1. Compile chemesis following instructions is chemesisREADME
2. Change chemesis path in Python scripts in main directory from '/home/asia/genesis-2.4/' to your chemesis path.
3. Run make_timetables.py to generate presynaptic stimulation patterns.
4. To generate article figures:
Fig 1 IF curves:
run MSsimSyn.g and specify paradigm IF. To generate the figure run fig_0_article.py in SimData
Fig 2:
change calciumdye to 2 in MScell/Ca_constants.g
run Fig_2_distance.py and Fig_2_PSP.py
for 3_AP run MSsimSyn.g, specify paradigm 3_AP and specify location:
secdend11,tertdend1_1,tertdend1_2,tertdend1_3,tertdend1_4,tertdend1_5,tertdend1_6,tertdend1_7
to produce figure run fig_1_article_4_panel.py in SimData
remember to change calciumdye back to 0
Fig 3:
run Fino Pre, Fino Post, P_and_K Pre, P_and_K Post, Shen Pre and Shen Post using MSsimSyn.g
run fig_2_article.py
Fig 4:
if you didn't run Fino Pre, Fino Post, P_and_K Pre, P_and_K Post, Shen Pre and Shen Post using MSsimSyn.g before, do it.
Run Fino_Pre_dends.py PandK_Pre_dends.py  Shen_Pre_dends.py
Run 1_PSP with high resolution using MSsimSyn.g 
You can either comment two last lines, generate the stimulation files and then use a batch file to run them with genesis or uncomment two last lines and run them via python. Beware the second option is not going to be parallel and genesis simulations will run sequentially.
When the simulations are done, in SimData directory comment lines 305-318 in calclulate_weights.py, run calculate_weights.py, then distance.py and finally fig_3_article_5_panel.py
Fig 5:
Run Fino_ISIs_no_L.py,  Fino_ISIs_no_NMDA.py,  Fino_ISIs.py.
You can either comment two last lines, generate the stimulation files and then use a batch file to run them with genesis or uncomment two last lines and run them via python. Beware the second option is not going to be parallel and genesis simulations will run sequentially.
Change the directory to SimData. If lines 305-318 of calculate_weights.py are commented, uncomment them. Run calculate_weights.py, then ISIs_data.py and finally run fig_4_article_4_panel.py
Fig 6:
Run scripts generated by Fino_Pre_dends.py with chemesis to obtain tonic and phasic GABA simulations. Set tonic and phasic GABA switch in SimParams.g (if you have not generated fig 4, run  MSsim_Fino_Pre_location_tertdend1_*_ISI_0.04_phasic.g and  MSsim_Fino_Post_location_tertdend1_*_phasic.g and then calculate_weights.py with  lines 305-318 commented and distance.py)
Go to SimData directory. Run fig_5_article.py

20161010 A replacement file SimParams.g was supplied by Joanna Jedrzejewska-Szmek