Postgraduate Study - University of Dundee

Postgraduate StudyGeneric Skills

2015 - 2016

School of Life Sciences

2 Postgraduate Study - Clinical Thesis and Transfer Committees

Contents

Message from the Head of Postgraduate Studies 3

Compulsory Elements of Generic Skills Training 4 in the School of Life Sciences

Optional Elements of Generic Skills Training 9 in the School of Life Sciences

Organisational and Professional Development (OPD) Dundee 11

School of Life Sciences University of Dundee 3

Message from the Head of Postgraduate Studies

This booklet is your passport to an outstanding range of specialist scientific training, generic skills courses, symposia, poster sessions and retreats, which will enhance your experience as a postgraduate student in the School of Life Sciences at the University of Dundee.

The specialist training will introduce you to the dedicated staff and cutting-edge facilities of our multidisciplinary Centre for Advanced Scientific Technologies, and will also cover core competencies in computational biology, statistics and image processing for Life Sciences.

Generic skills (from the same Latin root as ‘generate’) are the qualities of communicating, organizing, problem-solving, flexibility, positivity, ethics, initiative taking, creativity and resilience that will help you to build professional relationships, adapt to change and make a real impact in the world.

In recognition of the importance of generic skills training, the Government and UK Research Councils recommend that all postgraduate students must undertake 10 days (60 hours) of core and generic skills training each year (pro-rata for part-time students) for the first 3 years of study.

Your required 60 hours of training will include compulsory elements specified on pages 3 to 5 of this booklet. Your participation in these courses will be reported to your Thesis Monitoring Committee and in our annual returns to the UK Research Councils. Some of the compulsory courses in writing and presentation skills are timed to help you prepare the written reports, oral and poster presentations, and ultimately the papers and thesis that will be used to assess your academic progress.

How you fill the rest of your 60 hours will largely depend on your own strengths, weaknesses, interests and aspirations. Possibilities include the following:

• Workshops run within the School of Life Sciences and the University of Dundee Organisational and Professional Development (OPD) unit, as described on pages 4-12 of this booklet. OPD and Life Sciences have worked closely together to develop engaging workshops that are specially tailored to the needs of our students.

• Demonstrating to undergraduate students (up to 3 days per year),

• Time spent organizing a symposium/conference, for which support is given,

• Time spent preparing for a presentation when feedback is given from your supervisor/ senior lab members as to the delivery,

• Outreach/Public Engagement activities and training for these (e.g. Researchers in Residence activities).

Perhaps, one of the most challenging of generic skills is time management – how to protect your precious research time without sacrificing your personal and generic skills training needs!

Look after yourself, and take full advantage of the opportunities and support that are available to you.

Good luck.

Professor Carol MacKintosh, Head of Postgraduate Studies

August 2015

Compulsory Elements of Generic Skills Training in the School of Life Sciences

The elements outlined in the table below are compulsory and you are expected to attend as part of your PhD programme studies. Please note that records of attendance will be taken. We would also appreciate that you provide feedback on our training by completing a short questionnaire after each session which can be found here www.lifesci.dundee.ac.uk/generic-skills-training-feedback. We will send a reminder after each event.

The number of hours of generic skills training is indicated in brackets next to the title.

Year Month Description

1 October Postgraduate Induction (3 hrs): This event is designed to provide information on the process of doctoral research and give new researchers essential information to start their research with a clearer view of:

• What is expected of research students

• The role of the supervisor

• Maintaining motivation

• Potential problems and strategies to avoid them

• Sources of additional support

There will also be an introductory talk about the Programme by the Postgraduate Course Organisers.

All October Introduction to Research Statistics for BioScience Research Staff and Postgraduate Researchers (Steve Hubbard) (12hrs): This course introduces statistical analysis using the freeware program R and its associated graphical user interface RStudio. The following topics will be covered in the order given:

• The use of RStudio to import data from Excel, and to explore its properties using graphics.

