План доклада

1. BioUMLинтегрированная среда для моделирования биологических системBiosoft.RuЛабоработория Биоинформатики КТИ ВТ СО РАНhttp://www.biosoft.ru

2. 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.

3. BioUML BioUML - Biological Unified Modeling Language – это интегрированная расширяемая среда для визуального моделирования биологических систем.

4. 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.

5. 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.

6. Database search engine Specifying 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.

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

8. 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.

9. %constants declaration global k_1 k_2 k_3 k_E0 k_Km v_blood v_liver k_1 = 0.1 k_2 = 0.05 k_3 = 0.01 k_E0 = 1.0 k_Km = 0.1 v_blood = 100.0 v_liver = 100.0 %Model variables and their initial values y = [] y(1) = 100.0 % y(1) - $blood.A y(2) = 0.0 % y(2) - $liver.A y(3) = 0.0 % y(3) - $liver.B y(4) = 1.0 % y(4) - $liver.E %numeric equation solving [t,y] = ode23('pharmo_simple_dy',[0 200],y) %plot the solver output plot(t, y(:,1),'-',t, y(:,2),'-',t, y(:,3),'-',t, y(:,4),'-') title ('Solving pharmo_simple problem') ylabel ('y(t)') xlabel ('x(t)') legend('$blood.A','$liver.A','$liver.B','$liver.E'); BioUML modeler Automatically generated script file for model simulation and graphic result presentations.

10. 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]

11. Architecture overview

12. Meta model n n Dynamics model n Compartment nodes:Node[] edges:Edge[] Node location:Point image:Image DiagramElement kernel:DataElement title:String view:View role:Role n Equation variable:Variable equation:String Edge in:Node out:Node Role diagramElement MatlabODEModel generateModel():File[] Variable initilaValue:double ExecutableModel variables:Variable[] constants:Constant[] Constant value:double Diagram type:DiagramType 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.

13. Architecture overview

14. ru.biosoft.access • библиотека для доступа и объектно-ориентированного представления информации из гетерогенных баз данных

15. 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)

16. 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

17. ru.biosoft.access типы DataCollection • VectorDataCollection • FileDataCollection • SQLDataCollection (SQLTransformer) • DerivedDataCollection • TransformedDataCollection (Transformer) • FilteredDataCollection (Filter) • UnionDataCollection

18. Entry - name - text Entry - name - text Entry - name - text TransformedDataCollection Sequece - name - sequence - sites[] Sequece - name - sequence - sites[] Sequece - name - sequence - sites[] Transformer FileDataCollection File Data ID 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; FTintron 462..611

19. Entry - name - text Entry - name - text Entry - name - text TransformedDataCollection Sequece - name - sequence - sites[] Sequece - name - sequence - sites[] Sequece - name - sequence - sites[] Transformer FileDataCollection File Data ID 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; FTintron 462..611

21. BeanExplorerhttp://www.beanexplorer.com • компонетная технология (расширения JavaBeans) для автоматической генерации пользовательских интерфейсов и публикации данных в различном виде.

22. View • Java Swing UI • tree tables • dialogs • tables • HTML • text view • form • table • WML • text view • form • table Model Simple Property Property Inspector Component Model Property Inspector Property Inspector Array Property Composite Property Component Factory Problem domain data Meta data Class instance (MetaClass) Component (Bean) Component (Bean) Component (Bean) BeanInfo (BeanHelpers Extention)

25. 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….

26. 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 Click or press any key to continue….

27. 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. Click or press any key to continue….

28. 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 Click or press any key to continue….