Professional Development
ISMB 2008 Tutorial
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References
• The PLoS Computational Biology Ten Rules
Collection and references contained therein
• These can be found on-line at
http://collections.plos.org/ploscompbiol/tensi
mplerules.php
• They are also included as an appendix to these
slides.
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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
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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
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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
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Introduction
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Background
• How did the course come about?
• What is the background (bias) of the
instructor?
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Motivation
How We Spend Our Time
Task
Percent Time
Key Elements
Collaboration
20%
Science driver, but never taught how to
collaborate
Lecturing (Internal and
External)
10%
Various drivers, but never taught how to
lecture
Writing Grants
10%
Science driver, but never taught how to
write a grant
Managing People
20%
Dealing with HR (visas, hires, reference
letters); people have/are problems
Writing/Reworking Papers
15%
Science driver, but never taught how to
write a good paper
Reviewing
15%
Science driver, but never taught how to
write a good review
Mentoring
10%
Science driver, but never taught how to
mentor
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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
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Perspectives - Brenner
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Perspective - Lewitter
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Perspectives - Regev
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Perspectives - Sander
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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?
• 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”
…
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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/tensi
mplerules.php
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Download Statistics
Publication date >
Postdocto
Oral
Best
Getting
Getting
ral
Collabora Presentat
Researc Graduate
Published Grants
Reviewers Position tion
ions
Posters h
Students
Oct-05
Jan-06
Sep-06 Nov-06 Mar-07
Apr-07 May-07 Oct-07
Nov-07
Oct-05
Nov-05
Dec-05
2074
4032
1619
Jan-06
Feb-06
Mar-06
Apr-06
May-06
Jun-06
Jul-06
Aug-06
Sep-06
Oct-06
Nov-06
Dec-06
1517
1792
2454
1392
1239
1520
1076
986
1741
1671
1344
796
2174
2695
900
247
218
202
196
452
706
261
236
1432
2144
483
325
3972
2559
Jan-07
Feb-07
Mar-07
Apr-07
May-07
Jun-07
Jul-07
Aug-07
Collection launched
Sep 07
Oct-07
Nov-07
Dec-07
Total
680
711
668
718
1406
1100
822
984
244
216
181
344
705
410
307
212
347
375
241
290
689
310
280
204
1369
566
478
650
831
659
410
399
750
3232
1284
597
400
250
1814
3622
916
491
429
2369
2068
812
375
6130
2098
1438
1529
43537
2896
1206
878
808
16694
2123
537
603
568
10951
2258
768
1027
855
16801
2233
606
822
564
10738
3523
2805
1445
1249
16294
3259
1086
1230
906
12105
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5858
984
9158
74
4813
4887
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Part I
Doing Your Best Research
(more about attitude than specifics)
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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
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Basic Question as Asked by Hamming in his 1986
Lecture ‘‘You and Your Research’’
How Can you do Nobel Prize Winning
Research?
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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
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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
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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
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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
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Rule 5 - Make the Best of Your
Working 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)
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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
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Rule 7 - Believe and Doubt Your
Hypothesis 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
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Rule 8 - Work on the Important
Problems 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
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Rule 9 - Be Committed to Your
Problem
• 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
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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
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Discussion/Questions?
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Part II
Getting the Most from Your
Graduate Student Experience
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Rule 0 – What to Have When You
Graduate
• 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
• 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?
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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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Discussion/Questions?
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Part III – Writing the Best
Research Articles
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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 Thoughts
Quality is
Everything
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Emerging Metrics - Bourne
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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
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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
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Rule 3 – Pick the Right Journal
•
In order of Priority:
1. The quality of the journal as defined by impact factor,
Editorial Board and quality of reviews (this is a matter of
opinion!)
2. Be realistic about where the work can be published – it
will save time and frustration
3. The journal with the readership that is closest to your
work
4. Go open access (personal comment)
•
Use the pre-submission system to be sure it is the
right journal
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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
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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
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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
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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
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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
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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
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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
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Part IV
Giving Good Talks
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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 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
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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
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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
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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
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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
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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
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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
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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
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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.
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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
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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
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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
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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
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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
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Discussion/Questions?
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