Research Enrichment Program

One key aim of the Genes to Geoscience Research Enrichment Program (GGREP) is for researchers to encounter during their PhD new research questions and possibilities across a wider range of fields than just in their own lab. They will then be better prepared to take the lead as new cross-discipline fields emerge. The second key aim is for researchers to learn useful skills, at higher standard and more efficiently than by self-education.

• GGREP Module Menu for 2009
• Potential External Modules for 2009

GGREP MODULE MENU FOR 2009

1. Genes to Geoscience Seminars
   
   • Organizer Wade Tozer
   • 1.5 days equivalent.
   • Half hour introduction session; 12:30pm, Monday 23rd March, Ecology Lab meeting room (E8C 146).
   • Going to seminars is an essential part of a researcher’s life. Researchers who are innovative and successful over the long term typically go to at least 1-2 seminars a week. This module is designed to help you make the most of seminars and enjoy them at the same time. For this module you will attend at least 20 seminars throughout the year. Appropriate seminars include those in the Genes to Geoscience and departmental series. Other seminars may be counted by prior arrangement with the convenor. Conference presentations and lab meetings are examples that do not count towards the 20 seminars for the year.
   • Participants will be required to produce two products. One will be a notebook kept during the seminars, noting interesting questions and research possibilities arising. The other will be a two page (max) document in the form of a pre-proposal, making a case for a line of research arising from the seminars and notebook ideas.
   • There will be a 2009 “Best Genes to Geoscience Research Idea Award”, providing $1000 research funds. This will be awarded to the pre-proposal that is most innovative, most significant and most convincingly expressed.
   • End date and submission date for notebook and pre-proposal: Friday 30th October 2009.


2. The R programming environment: includes modules on (I) Introduction to R (II) Graphing in R (III) Statistics in R. GGQAC will hold an informal R Hackathon later in the semester for those wanting specific help with R problems.
   
   • Taught by Dr Andrew Allen and Dr Joshua Madin. Academics and postdocs welcome.
   • 3 full day modules – Tuesday 24th, Wednesday 25th and Thursday 26th March.
   • GGQAC R-Hackathon will be held on Thursday 28th May.
   • You may not know it yet, but as a scientist you need to learn R. R is software that is freely available on the internet for a number of different computer platforms (http://www.r-project.org/). This software has become the de facto standard in universities and businesses round the world because of its power and because off-the-shelf solutions exist for many problems (http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html). Even Google uses it!
   • GGREP offers a series of three one-day modules on R. If you are unfamiliar with R, take Intro to R first. Graphing in R and Statistics in R can be taken separately, but statistical analyses and plotting do go naturally hand in hand. This three-day sequence will be followed later in the first semester by an informal 1-day "Hackathon", where you can bring data and ask questions about how to use R for your specific problem. Also, the second-semester module on phylogenetic analyses will use R.
      
   • (I) Tuesday 24th March - INTRODUCTION TO R
     Please, bring your computer. We will begin by downloading R off the internet and installing it on your computer. If you don't have a computer, no problem, let us know and one will be provided to you for the day. Once your computer is set up, we will teach you the basics of the R programming environment. During the course, we will cover a number of topics including how to import data into R, the various kinds of data that R is capable of handling, the syntax of the R programming environment, how to manipulate these data using various graphing, statistical, and programming functions, and how to write your own functions. No programming skills will be assumed for this first day, so you have no excuse not to come.
      
   • (II) Wednesday 25th March - GRAPHING IN R
     R is capable of producing sophisticated, publication-quality graphics, but the number of functions available can be a bit daunting at first. This one-day short course will teach you many different skills, including: how to generate B&W and color plots in 1, 2, and 3 dimensions; how to incorporate additional dimensions by using different sizes, colors, and types of symbols; how to enhance plots by incorporating titles, legends, equations, and axis labels; how to plot spatial information on maps; and how to export plots into various file formats for use in other programs. During the course, special emphasis will be placed on plotting data using R programming techniques in order to automate and document how plots are generated. For the afternoon session you are encouraged to bring your own data to try out various plotting routines.
      