• Using descriptive statistics to understand data structures

• The use of keyboard shortcuts in R

• Checking assumptions – normality & constant variance

• t-test & analysis of variance (function aov); model simplification & model checking

• Transforming the response variable

• Multiple comparisons in analysis of variance

• Correlation; first & second order partial correlation

• Regression using lm (linear model); the independence of significance & explanatory power

• Analysis of covariance; the blending of analysis of variance and regression

• Model specification & model simplification – the minimal adequate model

The Workshop Aims and Objectives are as follows:

• To establish an understanding of data structures, dataframes & the import of data into RStudio

• To become familiar with all the main features of RStudio

• To understand descriptive statistics and their use in checking assumptions


• To understand the use and interpretation of analysis of variance & regression models

• To bring together analysis of variance and regression into analysis of covariance and the general linear model

• To understand model construction, simplification and checking

• How to overcome model problems – transformation & other solutions

1 November Writing Skills (Gordon Spark) (2hrs): Students should write a Research Plan (500-700 words) briefly describing the background and subject area of their project, what they expect to do, and generally how they expect to do it. Although this will require discussion with your Supervisor, he/she should not alter the writing, since this session is designed to help you with your own writing style. Please bring this piece of writing with you to the class and be willing to share and discuss it in small peer groups. You may also wish to email a copy of the work to Gordon ([email protected]) a few days before the session. This will allow him to identify any common issues to be discussed in the workshop, as well as providing individual feedback where appropriate. You are also welcome to email Gordon in advance of the session to suggest any specific areas of writing you would like to be covered during the workshop. Please note that regardless of whether you choose to send your work to Gordon, it is essential that you bring a paper copy along to the workshop in order to be able to participate and engage with the session.

1 December Modern Techniques in Biomedical Research (7 hrs) Proteomics and Mass Spectrometry (Doug Lamont): To improve our ability to identify proteins, elucidate structure and function, new technologies such as proteomics and mass spectrometry have been developed and advanced over the last few decades. These technologies have and are being used to solve a wide range of problems in biochemical research from confirmation of protein identity, through detailed analysis of chemical modifications on proteins, to measurements in relative expression differences between protein populations. Topics covered will include an overview of proteomics and mass spectrometry, ms theory and instrumentation, types of ms analysis including uses and limitations and quantitative proteomics methods. The presentation will also include details of who to contact, how to prepare samples and what services are available from the proteomics facility within the School of Life Sciences.

Accurate Quantitation in Proteomics (Sara Ten Have): In the rapidly developing field of proteomics, qualitative information about biological systems is no longer enough. We are now able, with the use of SILAC and various other labelling and label free methodologies, to quantify and even describe the rate of protein production and degradation, and the dynamics of post translational modification. Sara will describe some of the novel and exciting ways in which these techniques are being applied to proteomics in the School and how to apply these techniques to your research.

Bioinformatics (David Martin): Tools to understand data-rich biological research. Traditional sequence analysis. Structure bioinformatics. Data analysis from modern proteomics. Next generation sequencing.

Drug Discovery (Tony Hope): The Drug Discovery Unit in the School of Life Sciences. Translational Research. Combining chemistry and biology. Development of assays to support automatic high throughput screening of chemical libraries. The journey to turn a hit-molecule into a drug.

Light Microscopy (Sam Swift): Topics include a brief history of the light microscope and the basic principles concerning its use in the modern research lab, followed by an overview of the equipment and support available to research staff within the School of Life Sciences.

X-Ray Crystallography (Paul Fyfe): X-ray Crystallography is the most powerful method for determining the atomic three-dimensional structures of large biological molecules. This session will provide a brief introduction to the steps that form a typical structure solution pathway. It will also highlight the facilities and support available to aid structural biology research within the School of Life Sciences.

Human pluripotent stem cells (Lindsay Davidson): A introduction to human



embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) and their potential applications in cell biology and drug discovery, followed by a brief overview of the Dundee University Human Pluripotent Stem Cell Facility and available services.

Flow cytometry and fluorescent activated cell sorting (FACS) (Rosie Clarke) Flow cytometry and FACS are technologies widely used in biological and biomedical sciences. The basic concepts of flow cytometry and FACS will be discussed, as well as some of the more common techniques and how they can be applied to different cell systems. Details of services provided by the facility and how these services can be accessed will be discussed.

All February Introduction to Research Statistics for BioScience Research Staff and Postgraduate Researchers (Steve Hubbard) (12hrs): This course introduces statistical analysis using the freeware program R and its associated graphical user interface RStudio. The following topics will be covered in the order given:

• The use of RStudio to import data from Excel, and to explore its properties using graphics.

