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BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML platform
BioUML platform
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
Main topics
Main topics
Systems Biology
Systems Biology
Systems Biology
Systems Biology
Standard supports: SBML, SBGN, BioPAX, SED-ML, SBO, MIRIAM, CellML
Standard supports: SBML, SBGN, BioPAX, SED-ML, SBO, MIRIAM, CellML
SBML support
SBML support
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
CellDesigner support Ц comparison for 165 images from Panther DB and
CellDesigner support Ц comparison for 165 images from Panther DB and
SBGN support
SBGN support
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
Reactome
Reactome
BioPAX Ц import dialog
BioPAX Ц import dialog
BioPAX example (BioCyc)
BioPAX example (BioCyc)
TRANSPATH example
TRANSPATH example
State concept
State concept
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
SED-ML support
SED-ML support
SED-ML Ц import dialog
SED-ML Ц import dialog
SED-ML workflow
SED-ML workflow
Simulation
Simulation
Parameters fitting
Parameters fitting
Main features
Main features
Parameters fitting Ц user interface
Parameters fitting Ц user interface
CD95L module and results of fitting its dynamics to experimental data
CD95L module and results of fitting its dynamics to experimental data
Comparison with COPASI (10,000 simulations)
Comparison with COPASI (10,000 simulations)
Modular modelling Composite model of the Apoptosis Machinery Agent
Modular modelling Composite model of the Apoptosis Machinery Agent
Yuri Lazebnik УCan a biologist fix a radio
Yuri Lazebnik УCan a biologist fix a radio
Biologist view
Biologist view
2002 However, I hope that it is only a question of time before a
2002 However, I hope that it is only a question of time before a
TNF-? module (SBGN)
TNF-? module (SBGN)
Biologist view
Biologist view
Biologist view
Biologist view
Modular design
Modular design
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
Agent based modeling
Agent based modeling
Arterial Tree PDE agent
Arterial Tree PDE agent
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
Blood arterial preassure regulation: another build
Blood arterial preassure regulation: another build
Systems Biology
Systems Biology
Systems biology: reproducible highthroughput data analyses
Systems biology: reproducible highthroughput data analyses
BioUML Ц open source integrated platform for collaborative and
BioUML Ц 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 Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
ChIP-seq processing pipeline
ChIP-seq processing pipeline
Galaxy Ц analyses methods
Galaxy Ц analyses methods
Galaxy - workflow
Galaxy - workflow
Genome browser
Genome browser
Genome browser: main features
Genome browser: main features
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
Systems Biology
Systems Biology
BioUML: platform for collaborative research
BioUML: platform for collaborative research
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
BioUML Ц open source integrated platform for collaborative and
Main current works:
Main current works:
Systems Biology
Systems Biology
BioUML Ц LIMS (Laboratory Information Management System)
BioUML Ц LIMS (Laboratory Information Management System)
Market
Market
Market
Market
BioUML ecosystem
BioUML ecosystem
Acknowledgements
Acknowledgements

ѕрезентаци€ на тему: ЂBioUML Ц open source integrated platform for collaborative and reproducible research in systems biologyї. јвтор: Anja. ‘айл: ЂBioUML Ц open source integrated platform for collaborative and reproducible research in systems biology.pptї. –азмер zip-архива: 11250  Ѕ.

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

содержание презентации ЂBioUML Ц open source integrated platform for collaborative and reproducible research in systems biology.pptї
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1 BioUML Ц open source integrated platform for collaborative and

BioUML Ц open source integrated platform for collaborative and

reproducible research in systems biology

Fedor Kolpakov, Institute of Systems Biology Ltd. Alexander Kel, geneXplain GmbH

www.biouml.org

2 BioUML platform

BioUML platform

BioUML is an open source integrated platform for systems biology that spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description, visual modeling and analyses of complex biological systems. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. Plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins. BioUML platform consists from 3 parts: BioUML server Ц provides access to biological databases; BioUML workbench Ц standalone application. BioUML web edition Ц web interface based on AJAX technology

3 BioUML Ц open source integrated platform for collaborative and
4 Main topics

Main topics

supported standards: SBML, SBGN, BioPAX, SED-ML, SBO, MIRIAM, CellML some examples, CellDesigner extension support state concept SED-ML as workflow Modular modelling: composite models, agent based models systems biology Ц reproducible highthroughput data analyses: analyses: algorithms, scripts, workflows integration with R/Bioconductor, Galaxy data: microarrays, NGS, ChIP-SEQ visualization: genome browser BioUML Ц as platform for collaborative research Amazon EC2 servers data repository - groups, projects, import/export, FTP upload chat, history current works: Biostore, LIMS ( laboratory information management system)