   • (III) Thursday 26th March - STATISTICS IN R
     You will be introduced to some of the most common statistical procedures used in R including: linear regression, generalized linear models, analysis of variance/covariance, correlation analyses, and diagnostic statistics. Common non-parametric statistical procedures will also be discussed, along with bootstrap resampling procedures, which allow statistics to be calculated for data that do not uphold normality assumptions. Time permitting, more exotic procedures like non-linear regression and classification and regression trees will be covered. In order to make these ideas more concrete, emphasis will be placed on using programming tools in R to generate "null" data that will then be analyzed using statistical procedures. If some (or all) of these topics seem unfamiliar to you, don't worry, background materials will be presented during the class. Feel free to bring your data for analysis in the afternoon session.
      
   • (IV) Thursday 28th May - GGQAC R HACKATHON
     Bring your data, bring your computer, and most importantly, bring your questions on how to use R for your research! Experienced R users will be available to answer your questions. Depending on interest, the level of participation, and how difficult your problems are, this R hackathon might go for an hour or it might go all day. Note, the R hackathon is not a GG module and does not count towards the 3-5 day per year time commitment.


3. New opportunities from new equipment
   
   • Organized by Mariella Herberstein, various contributors. Two half-days, (2pm – 4pm) on Monday 6th and Thursday 9th April. Academics and postdocs welcome.
   • Takes the form of a tour round some items of equipment. The aim is to get ideas what kinds of question can be asked. If you decide the equipment is useful for your research, you can get more detailed training later about how to use it.


4. Writing for journals and citation metrics
   
   • Organizer Mike Gillings, various contributors
   • 1 day, Thursday 30th April.
   • An introduction to authorship as a scientist. For practice, you will draft a small research proposal during the day. As incentive, a research grant of $1000 will be offered for the best draft proposal to undertake research that bridges disciplines.


5. Public Relations in science
   
   • Organizer Greg Welsh
   • Half day, morning of Wednesday 13th May.
   • Science often has an uneasy relationship with the media. It is no coincidence however that many successful and well renowned scientists are well skilled in public relations. With some understanding and appreciation of PR, you too can tap into the positive force of the media, while steering clear of the potential traps and pitfalls. This module is an introduction to public relations and an insight into how the media industry works - particularly in relation to the scientific community. What is the media? What forms does it take? It will describe why it is important, what makes "news" and illustrate how you can best present your research to make it news worthy while maintaining the integrity of your work. To help illustrate how science works in the media you will have the opportunity to write and receive feedback on your own press release.


6. Where biology, geology and chemistry meet
   
   • Organizer Simon George
   • 1 day, Wednesday 10th June. Academics and postdocs welcome.
   • Lectures and exercises at the interface of proteomics, molecular biology and organic geochemistry; how microorganisms affect geological deposits and vice versa; biomarkers in present-day environments; chemical record of life on earth; extraterrestrial biomarkers.


7. Colour: concepts and measurement.
   
   • Organizers Mariella Herberstein and Darrell Kemp,
   • half-day, Wednesday 24th June. Academics and postdocs welcome.
   • How to quantify colour for different plants or animals; colour and contrast; colour signals and communication between animals or plants and animals.


8. Genes to Geoscience Outlook
   
   • Organizer Mark Westoby. 12 or more speakers, including some invited from beyond Macquarie.
   • 2 days, Thursday 30th and Friday 31st July. Academics and postdocs warmly encouraged. Lunches provided.
   • This is the flagship of the Genes to Geoscience program. It is a research and research planning festival for academics, as well as a GGREP module. Genes to Geoscience postgraduates should take it at least once during their PhD. Speakers (mornings) will pick out the most exciting trends and possibilities in their fields. Structured discussions (afternoons) will develop research possibilities that take advantage of bridging disciplines. An award ($1000 research fund plus certificate) will be offered for the most intelligent and constructive contributions from a student.


9. Transition from PhD to research career
   
   • Organizer Michelle Power, various contributors
   • 1 day Wednesday 5th August. Academics and postdocs welcome.
   • This module will be of most interest to PhD researchers interested in pursuing postdoc fellowships and research careers. Topics include:
     
     • Planning and taking opportunities during your early career researcher years (ECR; first 5 years after PhD).
     • Building your track record and your CV
     • Grants and Fellowships available
     • Deciding who to collaborate with (including industry partners) and sustaining collaborations.
     • Developing your own research directions
     • What's needed to make your grant proposals competitive? Advice, plus first drafts from you and feedback from an experienced panel.


