FedericoV

D:\Coding Projects\sklearn\sklearn\feature_selection\selector_mixin.py:7: DeprecationWarning: sklearn.feature_selection.selector_mixin.SelectorMixin has been renamed sklearn.feature_selection.from_model._LearntSelectorMixin, and this alias will be removed in version 0.16
  DeprecationWarning)
D:\Coding Projects\sklearn\sklearn\pls.py:7: DeprecationWarning: This module has been moved to cross_decomposition and will be removed in 0.15
  "removed in 0.15", DeprecationWarning)
EE................FF...FFSS..............S..............................................E....E.................................SSS.........E.......................D:\Coding Projects\sklearn\sklearn\externals\joblib\test\test_func_inspect.py:122: UserWarning: Cannot inspect object <functools.partial object at 0x00000000084B5B88>, ignore list will not work.
  nose.tools.assert_equal(filter_args(ff, ['y'], (1, )),
...................................................................................................................................

FedericoV

 Volume in drive D is Storage
 Volume Serial Number is C827-0D77

 Directory of D:\Coding Projects\sklearn\sklearn\svm

07/28/2013  12:05 PM    <DIR>          .
07/28/2013  12:05 PM    <DIR>          ..
07/28/2013  11:16 AM            28,069 base.py
07/28/2013  11:41 AM            23,435 base.pyc
07/28/2013  11:16 AM             2,627 bounds.py

FedericoV

------------------------- OpenOpt 0.505 -------------------------
solver: ralg   problem: unnamed    type: DFP
 iter   objFunVal   log10(maxResidual)   
    0  2.944e+06               0.60 
Traceback (most recent call last):
  File "/home/federico/Systems_Biology/Projects/p53_modeling/Code/dfp_2.py", line 34, in <module>
    r = p.solve('nlp:ralg', plot=1, iprint = 10)
  File "/home/federico/anaconda/lib/python2.7/site-packages/openopt-0.505-py2.7.egg/openopt/kernel/baseProblem.py", line 245, in solve
    return runProbSolver(self, *args, **kwargs)

FedericoV

import numpy as np
from scipy.integrate import odeint
from scipy.optimize import leastsq
import nlopt

def michelis_menten(y, t, *args):
    Vmax = args[0][0]
    km = args[0][1]
    St = args[0][2]
    P = y[0]

FedericoV

from assimulo.solvers import CVode
from assimulo.problem import Explicit_Problem

from scipy.integrate import odeint
from scipy.optimize import fmin_l_bfgs_b

import numpy as np
import nlopt
import matplotlib.pyplot as plt

FedericoV

from assimulo.solvers import CVode
from assimulo.problem import Explicit_Problem
import numpy as np

class MyProblem(Explicit_Problem):
    def __init__(self, y0):
        Explicit_Problem.__init__(self,y0=y0)
        self.text = "Test"
    
    #Define the rhs

FedericoV

from assimulo.solvers import CVode
from assimulo.problem import Explicit_Problem
import numpy as np

class MyProblem(Explicit_Problem):
    def __init__(self, y0):
        Explicit_Problem.__init__(self,y0=y0)
        self.text = "Test"
    
    #Define the rhs

FedericoV

exp_sim.iter = 'Newton'
exp_sim.discr = 'BDF'
exp_sim.rtol = 1e-4
exp_sim.atol = 1e-4
#exp_sim.pbar = [1,1,1] #pbar is used to estimate the tolerances for the parameters
exp_sim.report_continuously = True #Need to be able to store the result using the interpolate methods
exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
exp_sim.suppress_sens = True
exp_sim.verbosity = 50

FedericoV

!******************************************************************************
!*                      Code generated with sympy 0.7.3                       *
!*                                                                            *
!*              See http://www.sympy.org/ for more information.               *
!*                                                                            *
!*                      This file is part of 'autowrap'                       *
!******************************************************************************

REAL*8 function autofunc(Gal, empty, fullbound_RE, fullbound_closed_RE, k_base_synt_p53, k_bindleft_p53_RE, k_bindright_p53_RE, k_deg_p53, k_max_synt_p53, k_sat_p53, k_transclosed, k_transhalf, k_transopen, k_unbindleft_p53_RE, k_unbindright_p53_RE, leftbound_RE, p53, rightbound_RE)
implicit none

FedericoV

{
 "metadata": {
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {