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Professional Development ISMB 2008 Tutorial. References. The PLoS Computational Biology Ten Rules Collection and references contained therein These can be found on-line at http://collections.plos.org/ploscompbiol/tensimplerules.php They are also included as an appendix to these slides.

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professional development ismb 2008 tutorial

Professional DevelopmentISMB 2008 Tutorial

PLoS Professional Development Tutorial

references
References
  • The PLoS Computational Biology Ten Rules Collection and references contained therein
  • These can be found on-line at http://collections.plos.org/ploscompbiol/tensimplerules.php
  • They are also included as an appendix to these slides.

PLoS Professional Development Tutorial

mentors plos comp biol editors
Mentors PLoS Comp. Biol. Editors
  • Philip Bourne – UC San Diego
  • Steven Brenner – UC Berkeley
  • Fran Lewitter – Whitehead Institute
  • Aviv Regev - MIT
  • Chris Sander – Sloan Kettering, New York
  • Each of us represents different career points and a unique perspective

PLoS Professional Development Tutorial

format
Format
  • This tutorial consists of four sessions in which we will discuss a variety of topics. In teaching some of this material in a graduate course at the University of California San Diego it became apparent that the best formula is for the instructor to provide enough content to stimulate discussion, for it is through that dialog that the best learning experience is to be had
  • Be prepared to contribute

PLoS Professional Development Tutorial

agenda
Agenda
  • Introduction
  • Part I – Overview – Doing the Best Research
  • Part II – Getting the Most from Your Graduate Student Experience – collaborating, reviewing, posters, getting a job ….
  • Part III – Writing the Best Research Articles
  • Part IV – Giving the Best Talks

PLoS Professional Development Tutorial

introduction

Introduction

PLoS Professional Development Tutorial

background
Background

How did the course come about?

What is the background (bias) of the instructor?

PLoS Professional Development Tutorial

7

motivation how we spend our time
MotivationHow We Spend Our Time

PLoS Professional Development Tutorial

perspective bourne
Perspective - Bourne

BS, BS (Hon.), PhD at same provincial Oz university

2 good postdocs in Europe and the US

Left academia (sort of) for the IT world for 12 years

14 years in academia – Research Scientist, Adjunct Prof., Prof.

Immersed himself in an emerging discipline

Many diverse research interests

PLoS Professional Development Tutorial

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perspectives brenner
Perspectives - Brenner

PLoS Professional Development Tutorial

perspective lewitter
Perspective - Lewitter

PLoS Professional Development Tutorial

perspectives regev
Perspectives - Regev

PLoS Professional Development Tutorial

perspectives sander
Perspectives - Sander

PLoS Professional Development Tutorial

thus this tutorial is
Thus This Tutorial Is…

How to be the best scientist you can be

Providing no scientific content at all, simply advice on professional development

The opportunity for you to engage in an active dialog about your career concerns. If we do not have that dialog we have failed!

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how did this course come about
How Did This Course Come About?
  • About 3 years ago the student council of the International Society for Computational Biology (ISCB) asked PB to give them a lecture on how to get published based on his role of EIC of PLoS Comp. Biol.
  • The exchange that took place was one of the most fun lectures he have ever given
  • In trying to capture that moment he wrote an Editorial “Ten Simple Rules for Getting Published” …

PLoS Professional Development Tutorial

how did this course come about16
How Did This Course Come About?
  • It was downloaded a large number of times
  • Folks started to approach him with other ideas for Ten Simple Rules
  • To date there is a “Ten Rules” series downloadable from http://collections.plos.org/ploscompbiol/tensimplerules.php

PLoS Professional Development Tutorial

download statistics
Download Statistics

PLoS Professional Development Tutorial

part i doing your best research more about attitude than specifics

Part IDoing Your Best Research(more about attitude than specifics)

PLoS Professional Development Tutorial

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doing your best research a philosophical perspective adapted from richard hamming
Doing Your Best Research – A Philosophical Perspective Adapted from Richard Hamming
  • Richard Hamming 1915 – 1998
  • Mathematician
  • Know to many of us for the Hamming Distance
  • Winner of the Turing Award

from http://en.wikipedia.org/wiki/Richard_Hamming

PLoS Professional Development Tutorial

basic question as asked by hamming in his 1986 lecture you and your research
Basic Question as Asked by Hamming in his 1986 Lecture ‘‘You and Your Research’’

How Can you do Nobel Prize Winning Research?

