMMS accelerator design)
MedAustron (Austria)
Department of Medical Radiation Physics of Karolinska
Institutet
• MAMMOGRID (see
http://www.gridstart.org/MAMMOGRID.shtml
and
http://mammogrid/vitamib.com/
The goal of the Project #2887:
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to develop the concept and the Technical Proposals for the
construcion in St.Petersburg of the new medical facility for the
ion-beam therapy – the North-West Regional Centre of Hadron
Therapy and Diagnostics of Oncology Deceases. The latest world
achievements in the ion beams therapy using protons and carbon
ions, the modern nuclear physics methods of radiation treatment
control and the newest methods of precise diagnostic of oncology
deceases will be taken into account. The latest developments in
the information technologies based on the distributed data
analysis will be used as a base for the demonstration of two
prototypes of mass scale diagnostic systems.
The Center is assigned to the efficient diagnostic and treatment of a
wide range of oncology deceases resulting in the localized deep
seated tumors, situated near the Organs at Risk that are not
suitable for the conventional beam therapy methods using photon
beams.
Participants:
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V.A.Fock Institute of Physics of Saint-Petersburg State University
(Fock Institute of Physics SPbSU, Ministry of Education, RF)
Federal State Unitary Enterprise “D.V. Efremov Scientific-research
institute of Electrophysical apparatus” (FSUE NIIEFA, MinAtom)
Central Design Bureau of machine Building (CDBM, MinAtom RF)
St.Petersburg City Clinical Oncology Centre (SPbCCOC,
St.Petersburg Health Protection Committee)
Central Research Institute of Roentgenology and Radiology, St.
Petersburg (CRIRR)
Petersburg Nuclear Physics Institute named after
B.P.Konstantinov, (PNPI, RAS, Gatchina)
Research Institute of Hygiene, Occupational Pathology and
Human Ecology (RIHOPHE, Federal Bureau of Medical and
Biological Extreme Problems, the Ministry of Health of Russian
Federation)
Project leader
Grigoriy A.Feofilov
Ph.D.
Project Technical
Coordonator (Accelerator)
Al’bert V.Stepanov
D.Sc.i.
FSUE NIIEFA
Submanager
Al’bert V.Stepanov
D.Sc.i.
PNPI
Submanager
Nikolai K.Abrosimov
Ph.D.
CDBM
Submanager
Nikolai A.Odintsov
Project Scientific
Coordinator (Medicine)
Sergei I.Chikrizov
Ph.D.
SPbCCOC
Submanager
Sergei I.Chikrizov
Ph.D.
CRIRR
Submanager
Valerii M.Vinogradov
Professor, D.Sc.i.
PI HOPHE
Submanager
Andrei S.Radilov
D.Sc.i.
Project Economist
Olga V.Sobol’
Project Coordinator
(Diagnostics systems)
Vladislav A.Shishov
Ph.D.
FSUE NIIEFA
Submanager
Al’bert V.Stepanov
D.Sc.i.
PNPI
Submanager
Nikolai K.Abrosimov
Ph.D.
Fock Instutite of
Physics SPbSU
Submanager
Olga V.Sobol’
Hadron Therapy in the Baltic region
Baltic Light Project (Anders Brahme, Department of
Medical Radiation Physics of Karolinska
Institutet, Stockholm):
Joint creation of 2 centers of excellence for the
hadron therapy of deeply seated tumors
(Stockholm-St.Petersburg)
GRID – is a technology that is needed for:
1. Advanced treatment planning
2. Medical images transfer between centers
3. Advanced diagnostics
Perspectives
• The Center should include a specialized medical accelerator
of protons and/or carbon ions with the beam delivery
system to the places of therapy, and the additional
accelerators for the production of medical isotopes used
for the PET diagnostics. Standard medical electron
accelerator and the narrow focused well studied photon
beams should be used as an additional tool for the
radiologist. The centre should be equipped with the high
precision systems of the automated dose distribution
control during the therapy that will guarantee the high
quality and efficiency at all stages of the medical process.
• The centre should be also connected with the intellectual
system of medical examinations of the population based on
the latest developments of the GRID informational
technology.
Relevance
• The relevance of the Project is dictated by the
necessity to enroot the newest modern high
efficient methods of diagnostics and therapy of
oncology deceases in St.Petersburg and the
North-West region.
• The validation of medical, technical and
economical feasibility will be obtained in a close
cooperation with the European Centre for Nuclear
Research (CERN), European radiology centers
and in contact with ESTRO ENLIGHT - (European
Network for LIGht Ion Hadron Therapy), in
particular, with Med-AUSTRON (Vienna) and
Karolinska Hospital(Sweden).
