1. How to Write A Paper Iris Lindberg 2/04 With help from Map and Compass http://www.ibro.info/secondary/education/mapandcompass/M_and_C_intro.htm

2. What Is a Paper? Communicates a linked series of observations in a logical fashion Interprets data neither too much nor too little Provides historical and biological context Tells a story Moves the field forward

3. Assemble Your Data Most often present in the order it was obtained Re-order if this makes a more logical presentation First step: get a list of figures ready with the conclusions from each figure –Figure 1. Compound X lowers the amount of compound Y in HEK cells.

4. When to Write? After you think you have a good story All critical experiments are finished Before you finish tying up all of the loose ends –Writing up will show you clearly what controls/additional experiments still need to be performed

5. Choose a Journal Select before you write so format is appropriate Focus of journal should be appropriate –Are similar papers in this journal? Choose the best journal –Availability and readership –Ranking (“impact factor”) –Time to publication

6. In What Order Should Paper Be Written? Figures and Legends Results Methods (easy part!) Introduction Discussion Abstract Referencing Letter to the Editor

7. Just Do It Find a place where you will not be interrupted Set down a first draft and do not worry about style- just write! - you can edit later Better to write something than nothing Save mechanical stuff (references, methods, figures) for the days you have brain fog First draft should take 2 days!

8. Title “Working title” gives the paper an actual substance- can revise later Avoid jargon, symbols, and abbreviations Avoid “A study of”, “Research On”, “Use of” ; also “rapid” or “new” Brief but complete; 6- 12 words ideal Attracts potential audience and aids retrieval/indexing

9. Figures and Tables Easy to read and in logical order; not too many small panels – Ideally, figures should not need legends to be comprehensible – can figures be reduced without loss of legibility? (use the reducing Xerox machine to make sure fonts are large enough) –minimize “white space” Try different types of format: tables vs bar graphs vs. figures- which is easiest to interpret? –Tables provide exact information, while figures clearly show trends –Always give error estimates!

10. Make an Outline Will be based on the figure order Groups data in (4-5) bunches Use your outline to present the Results and follow it for the Discussion It is not uncommon to reorder the presentation after you have a draft

11. Introduction Orients the reader as to why the work was done (rationale) and why is important Should provide fair and comprehensive referencing of the current state field Short overview of the methods used to investigate the question Concludes with a brief summary of what was done (BRIEF!) Should cover all required subjects in a logical order in about 500-600 words Present tense

12. Results- Order Not necessary to present results in order obtained Present in most logical order

13. Results Succinctly describes each major finding, grouping appropriately in figures/panels. Every statement made in the results should be supported incontrovertibly by the data in the paper Try not to make interpretations as this is what the Discussion is for (not always possible)

14. Results Make sure results are internally consistent! There is no substitute for beautiful data (to convince the reader) Use the past tense when describing your data; but section titles/summaries can be present tense

15. Methods Easiest part to write if you have kept a good notebook Enables the reader to actually repeat the experiments Skip methods that can be found in Current Protocols- just cite Cite the source of all reagents used and where QC information is to be found Cite previous your papers whenever you can Past tense

16. Discussion Does not repeat the Results but rather takes each major finding presented in the results and discusses it in the context of how it relates to previous and future work, with comprehensive and appropriate literature citation. Often ends with a brief speculative statement or idea for future work (definitely a positive note) In the present tense

17. Abstract- write last! Summarizes the major findings in the broad context of the work Consists of two or three sentences of topic introduction Selected results (not all but the most important) Concludes with implications of work About 250 words

18. Editing- Global Save the journal space by writing concisely and by eliminating unnecessary or negative figures and tables Proof all text carefully for errors- –typos, omissions, inconsistencies in the data, redundancies, or errors in referencing. Expect to revise again and again- 10 times ? Until language is perfect –Take a break between drafts to get a fresh viewpoint

19. Editing- Global Major alterations- is the order correct? (easiest to understand, most logical) –Cut up and lay out differently Are all the correct elements in every section? Give your paper to colleagues for input on clarity Never give anyone anything that is not spell- checked If English is not your native language try to have a native speaker look at it

20. Editing/Polishing Paragraphs- does each form a cohesive unit with a topic sentence? Are they the right length- neither one or two sentences nor page-length? At end, a summarizing statement or introduction to next paragraph is very helpful

21. Writing Good Sentences Use active voice when possible Use the correct tense- present means it is true while past means it is true under a specific set of circumstances Do not switch tenses frequently

22. Writing Good Sentences Neither too short nor too long Avoid long strings of adjectives Avoid long strings of nouns

23. Writing Good Sentences and Words Use the best word for the job (for example, “utilize” is overused) Make sure punctuation and grammar are correct Omit all unnecessary words- the shortest phrasing is usually the best Limit the use of abbreviations unless standard (ATP)

24. Submitting Papers Write a simple direct cover letter to the Editor using his/her name Suggest three reviewers if at all possible No need to plug the paper in the letter Submit electronically if you have a choice as it will speed your review

25. Rebuttal Letter Thank the reviewers for their time. They did not have to spend it on your work! Address each criticism in numbered order Repeat or include the criticism in your answer You are allowed to argue one or two items but most items should be addressed precisely the way the referee indicates Conclude by saying that you feel the paper is improved and you hope it is now acceptable for publication

26. Reviewing Papers

27. Reviewing the Work of Others You cannot review a paper if you are simultaneously engaged in identical work You cannot review a paper if you have strong feelings (hate or love) for the authors; or have recently collaborated/mentored/been mentored Golden Rule applies- apply the standard you would apply to your own work (neither be too critical nor too soft) Be helpful rather than pejorative; soften criticisms with an initial positive statement

28. Reviewing- General Read the manuscript with a pencil in hand, making notes on the margins Is the English used up to par? (suggest editorial revision by a native speaker) Is it sloppily done? (referencing wrong, many typos etc) Is it appropriate for the journal audience?

29. Reviewing, continued Set down your thoughts in a numbered order – cite figure and/or page for each Do not take longer than two weeks Introduction –Is it sufficiently comprehensive and fair? –Does it provide a good rationale for the work? –Are all abbreviations clear or is there jargon?

30. Reviewing Methods Are the methods neither too detailed (common methods not described) nor insufficiently described? (primers) Could the work be repeated by an outside group? (amounts of starting material given etc) Are the methods clearly written? Are all sources given?

31. Reviewing Results Are the figures cited in order? Is the rationale for each experiment clear? Do the text conclusions agree with the result you see in each figure? –Watch for over-interpretation Would there be a better (more space-saving or clearer) way to present the results?

32. Reviewing Figures Accuracy – are stated results really present and really significant? –Does the figure number correspond to the correct figure? Presentation –is there a minimum of white space? –are figures sharp and clear? –Are all of the figures really necessary? Is the legend neither too long nor too short?

33. Reviewing the Discussion Does it simply repeat the Introduction? Does it provide alternative explanations for the data/ introduce necessary complexities? Is it about the same length as the results? Does it put the work in context and suggest further lines of experimentation? Most importantly: does it go too far?