Training

Computational Biology // Massey University

Software and Data Carpentry Workshops

We facilitate basic and more advanced hands-on computational workshops for scientists of all fields under the umbrella of the Software Carpentry and Data Carpentry foundation. A Software Carpentry workshop usually is a 2-day hands-on workshop teaching introductory skills whereas a Data Carpentry workshop teaches more advanced ans specialised skills. Examples of things we teach at a SWC workshop:

The Unix shell/command-line

The Unix shell ... helps people combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). [Software Carpentry]

Programming in R or Python

The best way to learn how to program is to do something useful, so this introduction to R/Python is built around a common scientific task: data analysis. Our real goal isn’t to teach you R/Python, but to teach you the basic concepts that all programming depends on. [Software Carpentry]

Version control with Git

Version control is the lab notebook of the digital world: it’s what professionals use to keep track of what they’ve done and to collaborate with other people. ... And it isn’t just for software: books, papers, small data sets, and anything that changes over time or needs to be shared can and should be stored in a version control system. [Software Carpentry]

Bioinformatics

We are teaching more advanced courses and workshops in genomics and transcriptomics to help you get started to analyse your data. Example workshops include transcriptomics/RNA-seq gene expression analysis, variant calling, genome assembly, metagenomics/metabarcoding and others.


Events // upcoming

Events // past

Contact

Dr. Sebastian Schmeier
Research Group Leader
Senior Lecturer in Bioinformatics/Genomics

Massey University, INMS
Auckland, New Zealand
+64 9 414 0800 (ext: 43538)

Publications // latest

Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics & Chromatin, 2017, accepted.

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Scientific Reports, 2017, doi: 10.1038/s41598-017-11237-6

Consensus molecular classification of colorectal cancer and association with the colonic microbiota. Diseases of the Colon & Rectum, 2017, 60(6):E90-E91 (In proceedings: Annual Meeting of the American Society of Colon and Rectal Surgeons)

Workshops // upcoming

[ Nov 2017 ] Software Carpentry Workshop, Massey University Auckland

Tweets // latest