Novelty
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The novelty of the project is in the application of the modern
developments in the field of accelerator technique, of the newest
detector systems of high energy and nuclear physics for the high
precision beam control for the irradiated tumors. The use of the
latest information technologies (GRID and MammoGRID) as the
main tool in distributed data storage and analysis is an important
component part of the project. Development of the technical
proposal for the efficient upgrade of the existing Gatchina
synchrocyclotron, evaluation of the modern medical machines
and the capabilities of Russian enterprises to produce them,
engineering design of carbon ion beams transportation systems
(including gantry), detailed model simulations of the tissue
irradiation process using the modern Monte-Carlo codes (like
FLUKA and GEANT) and the codes validation with the available
experimental data, are among the main tasks of this proposal that
might be of some interest to the European centers of the hadron
therapy.
Novelty (continued)
• Development and practical demonstration of two prototype
systems of mass diagnostics of oncology deceases is one of the
peculiarities of the present proposal. It is planned, in particular,
to carry out a diagnostic check of not less then 5000 patients of
Mammology City Oncology Center and to use the obtained data
for the MammoGrid analysis using the CERN-developed GRID
systems. The bank of mammograms will be created using the
available resources of St.Petersburg State University and the
efficiency of the computer aided diagnostics will be studied. It
is also planned to carry out another check of the early cancer
mass scale diagnostic based on the new methods of bloodserum laser spectroscopy developed in St.Petersburg. 10000
patients are to be checked and the risk group is to be formed
as a result of GRID based analysis.
Some future plans of GRID
applications: MAMMOGRID
Status of St.Petersburg mammal
gland screening (data of 2002)
• St.Petersburg’s decree (07.03.01) on “Special Oncology
Program for St.Petersburg for 2001-2005”
• St.Petersburg: the highest rate in Russia of oncology
decease
• Mammal gland cancer is No.1 since 1981
• 2163 new mammal cancer patients in 2002 (21,6% of all
oncology cases) (see Tables below).
• Mortality – about 9% of the all mortality is due to the
oncology
• 2003: 21861 women are registered total with a general
diagnosis of mammal gland oncology
• The population of women in St.Petersburg is 2544
thousand
Review workstation
IBM IntelliStation
2*T221
Scaner
(Vidar VXR-16)
Mammography station
(GIOTTO IMAGE-MR,
3000rpm tube, Focus 0.1/0.3)
Radio modem
11Mb/s
gridbox
100Mb/s
Cern(Central
Node)
SPbSU Informational-computing center
External net - channels
Марсов о поле
ул. Чайков ского
Глав ное здание
ул. Большая Морская
ул. Сев аст ьянов а
Пет родв орец
Площадь Победы
Some future plans of GRID
applications: Early diagnostics
of cancer
Early diagnostics of cancer
• Early diagnostics using the computer aided intellectual
diagnostic system developed by the Research Institute of
Hygiene, Occupational Pathology and Human Ecology
(RIHOPHE, St.Petersburg) includes the diagnostics terminal
with pupillometer, laser analyzer of the functional state of
the blood form elements and spectrometer of small
fractions of blood-serum, network resources of data
storage and transfer. Laser correlation method of bloodserum spectroscopy (LCS) allows to reveal the risk groups
with some pathologies forerunning the development of
tumors and to monitor the process of illness. Pupillometry
is capable to define at the early stage the changes of
organic and functional nature in the central nervous
system.
• Laser analyzer of the functional state of the blood form
elements helps to control the magnitude of the general
impact of the beam and drug therapy.
Possibility of a new GRID application to
very early cancer diagnostics
• This computer aided intellectual system is designed for
the mass scale examinations of population using the
computer methods of screening diagnostics. The risk
groups is formed as result that should go through the
deeper study in order to clarify the diagnosis and to get the
needed further treatment if necessary.
• The practical demonstration of the given system based on
the existing complex of diagnostic equipment and the GRID
system is planned at the high productivity computer
complex of SPbSU using the 1 GB/s communication
channel to St.Petersburg .
• The volume of data expected for one patient is about 30
MB.
• Data is expected to come with the mean intensity 2Mb/s.
• The previously developed methods will be used for the
examination of 10000 patients (a prototype of the
intellectual computer aided intellectual early diagnostic
system).
Some Perspectives for AliEn/gLite
applications in St.Petersburg
(hopefully, links to NordicGrid will also appear to solve some
practical tasks!)
General conclusions
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Data Challenge 2004 tests in SPbSU show that the AliEn works.
Future applications of GRID to the NEW PHYSICS at LHC are
exciting!
Scientific and educational potential of SPbSU is still high,
but in parallel, we have to remember that medical applications of our
knowledge could be very beneficial :
1. GRID is a must for the European centers of hadron therapy
2. GRID technologies should be at hand for any doctor
3. 1.5 mln of women population in St.Petersburg are the potential
candidates for the mass screening using GRID. A film+scanner
technology is proposed to demonstrate the feasibility of the
Mammogrid application in St.Petersburg region
4. Very early cancer diagnostics prototype is proposed for tests in
St.Petersburg using GRID
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We are ready to start!
Any cooperation is welcome!