5 Systems Biology

Systems Biology

Computational modeling

Experimental hypothesis validation

Experimental data

6 Systems Biology

Systems Biology

COMBINE

Computational modeling

Experimental hypothesis validation

Experimental data

7 Standard supports: SBML, SBGN, BioPAX, SED-ML, SBO, MIRIAM, CellML

Standard supports: SBML, SBGN, BioPAX, SED-ML, SBO, MIRIAM, CellML

8 SBML support

SBML support

import/export - level 1, 2, 3 (core) passed all tests from SBML test suite version 2.0.0 beta 1 (2010, April 2) extensions: CellDesigner SBGN-PD (own XML format) Biomodels full text search SBGN -PD (parse RDF annotation do determine specie types) layout algorithms on-line simulation Panther DB full text search reads CellDesigner extensions SBGN-PD

9 BioUML Ц open source integrated platform for collaborative and
10 BioUML Ц open source integrated platform for collaborative and
11 BioUML Ц open source integrated platform for collaborative and
12 BioUML Ц open source integrated platform for collaborative and
13 CellDesigner support Ц comparison for 165 images from Panther DB and

CellDesigner support Ц comparison for 165 images from Panther DB and

generated by BioUML

14 SBGN support

SBGN support

diagram types: PD Ц beta; ER, AF Ц alpha defined as XML graphic notation for BioUML graphic notation can be edited using BioUML graphic notation editor special extension for SBML Reactome - SBGN-PD full text search SQL version is used read diagram layout from Reactome BioPAX Ц SBGN-PD level 2 (beta), level 3 (alpha) auto layout TRANSPATH Ц SBGN-PD full text search auto-layout

15 BioUML Ц open source integrated platform for collaborative and
16 Reactome

Reactome

17 BioPAX Ц import dialog

BioPAX Ц import dialog

18 BioPAX example (BioCyc)

BioPAX example (BioCyc)

19 TRANSPATH example

TRANSPATH example

20 State concept

State concept

State describes changes between initial model and its variant: for simulation experiment (corresponds to SED-ML <changes>) for specific cell line or model conditions for history history of editing can be represented as set of states - each state corresponds to some model build or commitment to repository. State formalizes changes as following events: add element remove element change property. Changes in the state can be grouped into transactions. For example to remove reaction we need to remove reaction node and corresponding edges. Changes can be presented as: table of changes, changes are grouped into transactions by decorating corresponding diagram elements Internally, changes are core of BioUML undo/redo subsystem, that was further extended for the purposes above.

21 BioUML Ц open source integrated platform for collaborative and
22 BioUML Ц open source integrated platform for collaborative and
23 SED-ML support

SED-ML support

SED-ML import only SBML models are supported now stored in userТs project SED-ML changes presented as BioUML states SED-ML presented as workflow automated hierarchic layout on-line simulation

24 SED-ML Ц import dialog

SED-ML Ц import dialog

25 SED-ML workflow

SED-ML workflow

26 Simulation

Simulation

27 Parameters fitting

Parameters fitting

28 Main features

Main features

Experimental data Ц time courses or steady states expressed as exact or relative values of substance concentrations Different optimization methods for analysis Multi-experimentsfitting Constraint optimization Local/global parameters Parameters optimization using java script

29 Parameters fitting Ц user interface

Parameters fitting Ц user interface

30 CD95L module and results of fitting its dynamics to experimental data

CD95L module and results of fitting its dynamics to experimental data

Bentele M, 2004

Neumann L, 2010

31 Comparison with COPASI (10,000 simulations)

Comparison with COPASI (10,000 simulations)

Stochastic Ranking Evolution Strategy

Method

BioUML (4 cores)

BioUML (1 core)

COPASI (1 core)

Evolutionary Programming

Ц

Ц

1 min 58,2sec 1 min 31,3 sec 1 min 16,6 sec

Particle swarm

7,1 sec 7,7 sec 6,9 sec

22,4 sec 15,3 sec 22,5 sec

1 min 32 sec 1 min 26,4 sec 1 min 07,1 sec

7,5 sec 7,47 sec 6,9 sec

23,4 sec 23,5 sec 22,2 sec

1 min 25,0 sec 1 min 5,6 sec 1 min 8,8 sec

Cellular genetic algorithm

7,7 sec 7,5 sec 7,2 sec

25,5 sec 22,1 sec 20,8 sec

Ц

32 Modular modelling Composite model of the Apoptosis Machinery Agent

Modular modelling Composite model of the Apoptosis Machinery Agent

based model of arterial blood pressure regulation

33 Yuri Lazebnik УCan a biologist fix a radio

Yuri Lazebnik УCan a biologist fix a radio

ЧOr, what I learned while studying apoptosisУ. Cancer Cell, 2002, 2(3): 179-182

34 Biologist view

Biologist view

EngineerТs view

35 2002 However, I hope that it is only a question of time before a

2002 However, I hope that it is only a question of time before a

user-friendly and flexible formal language will be taught to biology students, as it is taught to engineers, as a basic requirement for their future studies. My advice to experimental biologists is to be prepared. Y. Lazebnik, 2002

2010 Standards in systems biology SBML Ц Systems Biology Markup Language SBGN Ц Systems Biology Graphics Notation

36 TNF-? module (SBGN)

TNF-? module (SBGN)