10. Phylogenetic Analysis
    
    • Organizer Andrew Allen
    • 1 day, Tuesday 22nd September. Academics and postdocs welcome.
    • The ever-increasing availability of molecular sequence data is opening up new research opportunities in ecology and evolution. To harness these opportunities, you first need to learn methods of phylogenetic analysis. Phylogenetic methods allow you to infer evolutionary relationships among lineages, and to rigorously test a broad range of hypotheses related to rates and modes of species-trait evolution, and relationships of species traits to ecological factors. R has emerged as a popular platform for implementing these methods because of its power, flexibility and large user base.
    • In this one-day course, you will be introduced to the most popular R "packages" used to perform phylogenetic analyses. You should attend this course if you already are planning on collecting and analyzing molecular sequence data as part of your research, if you are interested in learning more about R, or if you are curious about phylogenetic methods. A basic understanding of R is assumed, but feel free to come even if you are an R neophyte. Please bring your computer and your data.


11. Building and maintaining your research website
    
    • Organizer Joshua Madin
    • 1 day, Thursday 15th October. Academics and postdocs welcome.
    • Hands-on: you will have a website at the end of the day! A brief introduction to design concepts and HTML, and then a focus on using basic software (i.e., not Dreamweaver) to build and maintain a website. Please bring your own laptop.


12. Biomechanics: Biological structures and materials
    
    • Organizer Joshua Madin
    • 1 day, Thursday 29th October. Academics and postdocs welcome.
    • Concepts and methods from physics and engineering applied to biological materials (breaking corals, bending twigs, stretching silk and lots more).

POTENTIAL EXTERNAL MODULES FOR 2009

Postgraduate Course in Understanding Experimental Design and Statistics (run yearly), 2 week intensive course (9 AM - 5 PM, Monday-Friday): Monday 23 February to Friday 6 March, 2009

Available to: Honours students (enrol in Approved Topic 6108 ENV), Higher Degree (Pgd.Dip., MSc, PhD) students and external students from industry.
Griffith University - Gold Coast Campus, Queensland.
Enrolment costs are approximately $970 (normal HECS fee for a 10CP course) and includes the textbook used in the course.
Max. of 15 students - first come first serve basis = ENROL NOW !
For course information contact: A/Prof. Jean-Marc Hero: m.hero@griffith.edu.au

'Methods in Bioinformatics and Molecular Evolution' workshop, 14-17 April, 09: Hosted by the Australian Centre for Ancient DNA at The University of Adelaide.

This Network sponsored workshop will feature hands-on training from 4 international experts, in leading software packages for the analysis of genetic data. Serial SimCoal and BEAST are some of the programs covered.
Limited to 20 places only, so early registration is advised. Where: The University of Adelaide, North Terrace Campus

Note for EFN ECR members, 5 travel grants (up to $200 per applicant) are on offer to assist with costs to attend this workshop. Expressions of interest should be submitted to the Network Administrator, including a paragraph of your current research project and its relevance to the workshop.
Follow this link for details

National Workshops for Graduate Students and Other Scientists offered by the School of Biology, The Australian National University, Canberra 2009.

Plant Specialized (Secondary) Metabolism: Genetics, Biochemistry and Evolution
April 15-16, 2009
A course offered by Professor Eran Pichersky (University of Michigan, USA)
This two day workshop will explore the genetics, biochemistry and evolution of plant specialized metabolism. An optional one day workshop on headspace (volatile) collection and GC-MS analysis will also be offered if there is sufficient interest.
http://www.anu.edu.au/BoZo/workshops/

Genetic Analysis for Population Studies

July 10-17, 2009.
A course offered by Professor Rod Peakall (ANU) and Professor Peter Smouse (Rutgers University, USA)
This workshop covers a wide range of standard and new statistical procedures for the population analysis and is designed to ensure that students fully understand the procedures involved. For many of the analyses, students will learn to calculate the various statistics by hand, before attempting the self-paced, computer-based tutorial examples. Examples will be drawn from a wide range of organisms.
http://www.anu.edu.au/BoZo/workshops/

Analytical Methods for Population Genetics

October 5 to 9, 2009.
A course offered by Dr David Gordon and Dr Celeste Linde (ANU).
The workshop will present the theoretical framework and concepts necessary to understand the processes shaping the genetic structure of microbial and eukaryote populations. Participants will be introduced to the basic analytical principles underlying a range of public domain software that are available for the analysis of population genetic data.
http://www.anu.edu.au/BoZo/workshops/