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Lab Journal

• 2 March 2020: First meeting and discussion about the topic
• 3-7 March 2020: Studying bibliography
• 7 March 2020: Creation of repo and first coding attempts to have an idea of the framework
• 10 March 2020: First v0 of the code in Python with proper I/O
• 11 March 2020: Discussion about the code with Ivan, troubleshooting and fixes to the foundations of the code
• 13 March 2020: First v0 version of the code in Julia, at a first glance a factor 10-50 faster in computation (still easy to read outputs missing)
• 14-15 March 2020: v1 of the code in Python and Julia. ++ optimization in Py: splitting is sometimes observed for some initial conditions, longer run is needed..! Julia has been more difficult to optimize and still many steps required-->parallelize?
• 17-18 March 2020: running pre-preliminary simulations.
• 18 March 2020: Optimization and tests for multithread. It has been checked that the exact same numerical results are obtained and a computational times are reduced by 1/3.
• 19-20 March 2020: Waiting for results (one simulation up to t=1e5 with dt=.005 takes 18h approximately, MacBook late 2015, 1.1 GHz Intel Core M) and repo updates
• 21-28 March 2020: Trying to convert Ivan's code from Matlab to Julia, motivated by https://github.com/SciML/MATLABDiffEq.jl, no results obtained for N>150 for memory pressure issue.
• 29-31 March 2020: Using Matlab code from Ivan to obtain data, then Python routine for analysis and plot. Comparison with exact results ODE vs CME
• 6 April 2020: Attempt for a generalized version of system of CME solver in Julia
• 12-18 April 2020: SIR model
  • Julia and Matlab code: results are now matching!
  • SIR analytically studied
  • First sets of results
• 20 April - 5 May 2020: SIS model
  • SIS in Matlab + analysis (multiple corrections and updates needed)
  • SSA implementation
  • Time series analysis of the SSA and Maximum Likelihood Method between CME and SSA