Курсы английского
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BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
CellDesigner support – comparison for 165 images from Panther DB and
CellDesigner support – comparison for 165 images from Panther DB and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
Reactome
Reactome
BioPAX – import dialog
BioPAX – import dialog
BioPAX example (BioCyc)
BioPAX example (BioCyc)
TRANSPATH example
TRANSPATH example
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
SED-ML – import dialog
SED-ML – import dialog
SED-ML workflow
SED-ML workflow
Simulation
Simulation
Simulation
Simulation
Simulation
Simulation
Simulation
Simulation
Parameters fitting – user interface
Parameters fitting – user interface
CD95L module and results of fitting its dynamics to experimental data
CD95L module and results of fitting its dynamics to experimental data
CD95L module and results of fitting its dynamics to experimental data
CD95L module and results of fitting its dynamics to experimental data
CD95L module and results of fitting its dynamics to experimental data
CD95L module and results of fitting its dynamics to experimental data
Yuri Lazebnik “Can a biologist fix a radio
Yuri Lazebnik “Can a biologist fix a radio
Biologist view
Biologist view
TNF-? module (SBGN)
TNF-? module (SBGN)
Biologist view
Biologist view
Biologist view
Biologist view
Modular design
Modular design
Modular design
Modular design
Modular design
Modular design
Modular design
Modular design
Modules: clear specification of interfaces
Modules: clear specification of interfaces
Modules: clear specification of interfaces
Modules: clear specification of interfaces
Modular model of apoptosis
Modular model of apoptosis
EGF module (BMOND ID: Int_EGF_module)
EGF module (BMOND ID: Int_EGF_module)
Mitochondron module (BMOND ID: Int_Mitoch_module)
Mitochondron module (BMOND ID: Int_Mitoch_module)
Modular model allows us to combine both up-down and bottom-up
Modular model allows us to combine both up-down and bottom-up
Arterial Tree PDE agent
Arterial Tree PDE agent
Arterial Tree PDE agent
Arterial Tree PDE agent
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
Blood arterial preassure regulation: another build
Blood arterial preassure regulation: another build
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
JavaScript host objects allows to merge R/Bioconductor and Java/BioUML
JavaScript host objects allows to merge R/Bioconductor and Java/BioUML
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
ChIP-seq processing pipeline
ChIP-seq processing pipeline
Galaxy – analyses methods
Galaxy – analyses methods
Galaxy - workflow
Galaxy - workflow
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
BioUML – open source integrated platform for collaborative and
Market
Market
Market
Market
Market
Market
Картинки из презентации «BioUML – open source integrated platform for collaborative and reproducible research in systems biology» к уроку английского языка на тему «Курсы английского»

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BioUML – open source integrated platform for collaborative and reproducible research in systems biology

содержание презентации «BioUML – open source integrated platform for collaborative and reproducible research in systems biology.ppt»
Сл Текст Сл Текст
1BioUML – open source integrated 31min 07,1 sec. 7,5 sec 7,47 sec 6,9 sec.
platform for collaborative and 23,4 sec 23,5 sec 22,2 sec. 1 min 25,0 sec
reproducible research in systems biology. 1 min 5,6 sec 1 min 8,8 sec. Cellular
Fedor Kolpakov, Institute of Systems genetic algorithm. 7,7 sec 7,5 sec 7,2
Biology Ltd. Alexander Kel, geneXplain sec. 25,5 sec 22,1 sec 20,8 sec. –.
GmbH. www.biouml.org. 32Modular modelling Composite model of
2BioUML platform. BioUML is an open the Apoptosis Machinery Agent based model
source integrated platform for systems of arterial blood pressure regulation.
biology that spans the comprehensive range 33Yuri Lazebnik “Can a biologist fix a
of capabilities including access to radio?—Or, what I learned while studying
databases with experimental data, tools apoptosis“. Cancer Cell, 2002, 2(3):
for formalized description, visual 179-182.
modeling and analyses of complex 34Biologist view. Engineer’s view.
