Collaboration Workshop

Collaboration WorkshopThoughts for Young Scientists on How Best to Collaborate
Philip E. Bourne
pbourne@ucsd.edu
http://www.sdsc.edu/pb/
Much of the material presented here is draw from the PLoS Ten Simple Rules Collection Available Here
11/19/10
Collaboration Workshop

Intended Goal
Take away some pointers for how you can enrich your scientific career through interaction with others. That interaction is in turn dependent upon such issues as:
Doing the best science
Knowing how to collaborate
Communicating that science:
Writing good papers
Giving good talks
Making and presenting effective posters
Making the most of informal interactions
Being involved (societies, user groups, data depositor, curator etc.)
We will spend time on each of these
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Intended Audience
Graduate students
Postdoctoral fellows
Research scientists
Early stage faculty
Well anyone willing to listen really
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How Did I Arrive at My Perspective?
BS, BS (Hon.), PhD in chemistry at same provincial Australian university
2 good postdocs in Europe and the US doing structural biology
Left academia (sort of) for the IT world for 12 years
15 years in academia – Research Scientist, Adjunct Prof., Prof.
Immersed myself in an emerging discipline (bioinformatics/comp biol)
Pursue many diverse research interests (good or bad?)
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A Pot-pourri of What I Have Learnt Over the Years (the Bottom Line for You)
Do cutting edge science (ie pick the right problems)
Do it with the best people
Let your heart guide you not your head
If you are not excited every day by what you are doing you are doing the wrong thing
Never be intimidated
Plan to have impact
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How Did This Workshop Come About?
About5years ago the student council of the International Society for Computational Biology (ISCB) asked me to give them a lecture on how to get published based on my new role of EIC of PLoS Comp. Biol.
The exchange that took place was one of the most fun lectures I have ever given
In trying to capture that moment I wrote an Editorial “Ten Simple Rules for Getting Published” …
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How Did This Workshop Come About?
It was downloaded a large number of times
Folks started to approach me with other ideas for Ten Simple Rules
To date there is a “Ten Rules” series downloadable from http://collections.plos.org/ploscompbiol/tensimplerules.php
This became a graduate student course at UCSD and is accompanied by on-line versions of some of the lectures
I now get asked to give these workshops in various forums eg annual conferences
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Okay Enough Background .. Lets Get Started ..To State the Obvious More Scientists are Going to Want to Collaborate with You if You are Doing Interesting Work
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Doing Your Best Research – A Philosophical Perspective Adapted from Richard Hamming and Stated as Ten Simple Rules
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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Warning
This part of the workshop is like being on the couch
Subsequent parts provide more tangible advice
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Basic Question for Today 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 are sitting here sincerely not wanting to win a Nobel Prize then you are probably wasting 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 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 or contribute to making them better
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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 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
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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?
Improve science dissemination and comprehension through openness and rich content
Really understand using computational and systems biology what happens when we take a drug
Change the way evolution is studied so that we can:
Further prove we are a product of our environment
Understand the evolution of proteins through their structures
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 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.’’
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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 – you cant do it alone
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Discussion/Questions?

