Progress Report

This page lists the weekly progress of the project
and the minutes of my weekly meet with Dr. Alicia

COMMUNITY BONDING PERIOD

WEEK 0 + WEEK 1 - 23rd April to 6th May, 2018

No. Title Description Links if applicable
1. What did I get done this week?
1 Set up blog Set up the basic structure of blog. The blog has been divided into 3 parts. They are
1. About Project
2. Progress Report(which you are viewing right now)
3. About me		 https://arnab1896.github.io/
2 Introduction of OpenWorm Community Introduced myself during #Office-Hours on OpenWorm's Slack channel. Got to know other GSoC candidate and senior developers N/A
3 Discuss Communication rules with mentor It was decided that every Thursday around 7-8 pm IST I will have a Hangouts call with Dr. Alicea (mentor) to discuss progress of the week and plan for next week. For other discussion and code sharing related stuff, contact will be through Slack and email N/A
2. What do I plan on doing next week?
1 Deliver Presentation to DevoWorm community An in-detail presentation will be delivered to DevoWorm community somewhere between 9th - 13th May about the deliverables of the project. N/A
2 Build codelet to get a feel of the projects Write a python code to convert CSV/Excel type datasheet to XML-format document N/A
3 Run GraphViz and Gephi Run GraphViz and Gephi to execute some sample graphs and trees. Decide which is better and should be taken up for the project's deliverables N/A
4 Set up "About Me" "About Me" section needs to be set up on the blog https://arnab1896.github.io/page3_arnab
3. Am I blocked on anything?
1 Exams are over, so not blocked on anything now :) N/A
COMMUNITY BONDING PERIOD - Last week

WEEK 2 - 7th May to 13th May, 2018

No. Title Description Links if applicable
1. What did I get done this week?
1 Deliver Presentation to DevoWorm community A presentation was delivered to DevoWorm community on 12th May about the deliverables of the project. Video has been uploaded here: https://www.youtube.com/watch?v=HVYzkR2XrTQ
2 Built codelet to get a feel of the projects Repository has been set up Repository: https://github.com/arnab1896/GSOC-2018/tree/master/python_query_respond
3 Ran Gephi Ran Gephi on Windows with a sample dataset to check out it's features. By the way, Gephi has Java dependencies, so had to upgrade that. Gephi work has been currently put on hold to first get the python codes done. Some sample pics: https://github.com/arnab1896/GSOC-2018/tree/issue-8_branch/gephi_initial_try
2. What do I plan on doing next week?
1 Take the floor in Office Hours The May 23rd Office Hours has GSoC on its agenda. So, Afonso Pinto and me; we are going to talk about our project on Slack to the entire OpenWorm community N/A
2 Python Well, nothing much to describe, except that the codes will be taken forward N/A
3 Set up "About Me" "About Me" section needs to be set up on the blog https://arnab1896.github.io/page3_arnab
3. Am I blocked on anything?
1 Nope N/A
CODING PERIOD - PHASE I

WEEK 3 + WEEK 4 14th May to 27th May, 2018

No. Title Description Links if applicable
1. What did I get done this week?
1 Take the floor in Office Hours Took the floor on 23rd May Office Hours and gave talk on my project on OpenWorm's slack channel N/A
2 Python The way the codes are currently being morphed. There are two codes:-
1. Python Query Respond
2.Python dataset to XML generator/convertor		 Here are a couple of links:-
1. Query Respond
2. Dataset to XML
3 Waffle board of issues Got the waffle board of issue more organized with help from Dr.Alicea https://waffle.io/devoworm/GSOC-2018
2. What do I plan on doing next week?
1 Paper planning and documentation The reposiory size is increasing and with this, the need to keep documentation upto date is becoming important. So, coming two weeks, I plan to give the documentation a heads-up N/A
2 Python Well, nothing much to describe, except that the codes will be taken forward N/A
3 Set up "About Me" "About Me" section needs to be set up on the blog https://arnab1896.github.io/page3_arnab
3. Am I blocked on anything?
1 Nope N/A