• Using descriptive statistics to understand data structures

• The use of keyboard shortcuts in R

• Checking assumptions – normality & constant variance

• t-test & analysis of variance (function aov); model simplification & model checking

• Transforming the response variable

• Multiple comparisons in analysis of variance

• Correlation; first & second order partial correlation

• Regression using lm (linear model); the independence of significance & explanatory power

• Analysis of covariance; the blending of analysis of variance and regression

• Model specification & model simplification – the minimal adequate model

The Workshop Aims and Objectives are as follows:

• To establish an understanding of data structures, dataframes & the import of data into RStudio

• To become familiar with all the main features of RStudio

• To understand descriptive statistics and their use in checking assumptions

• To understand the use and interpretation of analysis of variance & regression models

• To bring together analysis of variance and regression into analysis of covariance and the general linear model

• To understand model construction, simplification and checking

• How to overcome model problems – transformation & other solutions

1 February/March Fluorescence Microscopy (Sam Swift) (1hr30) Workshop: Fluorescence Microscopy. Understanding the fluorescent light path, objective lenses, detectors, signal to noise ratio, tips and tricks.

Image Analysis (Graeme Ball) (2h30) Seminar: working with image data, designing experiments for analysis, basic image processing and analysis, making figures, image analysis software. Overview / tour of our image analysis facilities, opportunity to bring your own image analysis problems.


1 March Ethical Practice in Biological and Medical Research: Alan Fairlamb (3hrs). Claire Halpin; Bioethics and Public understanding Luke Newman; Use of animals in biomedical research

1 April Workshop on scientific writing Mike Stark (3hrs): to discuss the transfer report structure and the stylistic elements of scientific writing.

All April Intermediate Research Statistics for BioScience Research Staff and Postgraduate Researchers (Steve Hubbard): (12 hours) This course extends the introductory course, offered in the same series, by broadening the treatment of core topics such as analysis of variance and regression, and introducing new material based on the implementation of generalised linear models with binomial and poisson error structures. In particular, the following topics will be covered:

• A brief refresher of the use of the GUI RStudio to implement R

• The use of graphic and descriptive statistics functions in R to describe data and check data structure to match the assumptions made by parametric tests

• Linear, first, second and higher order partial and part correlation; use of the pairs function to visualise correlation and fit smoothers to the data

• Use of the lm function to fit general linear models to data; introducing polynomial terms into the model; model simplification & checking; using smoothers to identify possible polynomial terms

• Transformation of the response variable

• Non-linear least-squares regression using the nls function; selection of initial coefficient estimates for nls

• Use of the aov function in independent and paired designs

• A brief introduction to robust methods in analysis of variance; trimmed means

• Multivariate anova using function manova

• AIC values & automated model simplification using step

• GLMs with poisson errors (count data) & binomial errors for binary response variables or count data expressed as proportions

This workshop aims to:

• Remind participants of the main features of the RStudio GUI

• Teach participants how to use graphics and descriptive statistics to explore data structures & check underlying assumptions of testing

• Bring together the separate threads of analysis of variance, regression & correlation within the framework of the general linear model with normal errors & constant variance, introducing the additional topic of non-linear regression

• Introduce robust and multivariate forms of the general linear model

• Discuss automated as opposed to manual methods of model simplification, and their respective merits

• Introduce generalised linear models and the error structure families associated with them

Is there any pre-session work required for this workshop? (A submission of work, attendance at a previous session etc.)

Students MUST have some previous experience with statistics, R and preferably RStudio. Attendance at the introductory course earlier in the year is the best way to get this.


1 September Demonstrating (3 hrs): - all second year students will be required to attend a half-day School of Life Sciences specific workshop on Demonstrating. These sessions will provide essential information on what is expected of students during demonstrating in practical classes, including: Introducing participants to the role of a tutor or demonstrator, giving participants confidence in dealing with undergraduate students, examining the best way to encourage learning,

boundaries between demonstrator/tutor and student, and techniques for handling difficult situations.

