Showing posts from 2013

Embedding Python in C++: converting C++ vectors to numpy arrays, and plotting C++ vector contents using matplotlib

Getting started with FFTW for computing the Discrete Fourier Transform

grep: select non-matching lines

Comment out block of code in bash shell script

Unarchive and decompress .tar.bz2 and .tar.gz (Ubuntu 12.04)

Texas A&M ENG-LIFE Workshop + Journal Club

Journal club: the trend towards rapid "high-throughput" development

OpenGL vs Direct3D: A history

Journal club: One happy epigenetic family

Using Emscripten to compile C++ to JavaScript on Windows 8

Journal Club: Ugly dogs

Journal club wonkiness

Communicating science without undermining its complexities: different sizes of infinity

Comment and annotate PDF in Ubuntu (12.10)

Open terminal to current working directory from nautilus (Ubuntu 12.10)

awk and GNU parallel: problems with quotes

Journal club: Ontologies to hypotheses. UhLAWLNo

Journal club: On data generation and analysis

Modeling of convection

Code golf

Journal Club: Is statistical significance always biological significance?

Journal club: neuroscience entomology

Using awk: removing restriction site sequence from reads in fastq format

Using awk: bitwise operations and string manipulation

Journal Club: short ORFs and gene prediction

Journal club: uORFs, eukaryotic "operon"?

awk to transpose (super fast)

Journal club: publishable units?

Journal Club: Homologous recombination reporter lines

Change MySQL data file directory (Ubuntu 12.10 64-bit)

Journal club: sweet plots

Journal Club: Nucleosome prediction

Gamasutra Post: Overview of Motion Planning by Matthew Klingensmith

Journal club: Specialist phenomena stems from differential concentrations

Journal club - Green leafy volatiles

Gamasutra and Ars Technica posts on WebGL and JavaScript performance

Gamasutra post: Watch the intriguing '3-Sweep' 3D modeling technique in action

Questions about models to analyze selective pressures

Non-synonymous base substitutions

Nature Jobs article: Two-body blessing by J.T. Neal

Gamasutra post: Modeling by numbers by Jayelinda Suridge

Postmortem: stacksToVCF

Update Stacks installation

Bioconductor is out-of-date: update R to version 3.0 in ubuntu

mysql++ compile example Linux Ubuntu 32-bit (a.k.a. example of linking libraries, makefile, headers for C++)

compile mysql++ from source on Linux Ubuntu 32-bit

Queue command to run after existing command finishes

awk print every other line (or every Nth line) in fasta file

Create directory from R

MySQL Purge Binary Logs (aka MySQL is taking up too much hard drive space)

Location of MySQL database files on Linux Ubuntu

Compile Genome Analysis Toolkit (GATK) from source

VirtualLeaf tutorial: Fatal error message stepwise underflow in rkqs, with h=0.000000 and htry = 0.100000

Gamasutra post by Timo Heinapurola: "What documentation?"

Gamasutra blog post by Lee Perry: "One reason we see so many clones? Communication."

Make bootable USB Linux Ubuntu

Rename error in Linux VirtualLeaf tutorial: "Bareword "tutorial0" not allowed while "strict subs" in use at (eval 1) line 1."

Nature News article: Quantum boost for artificial intelligence

Beginnings with Git

Advice from a systems software engineer

compile errors in Linux VirtualLeaf installation

Configuring an IGV Genome Server