PLoS Professional Development Tutorial

rule 1 be honest with yourself
Rule 1 – Be Honest with Yourself
  • If you do not want to win a Nobel Prize this may be a waste of your time
  • If you do not want to win a Nobel Prize (or have some equivalent driver) you will not succeed
  • It is no good just wanting to be a me too you must want to make a difference

PLoS Professional Development Tutorial

rule 2 prepare your mind
Rule 2 – Prepare Your Mind
  • Winning a Nobel Prize is not a matter of luck
  • You not winning the Nobel Prize is not the fault of others
  • Face up to your shortcomings and work out how to overcome them either by your own efforts or in collaboration with the efforts of others

PLoS Professional Development Tutorial

rule 3 age is important
Rule 3 – Age is Important
  • You are smarter when you are younger but less experienced
  • The foundation for your success will likely come from your work at an early stage – 20’s to mid 30’s – There are exceptions e.g., the field of study may not have existed when you were that old
  • Experience will help you successfully build on that body of work

PLoS Professional Development Tutorial

rule 4 brains are not enough you also need courage
Rule 4 - Brains Are Not Enough,You Also Need Courage
  • This could perhaps be interpreted as ego
  • You need to strongly voice an opinion you believe in, even when everyone is against you
  • The irony is that research is about innovation, yet at the same time the scientific community is very conservative
  • You need to keep pushing those ideas orally and in print

PLoS Professional Development Tutorial

rule 5 make the best of your working conditions
Rule 5 - Make the Best of YourWorking Conditions
  • ‘‘It is a poor workman who blames his tools—the good man gets on with the job, given what he’s got, and gets the best answer he can.’’
  • The workplace is not about a fancy foyer it is about a place that fosters discourse and stimulates you e.g., MRC Cambridge
  • If the working conditions are not good find new ones soon (more on this in subsequently)

PLoS Professional Development Tutorial

rule 6 work hard and effectively
Rule 6 - Work Hard and Effectively
  • ‘‘Knowledge and productivity are like compound interest. Given two people with exactly the same ability, the one person who manages day in and day out to get in one more hour of thinking will be tremendously more productive over a lifetime.’’
  • “Hard work alone is not enough—it must be applied sensibly.”
  • The person that spends the most hours in the lab. is often not the best
  • Time management skills are critical
  • To work hard like this requires real passion that comes from the heart not the head

PLoS Professional Development Tutorial

rule 7 believe and doubt your hypothesis at the same time
Rule 7 - Believe and Doubt YourHypothesis at the Same Time
  • ‘‘When you find apparent flaws, you’ve got to be sensitive and keep track of those things, and keep an eye out for how they can be explained or how the theory can be changed to fit them. Those are often the great scientific contributions”
  • You must see the big picture – it is oh so easy not too
  • If your hypothesis is proven wrong know when to move on

PLoS Professional Development Tutorial

rule 8 work on the important problems in your field
Rule 8 - Work on the ImportantProblems in Your Field
  • “If you want to do great work, you clearly must work on important problems. . . . I finally adopted what I called ‘Great Thoughts Time.’ When I went to lunch Friday noon, I would only discuss great thoughts after that. By great thoughts I mean ones like: ‘What will be the impact of computers on science and how can I change it?’’’
  • Talk is cheap - So what are my current great thoughts?
    • Change the way science is disseminated through pubcasts
    • Up turn the pharmaceutical industry by reverse engineering every drug on the market
    • Decipher more evidence that we are a product of our environment
  • I dare you to go back and ask your PI what are her/his current great thoughts

PLoS Professional Development Tutorial

rule 9 be committed to your problem
Rule 9 - Be Committed to YourProblem
  • Success comes from the heart not the head
  • ‘‘So the way to manage yourself is that when you have a real important problem you don’t let anything else get the center of your attention—you keep your thoughts on the problem. Keep your subconscious starved so it has to work on your problem, so you can sleep peacefully and get the answer in the morning, free.’’
  • E.g., New York Times on superconductivity

PLoS Professional Development Tutorial

rule 10 leave your door open
Rule 10 - Leave Your Door Open
  • ‘‘There is a pretty good correlation between those who work with the doors open and those who ultimately do important things, although people who work with doors closed often work harder. Somehow they seem to work on slightly the wrong thing—not much, but enough that they miss fame”
  • The door is a metaphor – be open to every idea and person in your field

PLoS Professional Development Tutorial

slide31

Discussion/Questions?

