http://wiki.bakshilab.net/ 2026-04-14T22:20:00+00:00 http://wiki.bakshilab.net/ http://wiki.bakshilab.net/lib/tpl/dokuwiki/images/favicon.ico text/html 2020-04-07T21:48:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.bakshilab.net/doku.php?id=bsubtilis_model&rev=1586296090&do=diff B. subtilis model videos Varying Carrying Capacity Varying AHL threshold Varying Response Sharpness Varying Response Sharpness at different AHL thresholds Varying Response Sharpness at different food thresholds Diffusion Model Animation text/html 2020-04-07T22:02:24+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.bakshilab.net/doku.php?id=gh_diffusion_model&rev=1586296944&do=diff Diffusion PDE model code import numpy as np import matplotlib.pyplot as plt from numba import njit # For just-in-time compilation to LLVM from copy import deepcopy def create_circle(r, cx, cy): # Initial conditions - ring of inner radius r, width dr centred at (cx,cy) (mm) r2 = r**2 for i in range(nx): for j in range(ny): p2 = (i*dx-cx)**2 + (j*dy-cy)**4 if p2 < r2: u0[i,j] = Thot #create_circle(1, 5, 5) m = 0 def create_cell(H, R,… text/html 2020-04-07T21:59:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.bakshilab.net/doku.php?id=gh_image_analysis_pipeline&rev=1586296756&do=diff Image analysis pipeline code ### Imports import time import os import glob from PIL import Image, ImageEnhance import numpy as np from skimage.filters import threshold_otsu, threshold_niblack, threshold_sauvola import matplotlib.pyplot as plt from matplotlib.pyplot import figure import mahotas as mh from scipy import ndimage as ndi from skimage.morphology import watershed as sk_watershed import skimage from sklearn.cluster import MeanShift, estimate_bandwidth, DBSCAN import pandas as pd from … text/html 2020-04-07T21:57:19+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.bakshilab.net/doku.php?id=gh_persilico&rev=1586296639&do=diff Persister Model Code parallel_hybrid.py import numpy as np from numba import jit import random from pprint import pprint import time import helpers as h import plot_helpers as ph import h5py import pandas as pd from joblib import Parallel, delayed import os N = 250_000 delta = np.array( [ [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0], # RelA protein [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0], # SatA protein [0, 0, 1, 0, 0, 0,… text/html 2020-04-07T22:27:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.bakshilab.net/doku.php?id=gh_rotation_supplementary_material&rev=1586298436&do=diff Supplementary Materials to Georgeos Hardo BBSRC DTP rotation report 2 Sequences Videos B. subtilis model videos Code Persister Model Image analysis pipeline code Diffusion PDE model code