1&2 September Postgraduates in the School of Life Sciences (PiCLS) Symposium (6hrs) – Westpark Conference Centre. This symposium will be held in September 2015 and is a great opportunity to meet top researchers in the Life Sciences field. Prizes will be awarded to the best posters and student talks. Please note that this is compulsory for 1st and 2nd year students.

2 October Poster Session (4 hrs): Each 2nd year PhD student entering 3rd year displays a research poster in the WTB Complex. This forms the basis for discussion at their next Thesis Committee.


Optional Elements of Generic Skills Training in the School of Life SciencesUp to 3 days of demonstrating will count towards the requirement of 10 days per year transferable skills training undertaken by PhD students in SLS. Additional demonstrating can be undertaken (with supervisors’ consent) beyond the 3 days that count towards transferable skills training. Demonstrating will normally be restricted to students in their second and third years of PhD training. All PhD students will attend a compulsory half-day workshop on demonstrating, but demonstrating itself will be voluntary. Demonstrating will be remunerated.

Python Programming for Biologists (9 x 3hrs) – Biology is a data-rich field and the ability to handle it effectively is an important skill. This course will provide a program of training to bring you up to a basic level of competence in Python. The course will run on Wednesday afternoons in October/November and is designed with biology-specific examples. BBSRC EastBio and rotation students are expected to attend this course and it is highly recommended for all other first year PhD students. The course is run and provided by David Martin.

Error Analysis in Biology (6 x 1hr) – This popular and engaging lecture series is designed to raise understanding of, often poorly understood, key concepts including confidence intervals, error bars and distributions. This course is complementary to the Research Statistics for Bioscience course run by OPD. The series is presented by Marek Gierliński and draws on his experiences of moving from Astrophysics to Biology. The series will run in early 2016 and is highly recommended for all PhD students.

Introduction to Bioinformatics (approx. 21hrs overall) – This course is designed to introduce several Bioinformatics principles and methodologies. For example, familiarity with the linux commandline, protein sequence analysis, RNA-seq analysis and genomics. Students will gain basic Bioinformatics skills, knowledge of some commonly used tools and a better appreciation for reproducible science in Computational Biology. Students may choose to only do some aspects, but will need to ensure to do the specific pre-requisites available elsewhere in Generic Skills. The course will be provided by Geoff Barton, Chris Cole, David Martin and Pietà Schofield.

Writing Skills (Geoff Barton) (3 hrs) - this workshop for 2nd year students is designed to help students to write up their first scientific research paper and their PhD thesis.

Special seminars and workshops (1 hr each) will be organised during the course of your studies. These are organised both centrally (through OPD Dundee; www.dundee.ac.uk/OPD) and at SLS level.

Retreat for all 2nd year students (6 hrs). This one-day retreat is co-ordinated and organised by PiCLS and takes place in September. It provides an excellent opportunity to meet up with other students in your year, present your work to your peers and interact socially in a relaxed environment.

School of Life Sciences Annual Symposium (12 hrs) - Crieff Hydro: This is an important event for all PhD students that is normally held in March each year. It gives you the opportunity to learn about other Division’s research as well as meeting other PhD students within the School. There is also the opportunity to win a lucrative prize at the PhD poster session held during the 3 day symposium. Attendance costs for all first and second year PhD students are covered by the postgraduate programme.

Postgraduates in the School of Life Sciences (PiCLS) Symposium (6hrs) – Westpark Conference Centre. This symposium will be held in September 2015 and is a great opportunity to meet top researchers in the Life Sciences field. Prizes will be awarded to the best posters and student talks.

Lectures in mass spectrometry and proteomics (6 hrs) These will be six one hour lectures which will cover the absolute basics in mass spec and proteomics, including the newest methods developed in the last few years. This basic knowledge will help you in designing better experiments and understanding the possibilities as well as the limitations of proteomics. The lectures will be given by Matthias Trost, Sara ten Have and Tony Ly from Angus Lamond’s lab. The lectures will run in late October/November.

Identification & Evaluation of Enzyme Inhibitors in Drug Discovery - Walter Ward : (7.5 hrs) This workshop is open to all PhD students and will cover fundamental principles of identification and evaluation of enzyme inhibitors, and specific applications in drug discovery. Around half of current medicines function through inhibition of enzymes. It is therefore paramount to gain deep understanding of the principles and methods that underpin the identification and evaluation of enzyme inhibitors. The course will cover topics ranging from basic enzyme kinetics, inhibition mechanisms and binding thermodynamics, all the way to principles and applications of modern biophysical techniques, which are nowadays at the heart of modern drug discovery projects.


