PlantSimLab An Innovative Web Application Tool for Plant Biologists

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Melina Hicks
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1 PlantSimLab An Innovative Web Application Tool for Plant Biologists Feb. 17, 2014 Sook S. Ha, PhD Postdoctoral Associate Virginia Bioinformatics Institute (VBI) 1

2 Outline PlantSimLab Project A NSF proposal granted to Dr. Reinhard Laubenbach and his research collaborators in the Year 2011 Background & Innovativeness Software Architecture Integration with Existing Analysis Tools Discussions 2

3 Background Molecular level nonlinear networks of heterogeneous molecules control many plant processes, and systems biology provides a useful approach to plant biology, building on the integration of experimental biology with mathematical modeling But most plant biologists do not have the mathematical background needed to build an manipulate mathematical models well enough to use them as a tools for hypothesis generation Several software tools have been developed specifically for plant biology, such as simulation tools for pant tissue growth and development, curated knowledgebases of plant biological pathways and systems providing graph-based integrations of knowledge and gene functional inferences Provide functionality very different from PlantSimLab Currently, no modeling tool is available either for plant biology or for general systems biology purposes, which has the functionalities PlantSimLab envision for a tool useful to experimentalist

4 Innovativeness As a network modeling tool for plant biologists, PlantSimLab is to Enable them to build, validate, and use intuitive qualitative computer models, with a user interface that does not require mathematical or modeling expertise Play the role of a virtual lab, in which the user can interrogate an in silico model in ways similar to the how it is done in the lab No such tool is currently available A tool for the discovery of biological hypotheses and for the subsequent design of experiments to test these hypotheses Develop the software in close collaboration with the plant biology community, through use cases that drive software capabilities and interface features

5 Aims Develop the software tool PlantSimLab, which allows plant biologists without specialized mathematical background to Build qualitative dynamic mathematical models of molecular networks relevant to plant biology, Analyze them Use them as a tool for biological hypothesis generation Integrate PlantSimLab with existing network inference software such as Cyclone ADAM (Analysis of Dynamic Algebraic Models) Polynome

Software Architecture A web based application to eliminate the need for download and installation, thus platform-dependent issues Use of a dedicated server to accommodate user demand Automatic

6 Software Architecture A web based application to eliminate the need for download and installation, thus platform-dependent issues Use of a dedicated server to accommodate user demand Automatic launching computing instances in the cloud for users Client and Server Model Client HTML, JavaScript, AJAX Server PHP, MySQL Backbone Pipeline connects PlantSimLab to ADAM, Cyclone and Polynome, the existing mathematical analysis tools for model inference

7 Main Frame Features & Components JAVA version (old) Web version 7

8 - User Account Maintenance Sign-up Log-in Reset-password Use MySQL database for user profile and program execution data 8

9 - Top Menus & Menu Items JAVA version Web version 9

10 - Three Model Building Stages Buttons Model Editor, Experimental Setup, Results Viewer buttons replaced the color scheme of JAVA version for indicating the current network model building stages 10

11 - SBGN Edge Types Positive Influence Necessary simulation Unknown Influence Negative Influence JAVA Web 11

12 - Node Specification Table Configure Number of States Configure Node Color Configure Node Shape 12

13 - Case Specific Node States Specification Tables JAVA Web 13

14 - Edge Specification Table Pops up at clicking the Node Pops up at clicking the Edge JAVA Web 14

15 Model Construction Creating a New Node Step 1. Click Add Node Button & Click on Drawing board Step 2. Configure Node using Node Spec Table Step 3. Specify node states in Node States Table 15

16 - Creating an Activating Edge Step 1. Click Activating Edge Button Step 2. Click Source & Target node in order 16

17 - Creating an Inhibiting Edge Step 1. Click Inhibiting Edge Button Step 2. Click Target & Source Node in order 17

18 A Sample Completed Model JAVA Web 18

19 Generation of a State Transition Table

20 Cyclone run on a PlantSimLab Model 3 2 Cyclone generates an Analysis Results File PlantSimLab generates a State Transition Tables File

21 ADAM Run on a Sample Model ADAM is a web based software doing mathematical analysis on network models (htpp://adam.plantsim.org) < 20 nodes Simulates complete state space of the model and finds all attractors (steady states and limit cycles) & statistics about the size of components Nodes > 20 Computes fixed points for both deterministic and probabilistic networks, and limit cycle of the length specified by the user for deterministic networks

22 ADAM Run on a Sample Model Sample Model Input: f1 = x1+x2 f2 = x1*x2*x3 f3 = x1*x2+x3^2 Analysis of the state space: Number of components 4 Number of fixed points 4 Number of cycles 0 Fixed point, component size, stability (0 0 0), 1, 1.00 (0 0 1), 2, 1.00 (1 0 0), 3, 1.00 (1 0 1), 2, 1.00

23 ADAM Run on a Sample Model - continued State space graph: Dependency graph:

24 Header Design Preference? Users preferences on the choice of Header Image? 24

25 Discussions Challenges with the Pipeline backbone construction between PlantSimLab and the existing mathematical analysis tools Challenges with in-depth understanding of mathematical model analysis and the molecula plant biology Some difficulties with client side drawing (HTML vs Canvas drawing) Some of enhancements to make Use of Style sheet that enables SBGN style and more customization options for graphical model designs Improve the Resolution of the objects drawn in GUI 25

26 Thank you! 26

AMNH Gerstner Scholars in Bioinformatics & Computational Biology Application Instructions

PURPOSE AMNH Gerstner Scholars in Bioinformatics & Computational Biology Application Instructions The seeks highly qualified applicants for its Gerstner postdoctoral fellowship program in Bioinformatics