План доклада

BioUMLинтегрированная среда

для моделирования биологических систем

Biosoft.RuЛабоработория Биоинформатики КТИ ВТ СО РАН

http://www.biosoft.ru

План доклада

• BioUML– обзор основных возможностей системы– архитектура

• Используемые технологии– ru.biosoft.access – библиотека для доступа и

объектно-ориентированного представления информации из гетерогенных баз данных

– BeanExplorer – компонетная технология (расширения JavaBeans) для автоматической генерации пользовательских интерфейсов и публикации данных в различном виде.

BioUML BioUML - Biological Unified Modeling Language –

это интегрированная расширяемая среда для визуального моделирования биологических систем.

BioUML viewer. Left pane shows GeneNet database content that was incorporated as GeneNet module; central pane shows “Antiviral response” diagram; right top pane shows filters that are applied to the diagram, right bottom pane shows properties of “Mx” graph node.

BioUML editor. Components toolbar allows user to add into diagram component of specified type. By clicking on any diagram node user can edit corresponding database record using powerful component editor (left bottom). Search engine (center bottom) allows a user to search database to find all components interacted with selected one and add them into the diagram.

Database search engineSpecifying filter values for database fields user can select the needed records. Here we would like to select proteins that are regulated by interferons (we can use regular expression /.*IFN.*/ for this purpose) and which are monomers.

Results of search of components interconnected with “Hs:HSF-1-p” protein.

BioUML modeler. Strings above arrows are right sides of differential equations associated with graph edges; numbers – are initial values of corresponding variables associated with graph nodes. Bottom right – result of model simulation using MATLAB.

BioUML modeler

%constants declarationglobal k_1 k_2 k_3 k_E0 k_Km v_blood v_liverk_1 = 0.1k_2 = 0.05k_3 = 0.01k_E0 = 1.0k_Km = 0.1v_blood = 100.0v_liver = 100.0%Model variables and their initial valuesy = []y(1) = 100.0 % y(1) - $blood.Ay(2) = 0.0 % y(2) - $liver.Ay(3) = 0.0 % y(3) - $liver.By(4) = 1.0 % y(4) - $liver.E%numeric equation solving[t,y] = ode23('pharmo_simple_dy',[0 200],y)%plot the solver outputplot(t, y(:,1),'-',t, y(:,2),'-',t, y(:,3),'-',t, y(:,4),'-')title ('Solving pharmo_simple problem')ylabel ('y(t)')xlabel ('x(t)')legend('$blood.A','$liver.A','$liver.B','$liver.E');

Automatically generated script file for model simulation and graphic result presentations.

BioUML modeler

Function to calculate dy/dt for the model.

function dy = pharmo_simple_dy(t, y)

% Calculates dy/dt for 'pharmo_simple' model.

%constants declaration

global k_1 k_2 k_3 k_E0 k_Km v_blood v_liver

% calculates dy/dt for 'pharmo_simple' model

dy = [ -k_1*y(1)+k_2*y(2)

-k_3*k_E0*y(2)/(k_Km+y(2)/v_liver)-k_2*y(2)+k_1*y(1)

k_3*k_E0*y(2)/(k_Km+y(2)/v_liver)

0]

Architecture overview

Database

Module type (Database adapter)- data types- data types meta information- transformers- graph query system

Data types- compartment

- cell- molecule

- gene- RNA- protein

- reaction- relation

Diagram type (Diagram adapter)- diagram view builder- diagram semantic controllerDiagramElement

kernel:DataElementtitle:Stringview:Viewrole:Role

Node

location:Pointimage:Image

Edge

in:Nodeout:Node

Compartment

nodes:Node[]edges:Edge[]

Diagram

type:DiagramTypeRole

diagramElement

Constant

value:double

Variable

initilaValue:double

Equation

variable:Variableequation:String

ExecutableModel

variables:Variable[]constants:Constant[]

MatlabODEModel

generateModel():File[]

Meta model

Dynamics model

n

n

n

nDiagramElement


DiagramElement


Node


Node


Edge

in:Nodeout:Node

Edge

in:Nodeout:Node

Compartment


Compartment


Diagram

type:DiagramType

Diagram


diagramElement

Role

diagramElement

Constant

value:double

Constant

value:double

Variable

initilaValue:double

Variable

initilaValue:double

Equation


Equation


ExecutableModel


ExecutableModel


MatlabODEModel


MatlabODEModel


Meta model

Dynamics model

n

n

n

n

Diagram viewer/editor

Modeling tools MATLAB

XML

XSLT

HTML publisher

Database search engine

Graph layout & search engine

Database module

Formalized description and graphic notation for biological pathways

Diagram types- pathway - pathway simulation - generalized pathway

Meta model

Meta model provides an abstract layer to present structure of any biological system as a clustered graph that further can be visualized as a diagram or stored as XML files.

