Producing the manuscript

1. Producing the manuscript

2. BEFORE WRITING • At the start of research, think about experiments in terms of future papers, • Arrange the control, experimental and marker samples in the optimal sequence for future figures. It will save going them when you write the paper. • For figures, think about the best magnifications and orientations to show the important features. Keep consistent backgrounds. Record the magnifications for the scale bars! • It is easier to assemble all the data BEFORE writing the paper, than during the process.

3. BEFORE WRITING • If possible, give an informal ORAL presentation of the work before you start to write the paper. It will help you clarify the story you want to tell and can anticipate objections or misunderstandings that must be addressed in the text. • Think about the key conclusions of the paper- the important message that you want to put across. Do you have all the data and the figures to prove your point?

4. BEFORE WRITING • Assemble draft FIGURES and lay them out in order on a table or desk. • Decide what are the key points that you need to make, and write them out. Focus on hypotheses that you tested. • Decide on a paper format. Short format papers (e.g. Nature, Science, Current Biology, PNAS ) versus Long format (papers with Abstract, Introduction, Results, Discussion). This will strongly influence the style in which you write.

5. BEFORE WRITING • Resolve Authorship issues. Corresponding author is usually senior author. • Have printed copies of key references at hand. • Start a building a database for references. ENDNOTE will help format format references for different journals.

6. SHORT FORMAT PAPER • hardest kind of paper to write, even though it is the shortest. • Paper has to be concise and engaging, right from the opening sentence. • For some journals the first paragraph of a short format paper is also the abstract and describes both the significance of the work and the major achievements

7. LONG FORMAT PAPER General considerations: • Download Instructions for Authors. Note limitations like page number, word and/or character count, number of figures, fonts for Figures, number of references, word length of Abstract . It is best to know the limits in advance than have to go back and change the paper later. • Print out one or two examples of a high quality paper in your field in this journal. • Note specific styles (Italics/bold for headings; Hours/hrs; Fig/Figure and other special features)

8. Order of preparation • Authors and their order • Data • Methods • Results • Discussion • Introduction • Acknowledgments • References • Abstract and Title

9. Writing the manuscript The hardest part is getting started.

10. STARTING OUT • Adopt personal working style:pencil and paper versus computer. Set a deadline and establish a reward system! • It is best to just write something down and then edit it rather than to expect to write a perfect sentence straight away. • Just start writing the data as if you were describing them to your colleagues. Lay out general arguments and then go into details so that you prepare the readers for what follows and the logic you are going to use. • Expect to write multiple drafts, so keep track of them carefully. Word has an “Edit” program.

11. FIGURES and LEGENDS • Annotate figures and pictures with arrows • High resolution, at least 300 dpi • Low resolution images “pixel out.” • Do not forget scale bars! • Figures must have a short title. • Follow conventions of the journal precisely.

12. FIGURES • Figures are important. Cannot simply “drop” them into paper • Writers are immersed in the subject -- readers are not!! • When referring to a specific Figure/Section/Table, use upper case, otherwise use lower case: • The overview in Figure 3 is better than the other figures. • Should describe each item in a figure: “The icon in the upper left corner of the figure represents…” • Should motivate the figure: “This figure provides an overview of our system, including input …”

13. FIGURES (cont) • If they contain code, number each line • Refer to specific lines, or sets of lines, in the text • s/b either pseudo-code, or language specific (tell them what the language is!) • All elements of figure/graph s/b marked (key or legend) • Each figure should have a tag and a caption

14. LEGENDS for TABLES and FIGURES • Tables and Figures with their legends are separate pages, not imbedded in text of paper • Must stand alone and be very descriptive • Must spell out all abbreviations used each time • Must be large and clear (little white space) • Make sure they are numbered in proper order

15. BEFORE GIVING DRAFT TO SUPERVISOR • Check the Figures versus the text • Check the References versus the text • Check the Figure legends • In general, edit a paper after printing it out and reading it as a whole, rather than editing it on a computer screen where you can only see one page at a time. Once a page has scrolled off the screen the text tends to be forgotten! • Be psychologically prepared to throw out and rewrite whole sections and not to cling to the original. • Be flexible.

16. BEFORE SENDING TO THE JOURNAL • Have the paper read by several people. Listen to what they say, especially if same criticism comes up several times. • Check and recheck spelling, figures, references, legends etc • Reviewers can be really annoyed by careless editing and mistakes reflect badly on your science. • Ensure you have followed all the requirements of the journal about electronic submission etc • Some have a specific Checklist and Front Page format (key words; contact information; e-mail address etc

17. BEFORE SENDING TO THE JOURNAL • Include a cover letter outlining the originality and important findings of the paper and why it will be of interest to the typical audience of the journal you have selected. • Sometimes it is helpful to suggest possible referees, especially if the topic is unusual. • It can save time to send a “presubmission enquiry” to the editor. This should outline in the most persuasive way the importance of your paper. Then the editor can reply with either encouragement to send the complete paper for review or a polite suggestion that you send it to another journal

18. Responding to the First Critique • Expect the paper to be rejected • Only 5% of papers are accepted without revision • You will get disappointed • The reviewer will ask you to do things you can’t fix • At first reading, you won’t understand how the reviewer could possibly have misunderstood or been confused by your paper • Put the paper down for three days to let your anger subside.