WEEK 5 + WEEK 6 28th May to 10th June, 2018

No. Title Description Links if applicable
1. What did I get done this week?
1 Add functionality in query responder Users can now query for subsequent generations of cells through the loop on terminal N/A
2 Flowcharts and annotation Detailed flowcharts and annotations have added to divide the project into different logical parts and help users understand the modularity Link for README.md:-
README.md
3 Gephi Basic *.gml files were simulated in Gephi using Force Atlas layout. Users can lookout for some common issues they might face in the file given in link Gephi_Issues
2. What do I plan on doing next week?
1 Paper planning and documentation The reposiory size is increasing and with this, the need to keep documentation upto date is becoming important. So, coming two weeks, I plan to give the documentation a heads-up N/A
2 Python Codes will be taken forward. New functionality will be added to query responder N/A
3 Set up "About Me" "About Me" section needs to be set up on the blog https://arnab1896.github.io/page3_arnab
4 Gephi Get versed with other possible layouts in Gephi and types of graphs N/A
3. Am I blocked on anything?
1 Nope N/A

WEEK 7 + WEEK 8 15th June to 24th June, 2018

No. Title Description Links if applicable
1. What did I get done this week?
1 Documentation and planning Flowcharts were modified, README of main repository as well as Graph generator was modified N/A
2 Python New functionality of allowing users to analyse class of cells added N/A
3 Gephi Got versed with other possible layouts in Gephi and types of graphs N/A
2. What do I plan on doing next week?
1 Paper planning and documentation Financial Information Exchange type protocol for representing information can be set up https://en.wikipedia.org/wiki/Financial_Information_eXchange
2 Python Codes will be taken forward. New functionality will be added to query responder and graph generator N/A
3 Set up "About Me" "About Me" section needs to be set up on the blog https://arnab1896.github.io/page3_arnab
4 Gephi and overall picture Get versed with other possible layouts in Gephi and types of graphs N/A
3. Am I blocked on anything?
1 Nope N/A
CODING PERIOD - PHASE II

WEEK 9 + WEEK 10 + WEEK 11 25th June to 15th July, 2018

No. Title Description Links if applicable
1. What did I get done this week?
1 Wildcard and Exploratory These two features were started fresh N/A
2 Gephi and *.gml Basic framework for *.gml generation coded. Also, Gephi guide/README first draft written N/A
3 Phase 2 evaluation Phase 2 evaluation done N/A
4 Common ancestor First draft script of common ancestor coded in python N/A
2. What do I plan on doing next week?
1 Documentation Improve annotation for the existing codes. Also, improve README.md for all required folders N/A
2 Matplotlib Explore matplotlib for 3d simulation possibly og *.gml type files N/A
3 Unify features Unify all the existing features in a single script for ease of use and better architecture of the project N/A
3. Am I blocked on anything?
1 Nope N/A
CODING PERIOD - PHASE III - FINAL

WEEK 12 + WEEK 13 16th July to 29th July, 2018

No. Title Description Links if applicable
1. What did I get done this week?
1 Master bash script Master script will act as single point of entry for the project and has the execution pathways for all the features for user ease. N/A
2 Open Source article Started penning down my thoughts for the open source world related article that I plan to publish during final evaluation N/A
3 Final evaluation preparation Documentation, annotation, flowcharts/pics and README improvements. Also, many miniscule bug fixes to outputs and codes in the already existing features N/A
2. What do I plan on doing next week?
1 Feature improvements Improve feature 7 by solving weird bug that is causing incomplete written file of lineages. Also, improve the XML generator feature and get it ready N/A
3. Am I blocked on anything?
1 Nope N/A

WEEK 14 + WEEK 15 30th July to 14th August, 2018

No. Title Description Links if applicable
1. What did I get done this week?
1 Feature improvements Improved feature 7 by solving weird bug that was causing incomplete written file of lineages. Also, improved the XML generator feature and get it ready N/A
2 Open Source article The article was finally published both on my blog as well as synthetic diaries My Personal Blog
Synthetic diaries
3 .gitignore To avoid the *.gml and some *.txt files from causing unnecessary clutter with every git commit, implemented a .gitignore file N/A
4 Final Evaluation Getting ready for final evaluation. Making final polishing efforts and tying things up together in a proper bundle. N/A
2. What do I plan on doing next week?
N/A
3. Am I blocked on anything?
N/A