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Conor Lawless CnrLwlss

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CnrLwlss / Harmonograph.py
Created May 6, 2015 21:57
Simulate an arbitrary number of linked oscillators (harmonograph), drawing output to .png file.
import numpy as np
import math
import matplotlib.pyplot as plt
import webbrowser
def makePlot(xvals,yvals,fname="harmonograph.png",fopen=False,w=50,h=50,width=0.1):
maxs=[np.max(np.abs(xvals)),np.max(np.abs(yvals))]
farthest=max(maxs)
drw=plt.figure(1)
@CnrLwlss
CnrLwlss / Vicky_Ztest.py
Created March 13, 2015 16:30
Z-test in python and alternative...
# Demonstrating significant differences between a
# vector of measurements and a single value
# Using the statsmodels package for doing test
# Using numpy to generate some fake data
from statsmodels.stats import weightstats as stests
import numpy as np
data=np.random.normal(loc=3.4,scale=0.1,size=100)
singleValue=3.3
@CnrLwlss
CnrLwlss / telo.hs
Created December 2, 2014 21:00
Simulating cell population dynamics with Haskell
data Cell = Cell {teloLength :: Double, birthDate :: Double, lifeSpan :: Double, seedCell :: Integer}
instance Eq Cell where (Cell t1 _ _ _) == (Cell t2 _ _ _) = t1 == t2
instance Ord Cell where (Cell t1 _ _ _) `compare` (Cell t2 _ _ _) = t1 `compare` t2
instance Show Cell where show (Cell t b _ _) = show t ++ " " ++ show b
data CellLine x = Senescent | Mother x (CellLine x) (CellLine x) deriving (Show, Read, Eq)
-- Functions modelling cell biology
shortenTelo :: Cell -> Cell
shortenTelo (Cell telo x y oldseed) = Cell (telo - delta) x y newseed
@CnrLwlss
CnrLwlss / ParallelSerialHaskell.hs
Created November 23, 2014 20:43
import Control.Parallel (par, pseq)
import Control.DeepSeq
import System.Environment (getArgs)
import Data.Time.Clock (diffUTCTime, getCurrentTime)
data Tree x = Empty | Node x (Tree x) (Tree x) deriving (Show, Read, Eq)
-- Create instance of NFData for Tree data type (defining "normal form")
instance NFData a => NFData (Tree a) where
rnf Empty = ()
@CnrLwlss
CnrLwlss / ParallelHaskellSO.hs
Last active August 29, 2015 14:10
Demo Haskell code for a SO question.
import Control.Parallel (par, pseq)
import Control.DeepSeq
import System.Environment (getArgs)
import Data.Time.Clock (diffUTCTime, getCurrentTime)
data Tree x = Empty | Node x (Tree x) (Tree x) deriving (Show, Read, Eq)
-- Create instance of NFData for Tree data type (defining "normal form")
instance NFData a => NFData (Tree a) where
rnf Empty = ()
@CnrLwlss
CnrLwlss / numerical_r.R
Created October 31, 2014 16:49
library(qfa)
numerical_r=function(obsdat,mkPlots=FALSE,span=0.5,nBrute=1000,cDiffDelta=0.0001){
# Generate numerical (model-free) estimate for maximum intrinsic growth rate
tims=obsdat$Expt.Time
gdat=obsdat$Growth
tmax=max(tims)
# Smooth data, find slope as function of time and maximum slope
gdat=log(gdat)
@CnrLwlss
CnrLwlss / GISFunctions.R
Last active January 19, 2017 13:08
Calculating genetic interaction strengths with qfa R package.
f(!("qfa" %in% rownames(installed.packages()))) install.packages("qfa", repos="http://R-Forge.R-project.org")
library(qfa)
GISReport=function(qfolder,cfolder,qTrtMed,cTrtMed,colName="MDRMDP",GISdirn=NULL,normalised=FALSE,wctest=FALSE,qStripRep=0,cStripRep=0,bootstrap=NULL,froot="QFA_EXPERIMENTS",makeImBrowser=FALSE,imTime=2.0,hpath=NULL){
cat("###### WORKING DIRECTORY MUST BE LOGS(2) ######\n")
cat("Query:",qfolder,qTrtMed,"Control:",cfolder,cTrtMed,"Directory:",GISdirn,"\n")
#################################################################
if(normalised){
quer=file.path(froot,qfolder,"ANALYSISOUT",paste(qfolder,"NORM_FIT.txt",sep="_"))
@CnrLwlss
CnrLwlss / Search.py
Created October 22, 2014 15:01
A demo Colonyzer script: looking for cultures in a wider search space
from colonyzer2.functions import *
import time, sys, os, numpy, PIL
print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
print("Note that this script requires a Colonyzer.txt file (as generated by ColonyzerParametryzer) describing initial guess for culture array")
print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
# Lydall lab file naming convention
# First 15 characters in filename identify unique plates
# Remaining charaters can be used to store date, time etc.
@CnrLwlss
CnrLwlss / QFA_ANALYSIS_LIST.R
Last active August 29, 2015 14:07
# To execute this script manually, in parallel on multiple CPUs:
# Rscript Scripts/QFA_ANALYSIS_INDIVIDUAL.R QFA0028 QFA0029 &
# Rscript Scripts/QFA_ANALYSIS_INDIVIDUAL.R QFA0030 QFA0031 &
library(parallel)
source("Scripts/QFA_ANALYSIS.R")
PLOSGenetics=sprintf("QFA%04d",c(28,29,30,31,35,36))
# NCPUs is the maximum number of CPUs the script can use on this node (should be less than 48 on cisban cluster)
NCPUs=47
cisbanNodes=TRUE
@CnrLwlss
CnrLwlss / PlotGrowthCurves.R
Created September 16, 2014 08:06
This is a short script to read in Colonyzer2 output after analysis of timecourse images of arrayed microbial cultures growing on solid agar surface. In this case it is assumed that the "time from inoculation" data are stored in the 4th element of an underscore delimited list embedded in the image filenames.
fnames = list.files(pattern="*.out")
datlist = lapply(fnames, read.delim,sep="\t",header=TRUE,stringsAsFactors=FALSE)
dat = do.call("rbind", datlist)
dat$ID=paste(dat$Barcode,dat$Row,dat$Column,sep="_")
dat$time=as.numeric(sapply(strsplit(dat$Filename,'_'), "[", 4))
dat=dat[order(dat$time),]
pdf("GrowthCurves.pdf")
by(dat,dat$ID,function(x) plot(x$time,x$Intensity,type="b",xlab="Time",ylab="Intensity",ylim=c(0,0.1),main=unique(x$ID)))
dev.off()