Citations added to allometric scale

cossorzano · Aug 9, 2017 · b16db6f · b16db6f
1 parent 8866594
commit b16db6f
Show file tree

Hide file tree

Showing 3 changed files with 32 additions and 8 deletions.
diff --git a/pyworkflow/em/packages/pkpd/bibtex.py b/pyworkflow/em/packages/pkpd/bibtex.py
@@ -70,6 +70,17 @@
   Url                      = {http://link.springer.com/article/10.1023/A:1007572803027}
 }
 
+@Article{Mahmood1996,
+  Title                    = {Quantitative prediction of in vivo drug-drug interactions from in vitro data based on physiological pharmacokinetics: use of maximum unbound concentration of inhibitor at the inlet to the liver},
+  Author                   = {Mahmood, I. and Balian, J. D.},
+  Journal                  = {J. Pharmaceutical sciences},
+  Pages                    = {411-414},
+  Volume                   = {85},
+  Year                     = {1996},
+  Doi                      = {http://dx.doi.org/10.1021/js950400y},
+  Url                      = {http://onlinelibrary.wiley.com/doi/10.1021/js950400y/full}
+}
+
 @Article{Rostami2004,
   Title                    = {In silico simulations to assess the in vivo consequences of in vitro metabolic drug?drug interactions},
   Author                   = {Rostami-Hodjegan, A. and Tucker, G. T.},
@@ -81,6 +92,17 @@
   Url                      = {http://www.sciencedirect.com/science/article/pii/S174067490400037X}
 }
 
+@Article{Sharma2009,
+  Title                    = {To scale or not to scale: the principles of dose extrapolation.},
+  Author                   = {Sharma, V. and McNeill, J. H.},
+  Journal                  = {British J. Pharmacology},
+  Year                     = {2009},
+  Pages                    = {907-921},
+  Volume                   = {157},
+  Doi                      = {http://dx.doi.org/10.1111/j.1476-5381.2009.00267.x},
+  Url                      = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737649/pdf/bph0157-0907.pdf}
+}
+
 @Article{Spiess2010,
   Title                    = {An evaluation of R2 as an inadequate measure for nonlinear models in pharmacological and biochemical research: a Monte Carlo approach.},
   Author                   = {Spiess, A. and Neumeyer, N.},

diff --git a/pyworkflow/em/packages/pkpd/protocol_pkpd_apply_allometric_scaling.py b/pyworkflow/em/packages/pkpd/protocol_pkpd_apply_allometric_scaling.py
@@ -37,7 +37,9 @@
 
 class ProtPKPDApplyAllometricScaling(ProtPKPD):
     """ Apply an allometric scaling previously calculated to an incoming experiment. The labels specified by the
-        allometric scaling model will be rescaled to the target weight. """
+        allometric scaling model will be rescaled to the target weight. Note that depending on the exponent of the
+        fitting you may want to use a different predictor (weight*maximum lifespan potential, or weight*brain weight)
+        see the rule of exponents (Mahmood and Balian 1996). """
 
     _label = 'apply allometric'
 
@@ -103,3 +105,6 @@ def createOutputStep(self):
     def _summary(self):
         msg = ["Target weight: %f"%self.targetWeight.get()]
         return msg
+
+    def _citations(self):
+        return ['Sharma2009','Mahmood1996']
diff --git a/todo_list b/todo_list
@@ -1,3 +1,7 @@
+Fitting plot should be more continuous
+Implement a test for allometric scaling and bootstrapping
+A bootstrapped population could be changed the experiment it refers to
+
 Generic analysis (signalAnalysis.py)
 Generic PD analysis
 Generic fitters (expression or func.py)
@@ -10,10 +14,3 @@ Population comparison between simulated data
 Batch effect via PCA
 Bootstrap on PD models
 Variance Inflation Factor
-
-# Files to revise
-wizard.py: createDrugSource, configureSource
-tk_ode.py: configureSource
-protocol_pkpd_ode_refine.py: configureSource
-protocol_pkpd_ode_bootstrap.py: configureSource
-protocol_pkpd_bootstrap_simulate.py: configureSource