Workshops for NCI, Python, R, Experimental design and Statistical Analysis

Description

The RSB Computational Biology and Bioinformatics Unit (CBBU), ANU Bioinformatics Consultancy (ABC), and ANU Statistical Consulting Unit (SCU) are organizing a series of workshops for students and staff from JCSMR, RSB, and Fenner School. Participants from outside of the three schools, including CSIRO and Uni. of Canberra, will be accepted if there are places available, on an individual basis.

The workshops will take place during the Semester 2 Teaching Break and will start at 9:30am, finish at 4:30pm with lunch break 12:30 – 1:30.
You will need to bring your laptop. We have a few laptops which we can lend for the course of the workshops.
To sign up please fill up and submit this form no later than October 25th. The workshops are offered at no cost. Number of places is limited to approx. 35, we will be giving priority to the Honours and PhD students and postdocs.

1. Introduction to NCI and use of Raijin supercomputer 1 day: Monday, 6th November

Delivered by an instructor from NCI and Marcin Adamski from JCSMR/RSB

  • How to get allocation and start using the machine.
  • Introduction to shell interface.
  • Logging in, accounting and monitoring usage.
  • Job submission and scheduling.
  • File system.
  • Software environment.

2. Programming with Python for Beginners 3 day: Wednesday – Friday, 8 – 10th November

Delivered by Bob Buckley and Cameron Jack from ABC

  • Introduction to programming with Python.
  • Variables and functions.
  • Program flow control: branches and loops.
  • Working with files.
  • Eliminating mistakes: debugging, asserts and commenting.
  • Building bigger programs: Modules and classes.

3. Introduction to R and RStudio, Programming in R; 2 days: Monday – Tuesday, 13 – 14th November

Delivered by Marcin Adamski from JCSMR/RSB

  • Introduction to R and RStudio.
  • Data types in R, and type conversions.
  • Loading and saving tab and coma delimited files.
  • Basic data exploration including plotting.
  • Data sub-setting, filtering and joining.
  • Adding new columns with calculated values.
  • Detecting and handling errors an missing values in the data.
  • Creating graphs and plots.

4. Experimental Design and Statistical Data Analysis; 3 days: Wednesday – Friday, 15 – 17th November

Delivered by Terry Neeman from SCU
Please note that this workshop requires basic knowledge of R. If you are not sure about your skills please first come to the workshop #3 - 'Introduction to R and RStudio'.

  • Structure of an experiment: response, treatment factors, blocking factors.
  • Introduction to the Statistical Model: Mean Structure (including Factorial models), Variance (blocking) structure.
  • Planning your experiment: sample size estimation, identifying sources of variation, randomised complete Block, Split Plot, incomplete block designs.
  • Data collection and Data Analysis: Exploring data (graphics and data summaries), review of data structures, linear models.
  • Practice in fitting linear and generalised linear mixed models to data using R. Interpreting and assessing model assumptions.
  • If time permits: Multiple hypothesis testing: false discovery rate and statistical models for genomic data analysis.

Please do not hesitate to contact Marcin Adamski if you have any questions.

Date & time

9am 6 November – 5pm 17 November 2017

Speakers

Various - see program

Contacts

 Marcin Adamski

Updated:  21 October 2017/Responsible Officer:  Director RSB/Page Contact:  Webmaster RSB