root/trunk/promoterActivity.m

function K = promoterActivity(well, mType, mName, absName, time)
% Compute the promoeter activity for a measure defined by WELL, MTYPE
% and MNAME, usin ABSNAME as the absorbance measure. TIME is optional and
% is otherwise computed as the common part between the measure and the
% absorbance curve.
%
%       dI(t)
%      -------
%        dt                I(t)
% K = --------- + gammaR --------
%      c A(t)             c A(t)
%
% well:     measure's well                                            [int]
% mType:    measure's type (RLU or RFU)                            [string]
% mName:    measure's name                                         [string]
% absName:  absorbance measure name                                [string]
% time:     (optional) sample computed                              [array]
%
% K:        reporter concentration computed                         [array]

% Copyright 2006-2007 INRIA
%
% This file is part of WellReader
% 
% WellReader is free software: you can redistribute it and/or modify
% it under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% WellReader is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
% GNU Lesser General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public License
% along with WellReader.  If not, see <http://www.gnu.org/licenses/>.

global WR;

if nargin == 5
    t = time;
else
    min1 = min(WR.wells{well}.(mType).(mName).time);
    max1 = max(WR.wells{well}.(mType).(mName).time);
    min2 = min(WR.wells{well}.Absorbance.(absName).time);
    max2 = max(WR.wells{well}.Absorbance.(absName).time);
    t = max(min1, min2):1:min(max1, max2);
end

dI = fnval(fnder(fit(well, mType, mName)), t); % signal derivative
A = fnval(fit(well, 'Absorbance', absName), t); % absorbance level
rC = reporterConcentration(well, mType, mName, absName, t);

gammaR = WR.global_parameters.([mType '_default_gamma']);
c = WR.global_parameters.plasmid_copies;

K = dI ./ (c .* A) + gammaR .* rC;

end