Federico Vaggi FedericoV

FedericoV / gist:6607867

Created September 18, 2013 11:30

Subclassing Explicit_Problem

	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 / gist:6607139

Created September 18, 2013 10:13

Assimulo and sensitivity

	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 / gist:6592288

Last active December 23, 2015 06:09

Inference of Parameters of an Ordinary Differential Equation using SciPy and nlopt

	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 / gist:6103306

Created July 29, 2013 09:56


	------------------------- 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 / gist:6098123

Created July 28, 2013 10:06

	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 / gist:6098092

Last active December 20, 2015 08:09

Build Attempt on Windows

	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, )),
	...................................................................................................................................