biological systems. Due to scripts (R, 352002 However, I hope that it is only a
JavaScript) and workflow support it question of time before a user-friendly
provides powerful possibilities for and flexible formal language will be
analyses of high-throughput data. Plug-in taught to biology students, as it is
based architecture (Eclipse run time from taught to engineers, as a basic
IBM is used) allows to add new requirement for their future studies. My
functionality using plug-ins. BioUML advice to experimental biologists is to be
platform consists from 3 parts: BioUML prepared. Y. Lazebnik, 2002. 2010
server – provides access to biological Standards in systems biology SBML –
databases; BioUML workbench – standalone Systems Biology Markup Language SBGN –
application. BioUML web edition – web Systems Biology Graphics Notation.
interface based on AJAX technology. 36TNF-? module (SBGN).
3 37Biologist view. Engineer’s view.
4Main topics. supported standards: 38Biologist view. Engineer’s view. Last
SBML, SBGN, BioPAX, SED-ML, SBO, MIRIAM, centaury: 50-70-th.
CellML some examples, CellDesigner 39Modular design.
extension support state concept SED-ML as 40Modules: clear specification of
workflow Modular modelling: composite interfaces. input/output. contacts.
models, agent based models systems biology 41Modular model of apoptosis. 13 modules
– reproducible highthroughput data 286 species 684 reactions 719 parameters.
analyses: analyses: algorithms, scripts, 42EGF module (BMOND ID: Int_EGF_module).
workflows integration with R/Bioconductor, Schoeberl B, et al: Nature Biotechnology
Galaxy data: microarrays, NGS, ChIP-SEQ 2002 Borisov N, et al: Molecular Systems
visualization: genome browser BioUML – as Biology 2009. Additions: Reactions of
platform for collaborative research Amazon protein syntheses and degradations.
EC2 servers data repository - groups, 43Mitochondron module (BMOND ID:
projects, import/export, FTP upload chat, Int_Mitoch_module). Bagci EZ, et al,
history current works: Biostore, LIMS ( Biophysical J 2006 Albeck JG, et al, PLoS
laboratory information management system). Biol 2008. Additions: Activation of CREB
5Systems Biology. Computational and deactivation of BAD by Akt-PP and
modeling. Experimental hypothesis ERK-PP Upregulation of Bcl-2 by CREB Bcl-2
validation. Experimental data. suppression by p53.
6Systems Biology. COMBINE. 44Modular model allows us to combine
Computational modeling. Experimental both up-down and bottom-up approaches.
hypothesis validation. Experimental data. top-down. bottom-up.
7Standard supports: SBML, SBGN, BioPAX, 45Agent based modeling. Ascape library
SED-ML, SBO, MIRIAM, CellML. is used main type of agents: - ODE agent -
8SBML support. import/export - level 1, arterial tree - plot.
2, 3 (core) passed all tests from SBML 46Arterial Tree PDE agent. Legend: P –
test suite version 2.0.0 beta 1 (2010, Pressure R – Resistance Q – Blood Flow V –
April 2) extensions: CellDesigner SBGN-PD Volume.
(own XML format) Biomodels full text 47
search SBGN -PD (parse RDF annotation do 48Blood arterial preassure regulation:
determine specie types) layout algorithms another build.
on-line simulation Panther DB full text 49Systems Biology. COMBINE.
search reads CellDesigner extensions Computational modeling. Experimental
SBGN-PD. hypothesis validation. Data Analysis.
9 Experimental data.
10 50Systems biology: reproducible
11 highthroughput data analyses. analyses:
12 algorithms, scripts, workflows integration
13CellDesigner support – comparison for with R/Bioconductor, Galaxy data:
165 images from Panther DB and generated microarrays, NGS, ChIP-SEQ visualization:
by BioUML. genome browser.
14SBGN support. diagram types: PD – 51
beta; ER, AF – alpha defined as XML 52JavaScript host objects allows to
graphic notation for BioUML graphic merge R/Bioconductor and Java/BioUML
notation can be edited using BioUML worlds. R world. Java/BioUML world.
graphic notation editor special extension 53
for SBML Reactome - SBGN-PD full text 54ChIP-seq processing pipeline.
search SQL version is used read diagram 55Galaxy – analyses methods.
layout from Reactome BioPAX – SBGN-PD 56Galaxy - workflow.
level 2 (beta), level 3 (alpha) auto 57Genome browser.
layout TRANSPATH – SBGN-PD full text 58Genome browser: main features. uses
search auto-layout. AJAX and HTML5 <canvas> technologies
15 interactive - dragging, semantic zoom
16Reactome. tracks support Ensembl DAS-servers
17BioPAX – import dialog. user-loaded BED/GFF/Wiggle files.