PLoS Professional Development Tutorial

part ii getting the most from your graduate student experience

Part IIGetting the Most from Your Graduate Student Experience

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rule 0 what to have when you graduate
Rule 0 – What to Have When You Graduate

PLoS Professional Development Tutorial

  • A break
  • A job which likely means:
    • The maximum number of high impact papers in quality journals – (ranges from 2 – 20+)
    • A post doc scholarship i.e. money
    • Excellent letters of recommendation from highly respected scientists
    • A committee that had a dialog about your research
    • A plan

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rule 1 here we go again let passion be your driving force
Rule 1 – (Here We Go Again) Let Passion be Your Driving Force

PLoS Professional Development Tutorial

You went into research with little experience – are you as good at it as you were coursework?

Are you excited about your work?

Do you like this life style?

If the answer to any of the above is no, what is your plan – you should always have a plan

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rule 2 is your mentor project and lab right for you
Rule 2 – Is Your Mentor Project and Lab Right for You?

PLoS Professional Development Tutorial

Are you getting the right level of mentoring? If not talk to your mentor, consider a second mentor, use your thesis committee

Is your mentor renown? If not, be sure to be able to get letters from a renown mentor

Is your mentor as enthusiastic about your project as others in the lab?

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rule 3 think independently
Rule 3 – Think Independently

PLoS Professional Development Tutorial

Having said that different students require different levels of mentoring in the end to succeed (particularly in academia) you have to be independent – Ask yourself how independent are you? Can you formulate your own research problems and carry it through?

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rule 4 life is all about balance
Rule 4 – Life is All About Balance

PLoS Professional Development Tutorial

It is my observation that the best scientists balance their career with other activities

Leave an unsolved problem do something unrelated and come back to it – a solution will often be obvious

Other activities often lead to scientific collaborations!

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rule 5 think ahead
Rule 5 – Think Ahead

PLoS Professional Development Tutorial

Do not wait until you are about to graduate to find a lab to do a post doc

Apply for Fellowships – money talks

Use your mentor and thesis committee to help find the right position

Learn to parallel process

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rule 6 remain focused on your hypothesis
Rule 6 - Remain Focused on Your Hypothesis

PLoS Professional Development Tutorial

Step back once a week and consider the big picture – Are you moving towards your big goals

Define the scope of your project with your mentor earlier rather than later – many mentors are happy to have cheap productive labor, but is it in your best interests to stay around?

Do not be scared of what the future holds

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rule 7 address problems earlier rather than later
Rule 7 – Address Problems Earlier Rather Than Later

PLoS Professional Development Tutorial

Your mentor should be more than a purveyor of good science they should be there for your professional development

Issues you are having your mentor will likely have experienced before – take advantage of that experience

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rule 8 networking its critical
Rule 8 – Networking – Its Critical

PLoS Professional Development Tutorial

The literature is the most important vehicle for your work but it is impersonal

Be personal - the connections you make are critical to your future career – give posters, do talks whenever you can both locally, nationally and internationally

Scan for important meetings and discuss your attendance with your mentor

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rule 9 build confidence and a thick skin
Rule 9 – Build Confidence and a Thick Skin

PLoS Professional Development Tutorial

Defend your work with knowledge not knee jerk reactions

Stand up for what you believe in

Be prepared for periods of failure – learn what you can from them, but get over them

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rule 10 make your thesis committee work for the privilege
Rule 10 – Make Your Thesis Committee Work for the Privilege

PLoS Professional Development Tutorial

Select a committee as early as possible – be involved in that selection criteria should be related science and how they can help you with your post doctoral career

Communicate with members regularly – use them as mentor backups

If you and your mentor seriously disagree consult other members of your committee

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slide44

Discussion/Questions?

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part iii writing the best research articles

Part III – Writing the Best Research Articles

Professional Development Series

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overarching thoughts
Overarching Thoughts …

Your publications are the most important metric by which you are judged as a scientist

That metric is increasingly easy to measure

H factor (ISI Web of Science)

Number of citations (ISI, Google Scholar)

Journal downloads

Your papers will be around long after you are gone – they are your scientific legacy

Think about that immutability as you write

Numbers (regrettably) are important

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overarching thoughts47

Overarching Thoughts

Quality is Everything

PLoS Professional Development Tutorial

emerging metrics bourne
Emerging Metrics - Bourne

PLoS Professional Development Tutorial

http://pubnet.gersteinlab.org/

rule 1 to write you have to read
Rule 1 – To Write You Have to Read
  • Read at least 2 papers per day in detail
  • Review papers through journal clubs and take note of the reviews of others
  • Put aside papers you and others think are of high quality to refer to as you write even if they are not related to the topic
  • Look at papers which have open review – learn to write better papers from those reviews

