ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/osprai/osprai/trunk/mdl_module.py
(Generate patch)
# Line 2 | Line 2
2   mdl: Example model functions module for SPRI data.
3   Christopher Lausted, Institute for Systems Biology,
4   OSPRAI developers
5 < Last modified on 100511 (yymmdd)
5 > Last modified on 100518 (yymmdd)
6  
7   Examples:
8   #import mdl_module as mdl
# Line 22 | Line 22
22   #param2['t3'] =    {'value': 270.0}
23   #data2 = simple1to1(time, data, param2)
24   """
25 < __version__ = "100511"
25 > __version__ = "100518"
26  
27  
28   ## Import libraries
# Line 63 | Line 63
63      It requires numpy arrays of times and starting data values.
64      params['t1']['value']   is time of injection for binding, (s)
65      params['rmax']['value'] is maximum response, (RIU)
66 <    params['conc']['value'] is concentration of analyte [A], (M)
66 >    params['conc']['value'] is stock concentration of analyte [A], (M)
67      params['kon']['value']  is on-rate of analyte, (1/Ms)
68      params['t2']['value']   is time of end binding & begin washing, (s)
69 <    params['koff']['value']  is off-rate of analyte, (1/s)
69 >    params['koff']['value'] is off-rate of analyte, (1/s)
70      params['t3']['value']   is time end of washing & data fitting, (s)
71 +    
72 +    It also can take an optional parameter useful for dilution series.
73 +    params['cofa']['value'] is concentration factor, (1/dilution factor)
74      """
75      ## Skip parameter validation steps for now.
76 <    t1 = params['t1']['value']
77 <    rmax = params['rmax']['value']
78 <    conc = params['conc']['value']
79 <    kon = params['kon']['value']
80 <    t2 = params['t2']['value']
81 <    koff = params['koff']['value']
82 <    t3 = params['t3']['value']
76 >    t1 = float(params['t1']['value'])
77 >    rmax = float(params['rmax']['value'])
78 >    conc = float(params['conc']['value'])
79 >    kon = float(params['kon']['value'])
80 >    t2 = float(params['t2']['value'])
81 >    koff = float(params['koff']['value'])
82 >    t3 = float(params['t3']['value'])
83 >    if ('cofa' in params.keys()):
84 >        conc *= float(params['cofa']['value'])
85      
86      """
87      Derivation:
# Line 129 | Line 134
134      params['koff']['value'] is off-rate of analyte, (1/s)
135      params['t3']['value']   is time end of washing & data fitting, (s)
136      params['kmtl']['value'] is rate of diffusion,  (RIU/Ms)
137 +    
138 +    It also can take an optional parameter useful for dilution series.
139 +    params['cofa']['value'] is concentration factor, (1/dilution factor)
140      """
141      ## Skip parameter validation steps for now.
142      t1 = params['t1']['value']
# Line 139 | Line 147
147      koff = params['koff']['value']
148      t3 = params['t3']['value']
149      kmtl = params['kmtl']['value']
150 <    
150 >    if ('cofa' in params.keys()):
151 >        conc *= float(params['cofa']['value'])
152 >        
153      """
154      Derivation:
155      d[AL]/dt = (kon*[A]*[L] - koff*[AL]) / (1 + kon*[L]/kmtl)

Diff Legend

Removed lines
+ Added lines
< Changed lines
> Changed lines