Dundee Imaging Facility Training Series (January – March)Week 1, Introduction to the Dundee Imaging Facility - Dr Sam Swift, Head of Imaging Seminar: Introduction to the Dundee Imaging Facility: Available technologies in the Imaging Facility, applications, points of contact and how to arrange access. Followed by short tours of the facility.

Week 2, Microscopy Basics -Dr. Bavishna Balagopal, Light Microscopy Scientific Officer Seminar, Microscopy Basic: Basic principles of microscopy [Kohler illumination, Bright Field, Dark Field & Phase contrast] from an optics perspective. Workshop: Hands on training using home built microscopy kits.

Week 3, Sample Preparation - Dr Paul Appleton, Imaging Applications Specialist Seminar: Methods for preparing biological samples for conventional transmitted light and fluorescence imaging will be covered. This will include conventional wax histology wax and cryosections as well as wholemount (unsectioned) samples. Practical demonstration of wax and frozen sample sectioning and staining.

Week 4, Fluorescence Microscopy - Dr Sam Swift, Head of Imaging * see compulsory section for 1st Years Workshop: Fluorescence Microscopy. Understanding the fluorescent light path, objective lenses, detectors, signal to noise ratio, tips and tricks.

Week 5, Super Resolution Microscopy - Dr. Bavishna Balagopal, Light Microscopy Scientific Officer Seminar : Limitations of conventional imaging techniques, concept of super resolution microscopy, variants of this technology, structured illumination microscopy (using OMX). Practical session on the OMX SIM.

Week 6, Imaging Tissue - Dr Paul Appleton, Imaging Applications Specialist Seminar: Fluorescence and label-free deep tissue imaging techniques; non linear illumination, two photon laser scanning microscopy, second harmonic and third harmonic imaging. Demonstration: technology in the Tissue Imaging Facility.

Week 7, Electron Microscopy - Dr Alan Prescott, Light and Electron Microscopy Applications Specialist Seminar: sample preparation and imaging approaches in Transmission and Scanning Electron Microscopy. Demonstration: technology in the Electron Microscopy Facility.

Week 8, Non-optical Imaging Technology - Dr Yongchang Fan, Electron Microscopy Applications Specialist Seminar: non-optical imaging modalities in the Dundee Imaging Facility; Atomic Force Microscopy, High Resolution Ultrasound and OCT.

Week 9, Image Analysis - Dr Graeme Ball, Image Analyst *see compulsory section for 1st years Seminar: working with image data, designing experiments for analysis, basic image processing and analysis, making figures, image analysis software. Overview / tour of our image analysis facilities, opportunity to bring your own image analysis problems.

Week 10, The Physics and Life Science (PaLS) lab - Dr David McGloin, associate Dean of Physics Seminar: an overview of the PaLS concept, current project and opportunities for collaboration.

Week 11, Drop in Session An opportunity to come and talk to us, bring your own samples and trouble shoot any problems you may be having. All of the Dundee Imaging Facility staff will be available to answer questions and all of the systems will be available.


Organisational and Professional Development (OPD) DundeeOPD is the University of Dundee’s transferable skills training unit for postgraduate research students and staff. You will receive monthly emails from OPD advertising workshops for the up-coming month where there are spaces available, however all workshops for the year can be viewed from their website (www.dundee.ac.uk/OPD), and it is recommended that bookings be made in advance as demand for workshops can be fierce. It should be noted that the programme is not static, and additional workshops will be run subject to demand (please put your name on the waiting list if a workshop is fully booked as you will be offered priority booking on additional dates), and subject to requests from postgraduate research students and staff (your suggestions are welcomed).

Some OPD training sessions are run for School of Life Science students only.

To book a place on an OPD training workshop, you will first need to login, then you can book or cancel places as required via the website. OPD recognises that all students have differing skills, and differing needs, and as such the decision of which training is appropriate should be made via discussions between the student and their supervisor. The School of Life Sciences has a number of mandatory training workshops, and some of these are organised with administration support from OPD. If a student is unable to attend a mandatory workshop, or feels that the workshop is inappropriate for their needs, this should be discussed with the School.

