Team:Wageningen UR/Notebook/Hetty
Modeling the spread Xylencer phages
By: Hetty Huijs
Hetty modeled the spread of our Xylencer phage and X. fastidiosa to help us determine where and when to apply our therapy. More information can be found on her result page.
May
Week 1 (13th of May – 19th of May)
Started working in the office, setting up my computer and tea collection.
Week 2 (20th of May – 26th of May)
Started writing proposal and attended the Dutch Biotechnology conference.
Week 3 (27th of May – 2nd of June)
Wrote proposal and looked for suitable models in literature.
June
Week 4 (3rd of June – 9th of June)
Read literature to compare models on spatial spread of X. fastidiosa. Also I started reading up and expanding my knowledge on dynamic modeling.
Week 5 (10th of June – 16th of June)
Worked on proposal for Safe-by-Design, and looked into modeling of interaction of X. fastidiosa and phages.
Week 6 (17th of June – 23rd of June)
Finalized proposal.
Week 7 (24th of June – 30th of June)
Started coding and making the Lotka-Volterra model.
July
Week 8 (1st of July – 7th of July)
Finalized Lotka-Volterra model.
Week 9 (8th of July – 14th of July)
Vacation and started looking into EFSA model.
Week 10 (15th of July – 21st of July)
Started encoding the different variables of the model for the spatial spread.
Week 11 (22nd of July – 28th of July)
Corrected the parameters for the Lotka-Volterra model as these were incorrectly calculated. Also worked on the script for the spatial spread model.
Week 12 (29th of July – 4th of August)
Started reading on finite difference approach and laplacian operators.
August
Week 13 (5th of August – 11th of August)
Prepared and gave presentation at MENSA in Gent.
Week 14 (12th of August – 18th of August)
After making the scripts for the iterations over the grid we ran into memory overload problems. Therefore I worked on script to minimalize memory usage.
Week 15 (19th of August – 25th of August)
Set up crowdfunding campaign.
Week 16 (26th of August – 1st of September)
I realized that there were problems with incorrect spread of the insects and looked for solutions and different approaches to coding this.
September
Week 17 (2nd of September – 8th of September)
Looked into using a Gaussian filter and convolve to model the spread of the insects over the grid.
Week 18 (9th of September – 15th of September)
Working on presentation of results up until now for chair group to receive feedback on approach of modeling and how to proceed.
Week 19 (16th of September – 22nd of September)
Fixed issues with convolve and running time, finalizing the correct spread of the insects.
Week 20 (23rd of September – 29th of September)
Looked into differences of Lotka-Volterra model and spatial spread model regarding growth rate of X. fastidiosa and fix problems.
Week 21 (30th of September – 6th of October)
Combined models and created the theoretical model on the spatial spread of the phages.
October
Week 22 (7th of October – 13th of October)
Started writing for the wiki and looked into running different simulations on the server for results. Also the scripts for data visualization were written.
Week 23 (14th of October – 20th of October)
Different simulations were run on the server and the wiki pieces were finalized.