PLoS Professional Development Tutorial

rule 2 learn to be objective about your work
Rule 2 – Learn to be Objective About Your Work
  • The best scientists are the most objective
  • It is easy not to be objective when you have buried yourself in it for months on end – see your work in a broader context – how will it impact science as a whole
  • It is easier for your mentor to be objective (it is only one of a number of projects going on in the lab) but still..
  • Have independent colleagues who can be objective review your first draft

PLoS Professional Development Tutorial

rule 3 pick the right journal
Rule 3 – Pick the Right Journal
  • In order of Priority:
    • The quality of the journal as defined by impact factor, Editorial Board and quality of reviews (this is a matter of opinion!)
    • Be realistic about where the work can be published – it will save time and frustration
    • The journal with the readership that is closest to your work
    • Go open access (personal comment)
  • Use the pre-submission system to be sure it is the right journal

PLoS Professional Development Tutorial

rule 4 learn to write well
Rule 4 – Learn to Write Well
  • This is critical to being a good scientist – it is not just about grammar, but comprehension
  • Take classes to improve your writing skills
  • This is valuable whatever your career path as you will need to present complex ideas clearly, logically and to a broad audience whatever in whatever you do
  • This will lead to less rejection and less rounds of editing

PLoS Professional Development Tutorial

rule 5 learn to live with rejection
Rule 5 – Learn to Live with Rejection
  • Being objective makes rejection easier
  • Even the best scientists get rejected frequently
  • Failure to do so has adversely impacted very good scientists
  • If all of the reviewers think you have written a poor paper – 9 times out of 10 you have – move on

PLoS Professional Development Tutorial

rule 6 learn to use the review process to your advantage
Rule 6 – Learn to Use the Review Process to Your Advantage
  • Good reviews will improve the paper significantly
  • Respond to all the points made by the reviewers
  • Do so in a polite and non-antagonistic way – particularly when the reviewer has not understood your point – consider it your fault not theirs
  • Respond in a way that is easy for the reviewer to comprehend:
    • Address every point head on in the response letter to the editor
    • Make it easy for the reviewer to see where you made changes e.g. with tracking

PLoS Professional Development Tutorial

rule 7 you know the rules for good science do not ignore them
Rule 7 – You Know the Rules for Good Science – Do Not Ignore Them
  • Novelty
  • Comprehensive coverage of the literature to establish your motivation and hypothesis
  • Good data and appropriate analysis
  • A thought provoking discussion

PLoS Professional Development Tutorial

rule 8 even if you obey rule 7 the message can be lost if
Rule 8 – Even if You Obey Rule 7 the Message Can be Lost If..
  • The paper is poorly organized – think logical flow not a blow-by-blow – think scholarship
  • There is not the appropriate use of figures and tables
  • The manuscript is not of the right length
  • You are not writing to the intended audience
  • You do not obey (to the letter) the Guide to Authors – particularly important for the methods section
  • The title does not convey the message
  • You overstate your case with words like “novel”, “new” and a host of other adjectives

PLoS Professional Development Tutorial

rule 9 start writing the paper on day 1 arguable
Rule 9 – Start Writing the Paper on Day 1 (Arguable)
  • Make a good bibliographic database to draw from as you go
  • Decide on the journal in which you will publish early
  • This implies the end result is a paper and not a new finding/knowledge – get real!
  • Draw up an outline
  • Structure the paper around the major results as found in figures and tables
  • Starting early makes it easier to finish – being the best at doing research is not enough – the world needs to know about it
  • As a PhD student this also implies you are writing your thesis as you do the work

PLoS Professional Development Tutorial

rule 10 become a reviewer early in your career
Rule 10 – Become a Reviewer Early in Your Career
  • Have your mentors give you the papers they are reviewing – write a review and discuss with your mentor to improve your reviewing
  • Look at the reviews others have written
  • Understand the review process – EIC, AEs, reviewers
  • Make reviewer-like comments in on-line journals that have that feature, like the PLoS journals
  • This will allow you to see your work in a new light

PLoS Professional Development Tutorial

part iv giving good talks

Part IV Giving Good Talks

Professional Development Series

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over arching thoughts
Over Arching Thoughts …

The science you are talking about is more important than the talk

Being a good speaker is a key element of being a good scientist

The best speakers are often the best scientists

Talk for yourself as well as others – talk to get feedback on your work and use it

If you are passionate about what you do your talks will be more compelling and enjoyable

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over arching thoughts61
Over Arching Thoughts
  • Work within the bounds of your personality
  • If you get no questions you screwed up
  • Even after what I am about to tell you sometimes I feel I give bad talks and I do not know why
  • Conversely sometimes I worry about giving a talk and it turns out much better than I expected
  • You should be able to give the same talk without visual aids

