omsai

## Plot heatmap in the style of Fig 1B-2:
## dx.doi.org/10.1371/journal.pgen.1006224.g001
library(ggplot2)

## Mock data of 50 rows, 10 columns and 2 strands.
value <- function(mean_ = 0, length_ = 10) {
    dnorm(seq(-1, 3, length = length_), mean = mean_, sd = 0.2)
}
noise <- function(length_ = 10) {
    rnorm(length_, mean = 0, sd = 0.1)

omsai

#!/bin/bash

# Informal scheduler for our shared compute server.
# 
# Run with "-h" for usage.

show_help () {
    name=$(basename $0)
    echo -e "Usage: $name [OPTION]
Informal scheduler for our shared compute server.

omsai

## Calculate power distribution of laser scanning photo-activation device
##
## Laser beam symbols used are from the beam power formula:
## [1] en.wikipedia.org/wiki/Gaussian_beam#Power_through_an_aperture
##
## References:
## [2] radiantzemax.com/kb-en/Goto50125.aspx
## [4] en.wikipedia.org/wiki/Beam_diameter#D4.CF.83_or_second_moment_width
## [5] en.wikipedia.org/wiki/Normal_distribution
##

omsai

commit :
	git add labnotes*.org
	git add Makefile
	git commit -m "ENH: Record up to $(shell date +%Y-%m-%dT%H:%M)"
	git push

.phony : commit

omsai

#!/bin/bash

# Use realpath for tilde expansion
pdf_file=$(realpath "${1}")

# Usage message if file does not exist
if ! [ -e "${pdf_file}" ] ; then
    echo -e "Usage: $(basename $0) <pdf_file>

Double-sided printing.  First prints the odd pages in reverse order,

omsai

$ emerge --info
Portage 2.2.20.1 (python 2.7.9-final-0, default/linux/x86/13.0/desktop, gcc-4.8.5, glibc-2.20-r2, 3.18.7-gentoo i686)
=================================================================
System uname: Linux-3.18.7-gentoo-i686-Intel-R-_Core-TM-_i5-4200U_CPU_@_1.60GHz-with-gentoo-2.2
KiB Mem:    16547692 total,   6993780 free
KiB Swap:    4456444 total,   4456312 free
Timestamp of repository gentoo: Wed, 07 Oct 2015 19:30:01 +0000
sh bash 4.3_p39
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p39::gentoo

omsai

#!/usr/bin/env sh

# Update to the latest Micro-Manager release.
#
# - Download and unpack the source tarball from GitHub mirror.
# - Update 3rdpartypublic svn repo.
# - Unpack ImageJ to new versioned directory.
# - Compile and install Micro-Manager to the ImageJ directory.

# Read the current release version

omsai

embryo	eye
embryo	trunk mesenchyme
embryo	branchial arch
embryo	hindgut diverticulum
embryo	heart
embryo	gut endoderm
embryo	head
embryo	surface ectoderm
embryo	neural ectoderm
embryo	otic placode

omsai

# Replace all spaces in file names with dashes.

find . -name "* *" -type f | \
    while IFS= read -r f ; do \
	mv "$f" "$(dirname "$f")/$(basename "$f" | tr ' ' -)" ; \
    done

omsai

# Create thumbnails in another directory.  Center resize and crop
# images to 150x150.

OBJDIR := ../tabs-square
IMG_SRC := $(wildcard *.jpg)
OBJS := $(addprefix $(OBJDIR)/,$(IMG_SRC))

$(OBJDIR)/%.jpg : %.jpg
	convert \
		$< \