DiagramElement


Node


Edge

in:Nodeout:Node

Compartment


Diagram


diagramElement

Constant

value:double

Variable

initilaValue:double

Equation


ExecutableModel


MatlabODEModel


Meta model

Dynamics model

n

n

n

n

Architecture overview

Database

Module type (Database adapter)- data types- data types meta information- transformers- graph query system

Data types- compartment

- cell- molecule

- gene- RNA- protein

- reaction- relation

Diagram type (Diagram adapter)- diagram view builder- diagram semantic controllerDiagramElement


Node


Edge

in:Nodeout:Node

Compartment


Diagram


diagramElement

Constant

value:double

Variable

initilaValue:double

Equation


ExecutableModel


MatlabODEModel


Meta model

Dynamics model

n

n

n

nDiagramElement


DiagramElement


Node


Node


Edge

in:Nodeout:Node

Edge

in:Nodeout:Node

Compartment


Compartment


Diagram

type:DiagramType

Diagram


diagramElement

Role

diagramElement

Constant

value:double

Constant

value:double

Variable

initilaValue:double

Variable

initilaValue:double

Equation


Equation


ExecutableModel


ExecutableModel


MatlabODEModel


MatlabODEModel


Meta model

Dynamics model

n

n

n

n

Diagram viewer/editor

Modeling tools MATLAB

XML

XSLT

HTML publisher

Database search engine

Graph layout & search engine

Database module

Formalized description and graphic notation for biological pathways

Diagram types- pathway - pathway simulation - generalized pathway

ru.biosoft.access

• библиотека для доступа и объектно-ориентированного представления информации из гетерогенных баз данных

ru.biosoft.access основные концепции

• DataElement –интерфейс, реализуемый любым элементом, который может быть извлечен из базы данных. – getName()– getOrigin()

• DataCollection (implements DataElement) – общий интерфейс для работы с базами данных:– getInfo(); getDataElementType(); isMutable()– getNameList(); iterator();– contains(String name); get(String name);– put(DataElement de); remove (DataElement de)

ru.biosoft.access основные концепции

• Repository

• DataCollectionEvent, DataCollectionListener - механизм для уведомления об изменениях (добавление, удаление и изменение элементов)

• DataCollectionFactory регистрирует все открытые DataCollections и обеспечивает доступ к ним

ru.biosoft.access типы DataCollection

• VectorDataCollection

• FileDataCollection

• SQLDataCollection (SQLTransformer)

• DerivedDataCollection– TransformedDataCollection (Transformer)– FilteredDataCollection (Filter)– UnionDataCollection

File DataID ADHBADA2 standard; DNA; VRT; 1145 BP....//ID AGHBD standard; DNA; PRI; 1959 BP....FT CDS join(367..461,612..816,921..1049)FT /note="alpha-A globin; FT intron 462..611

FileDataCollection

Entry - name - text

Entry - name - text

Entry - name - text

TransformedDataCollection

Sequece - name - sequence - sites[]



Transformer

File DataID ADHBADA2 standard; DNA; VRT; 1145 BP....//ID AGHBD standard; DNA; PRI; 1959 BP....FT CDS join(367..461,612..816,921..1049)FT /note="alpha-A globin; FT intron 462..611

FileDataCollection

Entry - name - text

Entry - name - text

Entry - name - text

TransformedDataCollection




Transformer

BeanExplorerhttp://www.beanexplorer.com

• компонетная технология (расширения JavaBeans) для автоматической генерации пользовательских интерфейсов и публикации данных в различном виде.

View

Meta data

Class instance (MetaClass)

Problem domain data

BeanInfo (BeanHelpers Extention)Component(Bean)

Component(Bean)

Component(Bean)

Model

Component ModelSimple Property

Array Property

Composite PropertyComponent Factory

HTML- text view - form- table

Java Swing UI- tree tables- dialogs - tables

WML- text view- form- table

Property InspectorProperty InspectorProperty Inspector

Rapid development using BeanExplorer

Our development projects are very often based on BeanExplorer™ (www.BeanExplorer.com) – software product that allows developers to generate rich set of User Interfaces (UIs) at run time from proper definition of data. Because of BeanExplorer our development is usually conducted faster than expected and coding time is reduced up to 50% or even more.

Click or press any key to continue….

http://www.beanexplorer.com/

Managing enterprise data using BeanExplorer

• BeanExplorer’s ability to generate User Interfaces (UIs) from definition of data makes it valuable tool for meeting requirements of many business applications. One of the typical examples is making enterprise data available in mobile environments


Scientific visualization

BeanExplorer technology has no replacement for scientific applications where highest degree of parameterization is often required. With BeanExplorer developers concentrate on modeling and experimentation rather than on mundane task of developing UIs because UIs are generated automatically.


Bioinformatics software

• TRANSPLORER TRANSPLORER was developed for

our German partner Biobase GmbH (www.biobase.de). TRANSPLORER is a software package for analysis of genomic sequences and discovering gene regulation mechanisms. It is based on sophisticated Match algorithm for recognition of transcription factor binding sites in DNA sequences which are then visualized using our MGL3 library


http://www.biobase.de/

Documents

План доклада