FedericoV

# Initialize the MPI-based pool used for parallelization.
pool = emcee.utils.MPIPool()

if not pool.is_master():
    # Wait for instructions from the master process.
    pool.wait()
    sys.exit(0)

nwalkers = 1500
ndim = len(params)

FedericoV

bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'
bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'
bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'
bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'
bash: module: line 1: syntax error: unexpected end of file
bash: module: line 1: syntax error: unexpected end of file

FedericoV

206c 736f 6461 2d2d 2020 6174 2074 2028
3d72 3129 2061 6e64 2073 7465 7020 7369
7a65 2068 2028 3d72 3229 2c20 7468 6520
2020 2000 000a 2020 2020 2020 2063 6f72
7265 6374 6f72 2063 6f6e 7665 7267 656e
6365 2066 6169 6c65 6420 7265 7065 6174
6564 6c79 2020 2020 2000 000a 2020 2020
2020 206f 7220 7769 7468 2061 6273 2868
2920 3d20 686d 696e 2020 2000 000a 2020
2020 2020 696e 2061 626f 7665 2c20 2072

FedericoV

conda list | grep qt
ipython-qtconsole         1.1.0                    py27_1  
pyqt                      4.10.4                   py27_0  
qt                        4.8.5                         0  
federico@FV-DESKTOP-FEM-UBUNTU:~/Systems_Biology/Projects/l-py-and-ducts/modeler$ conda list | grep vtk
vtk                       5.10.1                   py27_1  

FedericoV

query
http://string-db.org/api/tsv/resolveList

data
output=tsv&identifiers=%250Dhob1%250Dfim1%250Dscd1%250Dpom1%250Drho2%250Drho1%250Dpsd1%250Dalp14%250Dfor3%250Dpck2%250Dpck1%250Dalp6%250Dscd2%250Dskb1%250Dsid2%250Dtea1%250Dmal3%250Dtea4%250Dmkh1%250Dppb1%250Dkin1%250Dmob2%250Dcki2%250Datb2%250Dpal1%250Dmyo1%250Dgef1%250Dsty1%250Drga1%250Dshk1%250Dssp1%250Dpmk1%250Dact1%250Drgf1%250Dsts5%250Dtea2%250Darp3%250Dtea3%250Dtip1%250Defc25%250D&request=resolveList&species=4896


queryIndex	stringId	ncbiTaxonId	taxonName	preferredName	annotation
0	4896.SPBC21D10.12-1	4896	Schizosaccharomyces pombe	hob1	Protein hob1; Has a role in DNA damage signaling as a part of stress response processes
9	4896.SPBC119.08-1	4896	Schizosaccharomyces pombe	spm1	Mitogen-activated protein kinase spm1; Regulates cell integrity and functions coordinately with the protein kinase C pathway (pck1 and pck2). Involved the regulation of wall architecture, cell shape, cytokinesis in exponential and stationary phase, and metabolism of ions

FedericoV

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

FedericoV

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

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

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

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