19. Dealing with the consequences • VERY FEW PAPERS ARE ACCEPTED WITHOUT AMENDMENT • Read your reviews • Give your reviews and the original paper to someone else to read • Discuss what actions you can take to respond to reviews • Give yourself a deadline for rewriting and resubmission – don’t leave it too long! • Rewrite • Resend with a covering letter telling the Editor how you have responded to comments in the reviews (you don’t have to agree with everything but explain why you haven’t taken advice, as well as how you have taken it) • Wait again …. • Repeat if necessary …

20. Responding to reviewers Carefully prepare your responses Each comment should be addressed Each change should be stated Be enthusiastic Reviewer may be wrong Be tactful – thank the reviewers Do not respond to reviewers while upset Never call the editor Get help from other authors

21. Rewriting the Paper • Editor must see you took the review seriously • Even if rejected outright, respond to critiques completely before sending to new journal • If first reviewers were confused… • Use constructive tone to respond to same journal. Don’t be defensive. • Respond within one month • Familiarity with the paper will increase chances of acceptance • Author to upload point by point response to review under “supplemental content.”

22. Writing Advice • Write with precision • Simplify - avoid jargon • Quantify • Avoid figurative language • Be concise • Use the active voice • Choose the right level of detail • One paragraph = One thought • Provide logical connections • Rewrite with feedback

23. Writing Tips • Write with a partner/collaborator • You will keep each other on track • Three-hour blocks minimum…stay in the zone • Use the draft of the paper as a notepad • When to start next time • What new references you need • What new statistical analysis you need • Put brief citations at end of sentences

24. Writing Tips • If a paper is too complex: • Reviewers will not understand it • Reviewers will not believe it • Reviewers will not like it • If a paper is too simplistic • Reviewers think its nothing special • Even if the results are good

25. General writing tips • Make your problem relevant • Start with the “big picture” • Take the reader by the hand • Step by step explanation • Highlight innovation • Do not give too many equations • Do not give too much theoretical details • Do not try to make a tutorial

26. General writing tips • Do not use “very” but give the numbers • Avoid to use “novel” • Everything you do not cite should be novel • Use short sentences • Use simple words • One point per paragraph • First or last sentence is most important • The rest is explanation

27. General writing tips • If you are stuck: • Tell a friend what you did. • Use the words & slides like on your conference paper • Polish the text later • Let a fellow student read & comment • Ask native speaker to correct language • Polish, Polish, Polish • Reviewers hate mistakes!! • It iz raely anojing to raed tekst width misstakes

28. Revising • Set aside the paper for several days. • Look for logical gaps and inconsistencies. • Cut ruthlessly. Use simple, direct constructions. • Have others read the paper and give written comments.

29. Cut, Cut, Cut • Shorter sentences are clearer. • Shorter paragraphs are clearer. • Shorter papers are clearer. • Is it worth creating a 20-page masterpiece if no-one will read it?

30. Tips • Write the introductionafter you finish the paper • Although the abstract is first part of the paper you read, you should write it last, after writing the introduction. • Normally, abstract written first, then paper

31. Tips • Know the journal, its editors, and why you submitted the paper there • Pay close attention to spelling, grammar, and punctuation • Make sure references are comprehensive and accurate • Avoid careless mistakes • Read and conform to “Instructions for Authors”

32. “There is no way to get experience except through experience.” “Good judgment comes from experience. Experience comes from bad judgment”

34. Stage 1 • DECISION MAKING 1 • What do you want to say? • Who do you want to read it? • RESEARCH 1 • What is been said already and how might you contribute? • What publications might be suitable? • Why? • WRITING 1 • See if you can write a brief summary (abstract) of what you intend to write about.

35. Stage 2 • DECISION MAKING 2 • Decide on your target publication(s) in view of Stage 1 • RESEARCH 2 • Understand how your target publication(s) select work to be published – check the notes for contributors, make sure you understand the publication target audience, make sure you take note of their style, ensure that you know what they’ve already published on the topic; write to the Editor to see if they’d be interested in a piece like yours. Talk to others who have published in this outlet. • WRITING 2 • Go back to your summary – now that you know a bit more about where you want the piece to go, does it fit with the publication? Will readers of the publication want to engage with it? Are you willing to change it to fit? If not, go back to DECISION MAKING 2 and rethink – go round the loop again.

36. Stage 3 • READ back copies of the publication again • READ what ‘others’ have said in relation to what you want to write • Decide how you might build on what others have said • WRITE a first draft • Circulate your first draft to at least a few ‘others’ for comment • WRITE a second draft • Circulate again if necessary … repeat as necessary

37. Submission • Make sure you know exactly how to submit to the journal (electronic, hard copies etc) • Make sure you have followed their guidelines to the letter • Ask yourself honestly: • Have I related this paper to the journal’s aims? • Have I engaged with the work of others in the same area? Is my paper saying something fresh or could it be accused of being repetitious? • Is the purpose of my paper clear? • Is my argument well developed? • Are all my claims justified? • Is the style/length/format what’s requested by the journal? • Is my paper perfectly presented in terms of references, typing, grammar, conciseness etc? • SEND IT OFF

38. What happens next? • Editor/publisher decides if it fits with the outlet’s purpose • Editor/publisher decides if it’s in a fit state to be sent out for review • Editor/publisher sends out to reviewers (2 or 3) – remember that reviewers may well be people mentioned in your piece – particularly if you are challenging their work. Implication – always write as if they are going to read your work. • Reviewers normally review pieces which are anonymous – if you want to ensure that your work is read anonymously, have you remembered to anonymise eg self-references? • Remember that reviewers are usually not paid – therefore expect to wait a few months before hearing (some journals have targets, but Editors have no control over reviewers – they are doing them a favour!) • Editors will send decision plus review(s) back to you – don’t expect to see all of them. Editors will take into account reviewers’ views but, in the end, will have to come to a decision if reviewers disagree (or send out for another review). • Possible outcomes – accept, accept conditionally (minor amendments, major amendments), resubmit for new review, reject.