37 Biologist view

Biologist view

EngineerТs view

38 Biologist view

Biologist view

EngineerТs view

Last centaury: 50-70-th

39 Modular design

Modular design

40 Modules: clear specification of interfaces

Modules: clear specification of interfaces

input/output

contacts

41 Modular model of apoptosis

Modular model of apoptosis

13 modules 286 species 684 reactions 719 parameters

42 EGF module (BMOND ID: Int_EGF_module)

EGF module (BMOND ID: Int_EGF_module)

Schoeberl B, et al: Nature Biotechnology 2002 Borisov N, et al: Molecular Systems Biology 2009

Additions: Reactions of protein syntheses and degradations

43 Mitochondron module (BMOND ID: Int_Mitoch_module)

Mitochondron module (BMOND ID: Int_Mitoch_module)

Bagci EZ, et al, Biophysical J 2006 Albeck JG, et al, PLoS Biol 2008

Additions: Activation of CREB and deactivation of BAD by Akt-PP and ERK-PP Upregulation of Bcl-2 by CREB Bcl-2 suppression by p53

44 Modular model allows us to combine both up-down and bottom-up

Modular model allows us to combine both up-down and bottom-up

approaches

top-down

bottom-up

45 Agent based modeling

Agent based modeling

Ascape library is used main type of agents: - ODE agent - arterial tree - plot

46 Arterial Tree PDE agent

Arterial Tree PDE agent

Legend: P Ц Pressure R Ц Resistance Q Ц Blood Flow V Ц Volume

47 BioUML Ц open source integrated platform for collaborative and
48 Blood arterial preassure regulation: another build

Blood arterial preassure regulation: another build

49 Systems Biology

Systems Biology

COMBINE

Computational modeling

Experimental hypothesis validation

Data Analysis

Experimental data

50 Systems biology: reproducible highthroughput data analyses

Systems biology: reproducible highthroughput data analyses

analyses: algorithms, scripts, workflows integration with R/Bioconductor, Galaxy data: microarrays, NGS, ChIP-SEQ visualization: genome browser

51 BioUML Ц open source integrated platform for collaborative and
52 JavaScript host objects allows to merge R/Bioconductor and Java/BioUML

JavaScript host objects allows to merge R/Bioconductor and Java/BioUML

worlds

R world

Java/BioUML world

53 BioUML Ц open source integrated platform for collaborative and
54 ChIP-seq processing pipeline

ChIP-seq processing pipeline

55 Galaxy Ц analyses methods

Galaxy Ц analyses methods

56 Galaxy - workflow

Galaxy - workflow

57 Genome browser

Genome browser

58 Genome browser: main features

Genome browser: main features

uses AJAX and HTML5 <canvas> technologies interactive - dragging, semantic zoom tracks support Ensembl DAS-servers user-loaded BED/GFF/Wiggle files

59 BioUML Ц open source integrated platform for collaborative and
60 BioUML Ц open source integrated platform for collaborative and
61 Systems Biology

Systems Biology

COMBINE

Computational modeling

Experimental hypothesis validation

Data Analysis

Experimental data

Data repository for collaborative work

62 BioUML: platform for collaborative research

BioUML: platform for collaborative research

Amazon EC2 servers data repository groups projects import/export, FTP upload chat history (in process)

63 BioUML Ц open source integrated platform for collaborative and
64 BioUML Ц open source integrated platform for collaborative and
65 Main current works:

Main current works:

LIMS (Laboratory Information Management System) Biostore

66 Systems Biology

Systems Biology

COMBINE

Computational modeling

Experimental hypothesis validation

Data Analysis

LIMS

Experimental data

Data repository for collaborative work

67 BioUML Ц LIMS (Laboratory Information Management System)

BioUML Ц LIMS (Laboratory Information Management System)

is being developed by Data Integrated Solutions Inc. (Pittsburg, USA) start-up organized by Maxim Mikheev and Fedor Kolpakov experiment is represented as workflow automated management by laboratory equipment automated generation of tasks for laboratory staff automated upload of experimental data into repository automated row data analysis

68 Market

Market

Android market

AppStore

Android

MacOS, iPOD, iPhone

Platform

69 Market

Market

Android market

AppStore

Biostore

Android

MacOS, iPOD, iPhone

Platform

BioUML

70 BioUML ecosystem

BioUML ecosystem

Biostore

BioUML platform

Developers - plug-ins: methods, visualization, etc. - databases

Users - subscriptions - collaborative & reproducible research

Experts services for data analysis on-line consultations

provide tools and databases

use

provide services

71 Acknowledgements

Acknowledgements

Part of this work was partially supported by the grant: European Committee grant є037590 УNet2DrugФ European Committee grant є202272 УLipidomicNetФ Integration and interdisciplinary grants є16, 91 of SB RAS. BioUML team Software developers Biologists Nikita Tolstyh Ilya Kiselev Ruslan Sharipov Tagir Valeev Elena Kutumova Ivan Yevshin Anna Ryabova Alexey Shadrin

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