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About Lev Lafayette

Crocodile Logo

Lev Lafayette has an MBA (Technology Management) from the Chifley Business School, where he was on the Dean's List, a Graduate Certificate in Project Management from the same institution, and an honours degree from Murdoch University in Politics, Philosophy and Sociology which is commented upon by the Vice-Chancellor of the time. Many years later he completed a Graduate Certificate in Adult and Tertiary Education at the same institution.

He is a certified PRINCE2 Practioner, and an Adult and Workplace Trainer. Clearly not satisfied with one masters degree, he's started another, this time a Master of Education at the University of Otago. With a interdisciplinary approach, Lev's interests include the political implementation of universal pragmatics, the relationship between communications technology and society, and comparative economic systems. On again and off again, he plods his way through completing a PhD in Social Theory as well.

Professionally however, Lev is an experienced systems administrator, specialising in the Linux operating system and scientific applications, a project manager, systems engineer, and quality management systems coordinator, specifically for ISO 9001 (Quality assurance) and ISO 270001 (Information Technology Security). Previous employment and clients include several years working as a computer systems trainer and database management for the Parliamentary Labor Party in Victoria. Following this he worked for the Ministry of Foreign Affairs in Timor Leste (East Timor) managing their computer network and providing training and technical expertise to that Ministry in their first year of self-governance. Dr. Ramos-Horta provided the following comments on his work.

Lev works for the Victorian Partnership for Advanced Computing as a systems administrator for Linux clusters. As per that organisation, this site is mostly dedicated to issues concerning High Performance Computing, Scientific Computing and Supercomputing. Lev is involved in Linux Users of Victoria, having spent four years as President, two years as Public Officer, two years as Vice-President, a year as Treasurer and is now in his second years as an ordinary committee member.

The crocodile logo was designed by Victoria Jankowski. It was first used on the cover of Neon-komputadór, the first IT training manual for the Ministry of Foreign Affairs in East Timor which was printed and translated by the United Nations Development Programme. The crocodile represents the Timorese people and is the emblem of their land. The integrated circuit represents their independent connectivity to the wider world.

You can also find a political site that Lev subscribes to, The Isocracy Network, a synthesis of several progressive political orientations, and RPG Review which covers his interests in roleplaying and simulation games. As a secular humanist with an interfaith perspective, he manages and contributes to the Lightbringers website. He also has a livejournal, which will probably be quite boring to anyone who doesn't know him personally.

That's enough of me talking about myself in the third person like Cerebus The Aardvark.

MrBayes HPC Installation

Mr. Bayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Download, extract. Note that the developers have produced a tarbomb which will require a separate directory created before download. This has been raised as a bug.

Note that more recent versions of MrBayes make much better use of autoconfiguration tools.


cd /usr/local/src/MRBAYES
mkdir mrbayes-3.2.5
cd mrbayes-3.2.5

General Atomic and Molecular Electronic Structure System HPC Installation

GAMESS (General Atomic and Molecular Electronic Structure System (GAMESS)) is a general ab initio quantum chemistry package. You will need to agree to the license prior to download, which will provide a link to gamess-current.tar.gz

Download and extract, load the environment variables for atlas and gcc.


cd /usr/local/src/
tar gamess-current.tar.gz
cd gamess
module load atlas/3.10.2
module load gcc/4.9.1

JAGS (Just Another Gibbs Sampler) Installation

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.


cd /usr/local/src/JAGS
wget http://downloads.sourceforge.net/project/mcmc-jags/JAGS/3.x/Source/JAGS-...
tar xvf JAGS-3.4.0.tar.gz
mv JAGS-3.4.0 jags-3.4.0
cd jags-3.4.0
../config
make
make check
make install
make installcheck

The config script takes the following form


#!/bin/bash
install=$(basename $(pwd) | sed 's%-%/%')

MuTect Installation

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

For complete details, please see the publication in Nature Biotechnology:

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnology (2013).doi:10.1038/nbt.2514

Download after login.

PROJ.4 Cartographic Projections library installation

The PROJ.4 Cartographic Projections library was originally written by Gerald Evenden then of the USGS.

Download, extract, install.


cd /usr/local/src/PROJ
wget http://download.osgeo.org/proj/proj-4.9.1.tar.gz
tar xvf proj-4.9.1.tar.gz
cd proj-4.9.1
../config
make
make check
make install

The config file is a quick executable.


#!/bin/bash
./configure --prefix=/usr/local/$(basename $(pwd) | sed 's#-#/#')

Geospatial Data Abstraction Library Installation

GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats.

Download, extract, install.


cd /usr/local/src/GDAL
wget http://download.osgeo.org/gdal/1.11.2/gdal-1.11.2.tar.gz
tar gdal-1.11.2.tar.gz
cd gdal-1.11.2
../config
make
make install

The config file is a quick executable.


#!/bin/bash
./configure --prefix=/usr/local/$(basename $(pwd) | sed 's#-#/#')

Rosetta Proteins with SCons (and jam and cream)

Rosetta is a library based object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

You'll need a license

Download, extract, load scons, and compile.


cd /usr/local/src/ROSETTA
tar xvf rosetta_src_2015.19.57819_bundle.tgz
cd rosetta_src_2015.19.57819_bundle/main/src
module load scons
scons

SCons with Modules

SCons is a software construction tool (build tool, or make tool) implemented in Python, that uses Python scripts as "configuration files" for software builds.


cd /usr/local/src/SCONS
wget http://prdownloads.sourceforge.net/scons/scons-2.3.4.tar.gz
tar xvf scons-2.3.4.tar.gz
cd scons-2.3.4
python setup.py install --prefix=/usr/local/scons/2.3.4

Change to the appropriate modules directory, check for .desc and .version and .base, create a symblink to .base


cd /usr/local/Modules/modulefiles/scons
ln -s .base 2.3.4

Freesufer cluster installation

Freesurfer is a set of tools for analysis and visualization of structural and functional brain imaging data.

Check system requirements and download. Note that registration and a license key is required for functionality, but not installation.

Create a source directory, change to it, download, extract, discover that everything is bundled, create the application directory and move everything across.

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