PLoS Professional Development Tutorial

how do i know i gave a good talk
How Do I know I Gave a Good Talk?
  • You get invited back to talk
  • You get invited to talk by someone in the audience
  • Audience members follow up with you days or weeks later
  • People are not asleep or reading email

PLoS Professional Development Tutorial

rule 1 tell the audience what they want to hear
Rule 1 – Tell the Audience What They Want to Hear
  • Talk at a level of detail that matches the expertise of the audience
  • Do not talk up e.g. by saying “this is not my expertise but..” if it is not your expertise they do not want to hear it
  • Do not talk down in a condescending tone
  • Figure out who your audience will be before you prepare one slide

PLoS Professional Development Tutorial

rule 2 less is more
Rule 2 – Less is More
  • Do not try and say too much – your message will be lost
  • Be clear and concise – use visuals to help with this
  • Your knowledge will come across – do not try and tell the audience everything you know
  • No more than one slide per minute max.
  • Too many slides and you tend to talk to quickly – the message will be lost

PLoS Professional Development Tutorial

rule 3 only talk when you have something to say
Rule 3 – Only Talk When You Have Something to Say
  • Your time is precious – the audiences time is yours x the number of people in the audience – Do not waste it with preliminary material

PLoS Professional Development Tutorial

rule 4 make the take home message persistent
Rule 4 – Make the Take Home Message Persistent
  • Test – Ask audience members a week later what they remember from your talk .. If
    • They remember more that 3 points … no one will
    • They remember 3 points you regard as key – well done
    • If they remember 1-3 points but they were not key somehow your emphasis was wrong
    • They say “what talk” .. Figure that out for yourself

PLoS Professional Development Tutorial

rule 5 tell a story
Rule 5 – Tell a Story
  • People (that includes scientists) love a story
  • Include a human element i.e. make it different to a paper
  • Stories have beginnings that set the stage reveal the characters etc.
  • Stories have middles (the experiment and its results perhaps)
  • Stories have a big ending, often a surprise one

PLoS Professional Development Tutorial

rule 6 treat the floor as a stage
Rule 6 – Treat the Floor as a Stage
  • Entertain the audience – think ahead of time what will keep their attention and make them enjoy listening
  • Do not use techniques that are not in your personality. If you are not humorous by nature don’t try and start in front of an audience ditto telling anecdotes

PLoS Professional Development Tutorial

rule 7 practice and time your presentation
Rule 7 – Practice and Time Your Presentation
  • Practice will avoid going off on tangents – this can be dangerous – message is lost, don’t get to the big finish, talk about stuff that you know little about…
  • Practice with colleagues before the big audience – they will think kinder thoughts if you screw up
  • Practice speaking through journal club, group meetings etc.

PLoS Professional Development Tutorial

rule 8 slides
Rule 8 - Slides
  • Do not read the slide unless you wish to emphasize a point
  • Slides are a backup for what you are saying
  • Look at them on the big screen before the audience does
  • Focus on content not glitz
  • Avoid information overload
  • Use animations sparingly and effectively
  • Use navigation tricks

PLoS Professional Development Tutorial

rule 9 video or at least audio your practice presentations and review declared conflict
Rule 9 – Video or at Least Audio Your Practice Presentations and Review (Declared Conflict)
  • This is a very telling way of seeing bad habits e.g., umming and ahhring, scratching your head (or worse) ….
  • Work hard to correct those habits

PLoS Professional Development Tutorial

rule 10 provide appropriate acknowledgements
Rule 10 – Provide Appropriate Acknowledgements
  • This is important – Do not run out of time and so not do it
  • Acknowledge as you go
  • Use pictures
  • Acknowledge people you anticipate will be in the audience who have contributed
  • Include important references

PLoS Professional Development Tutorial

additional thoughts on slides
Additional Thoughts on Slides…
  • A picture really is worth a lot of words
  • Spend time on preparing persistent (e.g. introductory slides you will use over) slides – it is a rewarding experience and a skill worth developing
  • As much as possible a slide should have an understandable message on its own – Its might end up in Google images after all

PLoS Professional Development Tutorial

additional thoughts on slides74
Additional Thoughts on Slides
  • Reuse slides to emphasize a point
  • Provide a roadmap
    • Navigation on the bottom of the screen
    • Returning to the agenda indicating the point you are going to discuss next
    • Use recap slides
    • On the Web

PLoS Professional Development Tutorial

slide75

Discussion/Questions?

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