This document provides guidance on writing good scientific papers in 3 key points: 1. Start writing the paper on day 1 of the research to focus the work and define the appropriate level of detail. 2. Consider which journal is the best fit for the scope and level of the work. Maintain bibliographic databases and have colleagues review drafts. 3. Address all reviewer concerns in revisions by making changes obvious and without adding new science unless requested. Choose revision over defensiveness.

1. Writing a Good Paper Philip Bourne & Steven Brenner [email_address] [email_address] ISMB 2010

3. 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

4. The Facets and Believed Importance in a US Academic Career ISMB 2010

7. Okay your work is hot you, are working around the clock, now what? ISMB 2010

9. Which means… If you hate writing – get over it If you do not write well take classes – the earlier the better ISMB 2010

10. And Remember Each Day as you Write … what you put in the literature is your scientific legacy after all else is gone ISMB 2010

11. … 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

18. The Work is Never Finished, but the Paper is – Now What? ISMB 2010

21. Consider how PLoS Computational Biology works ISMB 2010

22. 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

26. Questions? ISMB 2010