Okay so now lets assume you are working on the most interesting problems in a stimulating environment. Collaborations will likely come your way.How should you respond?
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Intended Goal
Writing good papers
Giving good talks,
Making and presenting effective posters,
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Establishing a Successful Collaboration
PLoS Comp. Biol. 3(3): e44
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My Bias
I don’t like projects where I feel like I am a cog in a wheel
Do not think I am particularly good at collaboration
When I have a collaboration it is usually a long one
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My Publication Web
http://pubnet.gersteinlab.org/
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Experiences
IlyaShindyalov (Research - grants) – 29 papers
Helen Berman (PDB - contract) – 11 papers
Jeff Lakey (Reviews) – 14 reviews
Lei Xie (Research – grants) 13 papers
Worked with someone seriously effected by a bad collaboration
Collaborations come in different forms and require different rules
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Over Arching Thoughts …
From 1981 to 2001 the average number of authors on a paper rose from 3.9 to 8.4
Funding (e.g., NIH Roadmap is making us be collaborative; Janelia Farm)
Nothing in Professional Development makes sense, except in the light of evolution - collaboration provided an evolutionary advantage
Collaboration can be fun or a drag
Some collaborators become life long friends
Some collaborations never get off the ground
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Your success as a scientist depends very much on what other scientists think of your work and of you personally so…
They must know you personally – that often comes through collaboration
They must know you to have integrity
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Over Arching Thoughts
“The scale and complexity of today's biomedical research problems demand that scientists move beyond the confines of their individual disciplines and explore new organizational models for team science. Advances in molecular imaging, for example, require collaborations among diverse groups—radiologists, cell biologists, physicists, and computer programmers.” —National Institutes of Health Roadmap Initiative
Sean Eddy – The individual is the interdisciplinary team PLoS Comp Biol 1(1) e6
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Rule 1 – Pick Collaborations Carefully
Do not be lured by money
Do not be lured by a famous co-investigator
Be lured by a shared passion in the science
Consider all aspects of the collaboration – will it make a difference to my long term goals? Do I have the experience? Do I like the team? Can I deliver on time?
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Rule 2 – Decide Early
Early delegation of responsibilities is priceless
For a grant revisit the specific aims regularly
Consider an MOU
Discuss expectations for authorship early
Do not blind sight them with related publications – tell collaborators in the formative stages
Be comfortable early not uncomfortable late
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Rule 3 – Stick to Your Tasks
Do not digress from the agreed upon questions to be addressed without prior discussion with your collaborators
Do not just think your collaborators will be pleased with your change of emphasis
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Rule 4 – Be Open and Honest
Share all data, protocols, materials etc.
Holding things to your chest may be a short term advantage but it is a long term disadvantage – it relates to integrity
Be available but have your collaborator understand your availability
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Rule 5 – Mutual Respect is a Must
If you do not respect the scientific work of a potential collaborator – do not collaborate
Respect can change as a collaboration progresses – look for signs of change
Examples of mutual respect:
Advanced notice when you cant make a deadline
Open dialog about your limitations for a given task
Discussing being approached by others to collaborate on related issues
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Rule 6 – Communicate, Communicate, Communicate
Face-to-face is best, followed by video, followed by telephone, followed by email – email is asynchronous and brings out unseen personality traits
Shared project documents are good e.g. Google docs
Use scientific meetings for face-to-face – you can justify the cost and get other benefits
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Rule 7 – Protect Yourself from a Collaboration That Turns Sour
Projects often do not work out as planned – both you and your collaborators should have a mutually agreed upon Plan B before it is needed
Be sympathetic to life changes that impact a collaboration
If things do not work out think carefully how the impact on your career can be minimized
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Rule 8 – Always Acknowledge and Cite Your Collaborators
This applies to preliminary results
This applies even when you are not happy with the collaboration IF the collaborator has contributed anything at all
Make it clear who is responsible for what
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Rule 9 – Seek Advice from Experienced Scientists
Collaborations always present challenges
Use mentors to help resolve challenges – they have likely been there done that
Challenges can on occasion lead to major breakthroughs – do not give up too easily
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Rule 10 – Keep Good Collaborations Going
Why did Shindyalov and Bourne publish so many papers together?
Why did it end?
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Lets Analyze Photograph 51 As One Highly Visible Collaboration
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Collaborations Often Start Through Science You Have Already Communicated. It Follows the Better You Communication Your Science the More Collaborations You Can Foster
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Intended Goal
Writing good papers
Giving good talks,
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Writing the Best Scientific Paper
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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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Personal Experiences
Have one of the most cited papers in the biological sciences (~10,000) – hardly anyone has ever read it
Have papers that are highly read (as judged by downloads) but never cited
The work I am proudest of is not the most cited
As an Editor you see a lot of papers – both good and bad
Even the best scientists write bad papers - they just know how to work the system better
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Emerging Metrics - Gerwick
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Emerging Metrics - Bourne
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Acknowledgement
The following is a rework of the Ten Rules for Getting Published PLoS Comput Biol 1(5): e57 (there is a rule here - you can always improve your work)
Notes from Bill Gerwick “Writing a Research Publication – 21 Suggestions” which he has prepared for students
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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
Take lessons from http://www.nature.com/nature/dna50/archive.html
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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:
Do you read that journal?
The quality of the journal as defined by impact factor, Editorial Board and quality of reviews
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
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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