18BioPAX example (BioCyc). 59
19TRANSPATH example. 60
20State concept. State describes changes 61Systems Biology. COMBINE.
between initial model and its variant: for Computational modeling. Experimental
simulation experiment (corresponds to hypothesis validation. Data Analysis.
SED-ML <changes>) for specific cell Experimental data. Data repository for
line or model conditions for history collaborative work.
history of editing can be represented as 62BioUML: platform for collaborative
set of states - each state corresponds to research. Amazon EC2 servers data
some model build or commitment to repository groups projects import/export,
repository. State formalizes changes as FTP upload chat history (in process).
following events: add element remove 63
element change property. Changes in the 64
state can be grouped into transactions. 65Main current works: LIMS (Laboratory
For example to remove reaction we need to Information Management System) Biostore.
remove reaction node and corresponding 66Systems Biology. COMBINE.
edges. Changes can be presented as: table Computational modeling. Experimental
of changes, changes are grouped into hypothesis validation. Data Analysis.
transactions by decorating corresponding LIMS. Experimental data. Data repository
diagram elements Internally, changes are for collaborative work.
core of BioUML undo/redo subsystem, that 67BioUML – LIMS (Laboratory Information
was further extended for the purposes Management System). is being developed by
above. Data Integrated Solutions Inc. (Pittsburg,
21 USA) start-up organized by Maxim Mikheev
22 and Fedor Kolpakov experiment is
23SED-ML support. SED-ML import only represented as workflow automated
SBML models are supported now stored in management by laboratory equipment
user’s project SED-ML changes presented as automated generation of tasks for
BioUML states SED-ML presented as workflow laboratory staff automated upload of
automated hierarchic layout on-line experimental data into repository
simulation. automated row data analysis.
24SED-ML – import dialog. 68Market. Android market. AppStore.
25SED-ML workflow. Android. MacOS, iPOD, iPhone. Platform.
26Simulation. 69Market. Android market. AppStore.
27Parameters fitting. Biostore. Android. MacOS, iPOD, iPhone.
28Main features. Experimental data – Platform. BioUML.
time courses or steady states expressed as 70BioUML ecosystem. Biostore. BioUML
exact or relative values of substance platform. Developers - plug-ins: methods,
concentrations Different optimization visualization, etc. - databases. Users -
methods for analysis subscriptions - collaborative &
Multi-experimentsfitting Constraint reproducible research. Experts services
optimization Local/global parameters for data analysis on-line consultations.
Parameters optimization using java script. provide tools and databases. use. provide
29Parameters fitting – user interface. services.
30CD95L module and results of fitting 71Acknowledgements. Part of this work
its dynamics to experimental data. Bentele was partially supported by the grant:
M, 2004. Neumann L, 2010. European Committee grant №037590
31Comparison with COPASI (10,000 “Net2Drug” European Committee grant
simulations). Stochastic Ranking Evolution №202272 “LipidomicNet” Integration and
Strategy. Method. BioUML (4 cores). BioUML interdisciplinary grants №16, 91 of SB
(1 core). COPASI (1 core). Evolutionary RAS. BioUML team Software developers
Programming. –. –. 1 min 58,2sec 1 min Biologists Nikita Tolstyh Ilya Kiselev
31,3 sec 1 min 16,6 sec. Particle swarm. Ruslan Sharipov Tagir Valeev Elena
7,1 sec 7,7 sec 6,9 sec. 22,4 sec 15,3 sec Kutumova Ivan Yevshin Anna Ryabova Alexey
22,5 sec. 1 min 32 sec 1 min 26,4 sec 1 Shadrin.
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BioUML – open source integrated platform for collaborative and reproducible research in systems biology

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