National Resource for Network Biology GSoC'21

Now we headed towards the 2nd coding phase where I discussed with the mentor how the work and how to proceed. So this week and for the upcoming, we will focus on calling various plugins from a single plugin. For doing this we referred to some of the plugins like:-  Cell Counter LSM Toolbox And begin with certain small tasks like: Adding a question mark, after clicking launch Help window Adding an icon to any field/button, like in the LSM toolbox Adding a vertical divider, horizontal divider, controlling the width, the length Adding JPanel with logo  Adding GUIButton.java - Nikita Mahoviya

The results of the First evaluation were out and the efforts over the project brought us to the evaluation phase. So, I passed my first evaluation and received feedback about my work quality, interaction, and some personal approach too for dealing with the project. So here are some of the questions that were asked:- About the Student Did you contribute to National Resource for Network Biology (NRNB) before February 2021? Did you participate in open source before GSoC 2021? <if Yes then for how many years> How many years have you been participating in open source? Were you a GSoC student before GSoC 2021? <if Yes then name of the organization> Communication When did you first communicate with National Resource for Network Biology (NRNB) this year? How often do you interact with your mentor(s)? How do you communicate with your mentor(s)? How responsive are your mentor(s)? Experience What is your favorite part of participating in GSoC? What is the most challenging part of par...

  I discussed the progress of the GUI integration with Michael Sir and the errors I came across and then we concluded  that first we will separate the ‘LinePlot into  Line Plot by Time’ and  ‘Line Plot by Distance’ into two options and then proceed further for which referring the VCellPlugin and experimenting it was important.  I also started working upon the conversion of various other Groovy scripts into plugins taking the reference of VCellPlugin. - Nikita Mahoviya

This week was devoted to improving the presentation of the work that is our GUI. I had to put a warning message on the top of the window which reminds the user to activate the ImageJ service before proceeding, the message at the top of GUI had the chance of being ignored so instead of putting a message at the top I insisted on a pop-up dialog box which had the message: “Please make sure VCell is launched and Fiji Service is started (Under Tools)!” and that was quite favorable to the mentors. So now when we are ready with a set of plugins, we need to integrate them into a single plugin that calls other plugins to perform the task. So this week I had meetings with my mentors that were solely for the integration of plugins. The base was our VCellPlugin and then we added some Radio Buttons that did the task of:  Load File LinePlot by time LinePlot by distance at a time - Nikita Mahoviya

This week I was continuing the task of developing the chart.groovy and Display1Var1Time.groovy into a plugin. The learning process was amazing and wherever I got stuck I consulted my mentors and with them, I was successful in developing the Plugin for chart.groovy . So by now, we had 5 plugins over which we had to do some beautification that included: Putting a warning at the top of each window: "Please make sure VCell is launched and Fiji Service is started (Under Tools)". Initially, the interphase of ModelSearch.java was quite crowded, so had to make it much more presentable and appealing. Integrating the "Search and load" interface of ModelSearch.java into LinePlot.java.  In ModelSearch.java, the purpose of Load vars and Time was not clear initially as it was below variables and time, so to make it more meaningful, Load vars and Time should be shifted above. Removal of ModelType in the GUI of VCellPlugin.java Replacement of the java icon which appears on all GUI ...

14th June 2021 Checked for the functionality for the various groovy scripts which were to be converted to a plugin. Most of them were not functional as the libraries were outdated. 15th June 2021 I had a meeting with Michael sir regarding the various groovy scripts where the points of focus were:  Understand the relationship between Open2D.groovy and VCellPluginTest.java chart.groovy - try to wrap it as a VCellPluginChart.java Display1Var1Time.groovy - understand and wrap into a separate Plugin. 16th June 2021 Understood the code structure of VCellPluginTest, VCellPlugin, and VCellHelper and tried to emulate the same for VCellPluginDisplay and VCellPluginChart. 17th June 2021 In the meeting, we discussed and resolved the mistakes in the conversion of the chart.groovy into java and eventually leading to the development of the plugin ‘VCellPluginChart’. 18th June 2021 Reported the errors while running the ‘VCellPluginChart’ plugin and worked over the conversion of Display1Var1Time.gr...

7th June 2021: An introductory meet was organized by the organization admins for all the students and mentors of the GSoC’21 program. It was a fun experience as we met people from different parts of the world. We had to introduce ourselves by stating our name, the place we belong to and our favorite food so we also came to know about a variety of dishes loved all over the world.. 8th June 2021: A discussion with Michael sir about the newly created plugin in VCell for ImageJ which has been created from the groovy script. Currently, the plugin works for a single model of VCell, when it gets integrated with a GUI, it will respond to all the Models in VCell. 9th June 2021: Added try-catch block for checking the data type of input. Like at places where we have to enter integer values, if at times the user enters the value in the wrong data type, it will display an error message. Designed a layout that depicted the overall working of the project. 10th June 2021: Discussed the layout with Mic...