GSOC2017 : Develop Web Service of SBML model analysis

Hi all 1. What I did this week I mainly focused on the test of simulation execution for large model: red blood cell model[1]. I tried to execute simulation. 1.1 Demo of simulation for red blood cell model Fig1.1.1 : Demo of simulation for red blood cell model As you can see, the dynamic range of the expression for these species are wide. Therefore, the result is really difficult to see. So I tried to set the form to change it logarithmic scale. Fig1.1.2 : The logarithmic scale to visualize the simulation for red blood cell model. This implementation is also difficult to see. I will discuss it in [Discussion]. Moreover, I faced the other problem to scale logarithmic Fig1.1.3 : If the end time is changed to more than 60 for red blood cell model, the logarithmic scaling is crushed. This is specifically happened in the condition following Fig.1.1.3. I have already confirmed that logarithmic scaling is correctly worked for other models in almost all of simula...

Hi all 1. What I did this week I finished to implement the client side UI to change the initial value and parameter value in SBML model and server side program to execute simulation based on this change. I tried to change the html dynamically after SBML model is uploaded to server. 1.1 Demo of this implementation Fig 1.1.1 : Each tab will contain the initial value , local and global parameter in SBML model Fig 1.1.2 : After SBML model is selected, each parameter and this value are visualized. The value can be changed sliding the bar or changing the value of text box. Fig1.1.3 Other initial value changing widget. Fig1.1.4 After changing the initial value( example shows changing initial value of S1 from 0.5 to 0.05), simulation is executed and visualized. Fig1.1.5 If pushing tab of local or global parameter, you can also change these values. [Discussion] Current implementation is pretty annoying to scroll the tab. After scrolling it, simulation result ...

Hi all. 1. What I did this week I finished following tasks. 1) Implementation of simulation program by SBSCL This can let user get the option to execute simulation because the algorithm of numerical integration by SBSCL is different from COPASI. 2) Corresponding to SBML model including the Species in listOfParameters I assumed all species are included in listOfSpecies last week. However, my mentor, Matthias Koenig, advised me that some models( such as the models for Flux Balance Analysis) include the species in listOfParameters. This week I finished the implementation of simulation and parameter estimation by COPASI corresponding to such models. 3) Visualization of steady state analysis My last implementation in steady state analysis is only to open the download dialog for the result of steady state analysis. This was insufficient for users to catch the result easily. Therefore, I implement the visualization program to show the results based on COPASI UI's implementation...

Hi all! 1. What I did this week I mainly focused on creating test server this week. Using the server of a2hosting( https://www.a2hosting.com ) I created the server and configure the environment of this( ex : Installation of tomcat and Java8 , deploying war to tomcat etc). 1.1 Configuration of test server I created the server using a2hosting. The IP address and host name is following. IP : 162.249.4.254 Host name :  gsoctyamadaproject.com In this server, I installed Java8( http://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.rpm ) and Tomcat6( http://ftp.riken.jp/net/apache/tomcat/tomcat-6/v6.0.53/bin/apache-tomcat-6.0.53.tar.gz ). After that I configured some environment variables( such as JAVA_HOME and CATALINA_HOME etc). Then I send the war file of my project to this server and deployed it. Then I checked deployed URL can be connected. Fig 1.1.1 : Checking of connection to my server. Red rectangle shows that the...

Hi all! As always I will firstly explain what I did this week and discussion. Then I will confirm the task next week. 1. What I did this week As I mentioned last week, I mainly implemented the system for users to set the parameters of analysis( ex : End time of simulation, algorithm to execute parameter estimation such as Leven-Berg Marquardt and Genetic Algorithm etc) and execute it based on these parameters. Completing this task, it is important to set the system to send these parameters as JSON format to server side. 1.1 Major Implementation : Client side html and JavaScript to send the parameters of analysis( ex End time of simulation) to server side I mainly set the "Select form" for the selection of libraries and "Input form" for the parameters. Considering AJA JSON, these form's onchange property was set and the analysis is dynamically executed when the libraries or parameters are changed. The data of library and parameters are sent to client s...

Hi all! Today I will firstly explain what I did this week and discussion of this. And then I will confirm the task of next week 1. What I did this week I mainly focus on implementing parameter estimation analysis code using library of COPASI. Completing this task, I can say that fundamental implementation, Simulation, Steady state analysis and parameter estimation is finished and then I can focus on the implementation for users, such as client side UI to change the parameter of analysis. 1.1 Implementation : Server side Java code for analysis of parameter estimation First of all I implemented the analysis of parameter estimation using COPASI API because I am a little bit familiar with this library.  Executing parameter estimation, I supposed that the SBML model and experiment data( normally considered as time-course expression data) are sent from client side. In my implementation the analysis is executed and the result is arranged as JSON format using JSONIC library as I m...

Hi all! Firstly I will explain what I did this week and discussion of this. And then I will confirm the task of next week. 1. What I did this week 1.1 Implementation : AJA JSON system to visualise the result of simulation Last week I concentrated on the implementation of AJAX.  However, this is a little bit complicated because client side JavaScript should analyse the XML data from server side. Therefore, I changed the server side code to send the result as JSON format. Manipulating the JSON data in Java code,  I used the library of JSONIC(Jsonic ver1.3.10 and this is added in pom.xml of my project). Following my proposal, I planned to implement simple visualisation of analysis result. Therefore, I implemented client side visualisation system with AJA JSON. Following figure showed overview of my implementation and this has been already committed to GitHub repository and you can check that. Fig 1.1.1 : Client side html of simulation analysis Fig 1.1.2 : C...