Copyediting is on the decline – your mistakes will be left in the literature
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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 though 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
This will allow you to see your work in a new light
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Intended Goal
Writing good papers
Giving good talks
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Giving Good Oral Presentations
http://www.scivee.tv/pubcast/17500596
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My Bias
Given lots of talks – both good and bad – 31 plenary and keynotes in the past 3 years
Talked to between 5 – 5000 people
Talked on television
Talked on many subjects both science and IT
Talked to many different audiences – 3rd graders (most scary), investors, Nobel Laureates
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Experiences
Sydney Brenner
Dorothy Hodgkin
David Searls
Francis Crick
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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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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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Intended Goal
Writing good papers
Giving good talks
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Preparing and Presenting Posters
http://www.sicb.org/newsletters/fa97nl/sicb/poster.html
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My Bias
Have not personally made a poster for a long time
Encourage lab members to make posters and review their content – they need at least a poster to go to a conference
Encourage lab members to make “postercasts”
Post them on the walls after too
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Experiences
Given posters that have not generated a great deal of interest
Done “Statement posters” as well as research posters
Done “booth duty” with Sun Microsystems
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Posters are a key element of scientific communication and dissemination
Big names can be seen giving posters
They are different than other forms of communication and require special consideration
Snapshot of your current research
For a graduate student they are a major facet of your ability to interact
“Postercasts” make posters persistent (not always desirable)
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Should be a standalone experience if you are not there
If you are there engage people not intimidate them
Life long collaborations can start in front of a poster
Poster prizes count on your resume
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Rule 1 – Define the Purpose
Report latest unpublished work (most frequent)
Report a summary of a body of work
Specifically find collaborators
Spend the appropriate time depending on the longevity of the poster
Figure it being on an institutional wall after the meeting
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Rule 2 – Sell Your Work in 10 Seconds
You will likely be one of hundreds of posters – you need to fight for attention
Catch the attention of the person ambling by both with the written word and your elevator pitch
Consider casting your work in the form of addressing an important question which is prominent on your poster
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Rule 3 – The Title is Important
It may be the only thing the attendee sees before visiting the poster session
A title is your equivalent of a newspaper headline – short sharp and compelling
Unlike a newspaper headline it should not oversell your work
Make it understandable to a broad audience
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Rule 4 – Poster Acceptance Means Nothing
Poster acceptance usually says nothing about the scientific content – conferences need attendees – attendees can often only go if they are presenting – speaking slots are limited - enter posters
Follow up from a poster means everything – do good science and present it well
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Rule 5 – Note Similarities to Giving Good Talks and Writing Good Papers
Know your audience – provide the appropriate scope (breadth) and depth
Follow the proven formula for research
State the hypothesis to be tested and why
Show the major result
What does that say about your hypothesis
Conclude with what is next
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Rule 6 – Note the Differences to Research Papers
Message needs to be distilled but logical flow maintained
Posters (at least for now) allow you to be more speculative – they are not immutable
Use the poster as an attractant for other materials – supplementary information, reprints etc.
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Rule 7 – Layout and Format are Important (more on this when we review posters)
Remember the phrase “eye catching”
There is no need to cover every inch – guide the eye to the most relevant points
Unlike a research article a poster is not a sequential medium – guide the viewer through the logical sequence with numbers arrows, colored boxes etc.
Look at other posters to get ideas not on content but layout
Never use less than a 24-point font
Make sure the main points are at eye-level
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Rule 8 – Content Must Be Concise
Every aspect of the poster must convey the main message
Be clear concise and brief
Use pictorials as much as possible
Highlight the main points of those pictorials – e.g. bold emphasis, color coding in tables and figures
The abstract should say more than a paper abstract – it may go into an abstract book
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Rule 9 – Posters Should Reflect Your Personality
Unlike a paper a poster does not have to be dry and impersonal
Include a photo so you can be spotted even when you are not at the poster
Have the photo of you doing a hobby etc. – it starts the conversation also collaborations start often for non-scientific reasons
A viewer will likely remember more about you that your poster
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Rule 10 – The Impact of a Poster Happens Both During and After the Poster Session …
Work the crowd by being engaging, but not too engaging – one engaged viewer will attract others
Work all the audience at once – maintain eye contact with everyone
Make it easy for attendees to contact you after
For mature posters – have the poster on-line and accessible via a URL
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Rule 10 – The Impact of a Poster Happens Both During and After the Poster Session
Leave the attendee space and time
Have a sign-up sheet attached to your poster
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Additional Thoughts
What is right and wrong with the following posters?
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Closing Thoughts on What NOT to Do..
Just assume yours is the best poster
Ignore the instructions on poster size etc.
Assume content is all that is important
How you mount the poster does not matter
Do not use dark backgrounds
Do not stimulate the reader’s senses with many random colors
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Closing Thoughts on What NOT to Do
Require the reader stand for ½ hr 1cm from your poster
Have long titles in small font
Have the authors names and institution be the dominant visual
Invite collaboration through physical proximity
Require rigorous physical exercise to follow the logic of the poster
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Intended Goal
Writing good papers
Giving good talks
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Being Involved?
General Discussion
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Collaboration Workshop

by Philip Bourne on Nov 18, 2010

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Collaboration Workshop — Presentation Transcript