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Writing a Good Paper Philip Bourne & Steven Brenner [email protected] [email protected]...

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Writing a Good Paper Philip Bourne & Steven Brenner [email protected] [email protected] ISMB 2010
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Page 1: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Writing a Good Paper

Philip Bourne & Steven Brenner

[email protected]

[email protected]

ISMB 2010

Page 2: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

PB’s Perspective

• ~200 (50) papers and five books• 1982-1992 only a couple of papers• “Ten Rules” series + course in professional

development• Editor in Chief – PLoS Computational

Biology• Editor + reviewer for many years in different

disciplines (chemistry, IT, structural biology, comp biol)

ISMB 2010

Page 3: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Disclaimer

Everyone is different these are just guidelines we have found

useful and even these we do not necessarily agree on – consider what follows as 2 perspectives

Every academic/industrial laboratory is different – alternative

approaches may be more appropriate

ISMB 2010

Page 4: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

The Facets and Believed Importance in a US Academic Career

Good Papers

Teaching / Mentoring

Grants

Community Service

Good Talks/Networking

ISMB 2010

Page 5: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Good Papers Start with Good Science (duh) – Ask Hamming …

• Aim to do something very significant from the outset – ie work only on the important problems (with important people)

• Do it when you are young

• You need more than brains – you need courage too

• Luck favors the prepared mind

• Time management is critical

ISMB 2010

PLos Comp Biol 2007 3(10) e213

Page 6: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Good Papers Start with Good Science – Ask Hamming

• Work very hard and from the heart

• Some self doubt is a good thing

• Leave your door open

• Take time for the forest not just the treesISMB 2010

PLos Comp Biol 2007 3(10) e213

Page 7: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Okay your work is hot you, are working around the clock, now

what?

ISMB 2010

Page 8: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Start Writing the Paper on Day 1

• It will be easier to get it done• The mere act will help focus the work,

define the level of detail particularly if you choose the journal early (see discussion of scope in a minute)

• Much good research NEVER gets written up

• It is an object easily shared with colleagues

ISMB 2010

Page 9: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Which means…

If you hate writing – get over it

If you do not write well take classes – the earlier the better

ISMB 2010

Page 10: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

And Remember Each Day as you Write …

what you put in the literature is your scientific legacy after all else

is gone

ISMB 2010

Page 11: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

… And Always Look From a Distance

Try and see your paper as the reviewer will see it – believe me the reviewer will not see it as the best thing since sliced

bread even though you do!

ISMB 2010

Page 12: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

A Few Obvious Ingredients of a Good Paper

• Novelty – figure it out for yourself – do not rely on your PI

• Good coverage of the literature

• Good data

• Strong statistical support

• Clarity of presentation

• Thought provoking discussion

ISMB 2010

Page 13: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Avoid the Obvious Traps

• Don’t try and prove you are smart

• Avoid the kitchen sink syndrome

ISMB 2010

Page 14: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

How to Write a Good Paper - Pragmatically

• Maintain a good bibliographic database

• Consult a citation index (ISI, Google Scholar) and consider using that to annotate your database entries

• Use a tool like Mendeley to store annotations

ISMB 2010

Page 15: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

How to Write a Good Paper - Pragmatically

• Use other tools of the Web 2.0 world

• Have your colleagues critique your paper like object

• Become a reviewer early

ISMB 2010

Page 16: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Become a Reviewer (Critic) Earily

• Work through your mentor

• There are way more young people than old in this field – they want you to review

• Approach the program committee of conferences like this

• Approach the editorial staff of various journals

ISMB 2010

Page 17: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

How to Write a Good Paper - Pragmatically

• Identify good and bad papers in journal club and elsewhere and study them

• A good paper will likely tell a story and be enjoyable to read and follow which means pitched at the right level for the intended audience

ISMB 2010

Page 18: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

The Work is Never Finished, but the Paper is – Now What?

ISMB 2010

Page 19: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Choose the Journal Wisely

• Do you read that journal?

• Do you cite it in your work?

• Is it a top notch editorial board?

• Does it have highly accessed papers?

• What is the rejection rate?

• What is the average time to publication?

• Is it indexed in PubMed?

• Does the scope match your work!ISMB 2010

Page 20: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Understand the Publishing Process

• Use a presubmission inquiry if it is offered

• Suggest reviewers not because they might be easy, but because they will improve your work the most

• Understand the role of different editors, reviewers

• Understand the appeals process

ISMB 2010

Page 21: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Consider how PLoS Computational Biology works

ISMB 2010

Page 22: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Understand that the best scientists get rejected and/or have to make major revisions, they just know how to work the

process better

ISMB 2010

Page 23: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

The Post Review Phase

• Get over it • Do not get defensive unless it is really called for• Address EVERY aspect of the reviewers

concerns• Make it obvious to the reviewer through the

cover letter and the revised manuscript itself of the changes you have made

• Do not add new science unless it is called for

ISMB 2010

Page 24: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Example of What I Regard As a Good Paper

• A beautiful story• Foundation for further

studies on the use of structure to study evolution

• Concise

ISMB 2010

PNAS 2005 102(2): 373-378

Page 25: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Example of a Not So Good Paper

• Work not persistent• Unmaintainable• Good ideas but not

formulated until years later

ISMB 2010

Bioinformatics 2003 19(7) 897-898

Page 26: Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010.

Questions?

ISMB 2010


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