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Final Week : Create document and implement some minor UI

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Hi all
1. What I did this week
I created document and implement some minor UI this week.
1.1 Document
I created document. This document contains "Overview of this application", "Quick Start" and "How to use this application. "How to use this application" contains the document of simulation, steady state analysis and parameter estimation. These documents are basically constructed with the detail sentence and image of this application. In these document, user can change it using pagination.

Fig 1.1.1 : Overview of this document
Fig 1.1.2 : Simulation document with pagination( Previous and Next)
1.2 Some minor implementation
I implemented following minor UI. These are advised by my mentor.

1) Just after pressing confirm button in error message, target form is focused on.
2) Input file with ".xml" and ".sbml" ( both upper and lower case) is acceptable.
3) If the file is not readable, the error message happens( See below Fig1.2.1)
Fig …

Week14 : Pop-upping warning and error message

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Hi all.

1. What I did this week
1.1 Pop-upping error text in client side
I used bootstrap modal system to pop-up error text in client side. The error message is popping following situation.

1) The file is not selected
2) The value of some parameters are negative
3) SBML model is invalid.

1.2 Pop-upping warning text in client side
I used bootstrap modal system to pop-up warning text in client side. The warning message is popping following situation.

1)  SBML model has some incorrectness( by checking using the method "checkConsistency" of JSBML class SBML_Validator).

1.3 Demo of this implementation
Fig1.3.1 : The error message with that file is not selected.
Fig1.3.2 : The error message with that the parameter value is negative
Fig1.3.3 : The error message with that SBML model is invalid
Fig 1.3.4 : The waning message with the SBML has some incorrectness 
[Discussion]
The warning message is now used by output of SBML_Validater's return value. However, this value is a littl…

Week13 : Creating Docker image , setting the form to change the upper and lower bound for kinetic parameters in parameter estimation and fixing some bugs

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Hi all

1. What I did this week
1.1 Creating Docker image
I focused on creating Docker image this week. Docker image removes the connecting time to the server because the server in container of Docker is created in local environment. In addition, users are not worried about own model leak to the other.

1.2 Setting the form to change the upper and lower bound for kinetic parameters in parameter estimation.
My last implementation fixed the lower and upper bound of each kinetic parameter in parameter estimation. However, users sometimes want to change these value because the sensitivity of executing parameter estimation for each kinetic parameter is sometimes different. I tried local and global parameters in SBML model can be changed in my implementation.

1.3 Fixing some bugs
My mentors pointed out following bugs last week.
1) Not visualizing the result of analysis using Safari and FireFox( by Andreas)
2) Analysis activated even when the execution button is not clicked (by Andreas)
3) Hap…

Week12 : Download widget was created and all javascript code to execute ajax transfer is changed based on JQuery

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Hi all.

1. What I did this week
1.1 Minor implementation
Firstly I changed my Javascript code to execute ajax transfer based on JQuery.
This change let me to maintain these system easily.

1.2 Major implementation : Download widget to get the result of each analysis
I created this widget to get the result of each analysis as png format for graphical result and csv format for table result. This implementation is significantly important for users to get actual result and download it in their local environment.

1.3 Demo of major implementation( Example is Simulation's one)

Fig1.3.1 : The download tab is added in the "Result of Analysis"
Fig1.3.2 : After user finishes the analysis and click download tab, download dialog open. The file is zip including all the result of analysis. the result of each analysis is png format for graphical result and csv format for table result. 
Fig1.3.3 : The result gotten as png format( graphical result).
Fig1.3.4 : The result gotten as csv form…

Week11 : design of html for steady state analysis and parameter estimation and many minor implementation

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Hi All

1 What I did this week
1.1 Minor implementation discussed last meeting
I finished following implementation.

1. Adding the algorithm of differential evolution and particle swarm optimisation and eliminating genetic algorithm for parameter estimation analysis tool
2. Changing the identifier of species, compartment and kinetic parameter in client side UI to name attribute of SBML if it is defined for all analysis tool
3. Adding the units of species, kinetic parameter to table in client side UI
4. Changing the chart object in client side UI to singleton. This enables graph not to change suddenly
5. Elaborating the UI of parameter selection.
   5-1 If no parameter exists, the tab will be disabled to select
   5-2 If no parameter exists in initialAmount, selected tab is automatically changed to the tab    obtaining some parameters
   5-3 Adding the tab to change the compartment size
   5-4 Grouping species, compartment and kinetic parameter. Global parameter and local parameter belon…

Week10 : Designing of html using css and bootstrap library

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Hi all

1. What I did this week
1.1 The minor implementation discussed last week.
I finished following implementation discussed last week.

1. Adding Run button 2. Setting the form to change x axis to logarithmic scale 3. Setting visualized expression of each species to same result between COASI and simulationCore 5. Pop-uping the species ID when user hovers the mouse over the plot of expression 6. Setting the form to change the tolerance in simulation

Regarding "4. Grouping species, parameters and compartments in UI of changing these values" , I try to implementation from tomorrow.

1.2 Designing of top-page and simulation html
I used bootstrap to design html. This design can change responsively when the browser is changed or the space of canvas is changed.

1.3 Demo of design
Fig 1.3.1 Design of top page
Fig 1.3.2 Design of simulation page
Fig1.3.3 Design of simulation canvas and parameter change widget
[Discussion]
1) Current design
The banner of this design is provisional. T…

Week9 : Numerical table of the result from simulation and parameter estimation

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Hi all

1. What I did this week
I focused on the implementation of numerical table in the result of simulation and parameter estimation.

1.1 Demo of numerical table in simulation
Fig1.1.1 : The table of simulation result is visualized. Each row refers to time and column refers to the species.
 1.2 Demo of numerical table in parameter estimation
Fig1.2.1 : The table of parameter estimation result is visualized. First column refers to the reaction ID and second column refers to the parameter ID. Third and Forth column refer to the start value of this parameter and fitted parameter respectively.

[Discussion]
1) The implementation of the table
I finished this implementation of table. Following table shows my current progress.

Table 1 : Current implementation of visualisation UI : ○ means this is already finished and × means vice versa. Visualization UI Graphical Numerical Simulation ○ ○ Steady State Analysis × ○ Parameter Estimation ○ ○ As you can see, this table contents are really simple but basic …