You should consider taking training at appropriate times for your own needs, however below are workshop suggestions that may be of more relevance to particular years. All researcher specific workshops offered by OPD are mapped to the Researcher Development Framework. The entire OPD programme can be viewed on their website if you would like to see the full range of workshops available – www.dundee.ac.uk/OPD

Year 1: The Complete Researcher – PhD LaunchPad (Year 1) Introduction to research statistics for BioScience Postgraduates and Early Career Researchers Building good research habits (90 Minute session) Getting to Grips with Referencing - How to Cite Right and Avoid Plagiarism (Sciences) Practical Presentation Skills for Researchers Creating Academic Posters Using Publisher Presenting Your Poster Communicating Effectively with PIs and Supervisors Introduction to Demonstrating and Lab-based Practical Teaching Preparing a Submission for Thesis Monitoring Committee The Writing Process: Getting started with a literature review Mind Mapping using MindView 5 Business (upgrade from 4) Social Media Bootcamp: Sharing, Connecting & Building an Audience Planning Your Professional Career: An Introduction to The Researcher Development Framework - (RDF) Infographics, Data Visualisation, Animation - New Ways to Illustrate Your Research Good Laboratory Practice Project Managing your PhD

IT and University Systems Advanced Excel: Functions Tricks and Short Cuts Digital Image Manipulation - Illustrator Digital Image Manipulation - Photoshop


Year 2: The Complete Researcher – Making Progress in Your PhD (Year 2) Planning and Structuring Your Thesis Conflict Management (90 Minute session) Negotiation (90 Minute session) Layman’s Abstract: Summarise your Research for the Non-Specialist Writing-up, Proof-reading and Editing Your Work Communicating your Research Online: Digital Tools, Strategy & Impact The Enterprising Researcher IP and Commercialisation (Working Lunch) Intermediate research statistics for BioScience Postgraduates and Early Career Researchers Build a Research Website in Under Three Hours Presenting Science Visually Research Data Management at the University of Dundee Mastering Academic Style How to Write Research When There’s No Time Conference and Events Organising Preparing for Your Viva (Sciences) Design, Write & Storyboard your Academic Posters for Impact

IT and University Systems Creating Your Thesis in Microsoft Word

Year 3: The Complete Researcher – Finish Up and Move On (Year 3) Pitch Perfect: Public Speaking, Networking and Engaging Making the Transition: PhD to postdoctoral research Communicating with Impact Influence and Persuasion Skills Wow! Why? Aha! Communicating Complexity CVs, Covering Letters and Applications Enhancing Interview Skills - A Practical Approach Practice Job Interviews Building a flexible career plan (90 Minute session) Finding and making the best of a mentor for the next stage of your career (90 Minute session) Career Options with Your PhD Introduction to Project Management

If you are unable to attend a place that you have booked on an OPD training workshop, you can cancel this via the website up to 3 working days before the workshop, otherwise please let the unit know by phoning extension 88213, to ensure your place can be offered to students on the waiting list. For late cancellation of places, a valid reason is required as it is expected that you plan your time appropriately after placing a booking. Repeated late cancellation of places will be monitored by the School.

You can view the University’s Researcher Development Policy at www.dundee.ac.uk/opd/policies/researcherdevelopmentpolicy

Useful information for PhD students can be found on the CASTLE website: www.dundee.ac.uk/castle. The Centre supports students and staff in academic development and aids students’ employability offering 1:1 mentoring by appointment. Appointments can be made via online form. Other useful resources are available to access via the My Dundee, Groups and Communities online resources such as The Academic Skills Toolkit and Exam Revision Toolkit. There is also useful information on Digital Literacy which can be found here : www.dundee.ac.uk/library/learning/digital-literacies

The Centre also runs a series of workshops called Principles of Postgraduateness in Week 0 – there is a sign up form for this series on the welcome pages.




School of Life SciencesUniversity of DundeeDundeeDD1 5EH

Tel: 01382 385828www.lifesci.dundee.ac.uk/phdprog

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Postgraduate Study - University of Dundee