Science Paper Writing Workshop Arusha , Tanzania, November 18-22, 2013

1. Science Paper Writing Workshop Arusha, Tanzania, November 18-22, 2013 Chris Beadle, Peter Willadsen, Rob Skilton, Ethel Makila This course was designed by Peter Hairsine, CSIRO; further development by Greg Foliente and Mary Finlay-Doney

2. Agenda Day 1 08.30 Set-up workstations 09:00 Official Opening of Workshop by ??? 09:10 Administrative details 09:20Welcome and Introduction; Partnering for reviews – the trusted (Colleague 1) and distant reviewers (Colleague 2) (Chris B) 10:00 Morning coffee/tea 10:20 Seven-minute presentations 12:30 Lunch 13:15 Seven-minute presentations (cont.) 14:15 Concept Planning and the Original Contribution (Chris B) 14:45 Individual work on Concept Plan 15:15 Afternoon coffee/tea 15:30 Individual work on Concept Plan (cont.) 16:00 Review of Concept Plan with Colleague 1 16:30 Revision of Concept Plan 17.15 Appraisal and feedback for Day 1 17.30 The BecA-ILRI Hub (Rob S) 18.00 Finish and Welcome Reception at NMAIST CSIRO.Journal Writing

3. What is this course about? • Hands-on course • New skills to improve writing efficiency • Provides experience to transfer to your working groups • Creates time to produce an advanced draft • Vehicle for improving your institute’s working environment • Provides guiding principles for writing papers • However you should still maintain ownership of your own writing style CSIRO.Journal Writing

4. Why is paper writing important? • Rewarding in its own right • Contributes to global, regional and local knowledge • Means of recognition • Stimulates knowledge of the literature • Offsets underinvestment of time in reading and thinking CSIRO.Journal Writing

5. What needs to happen? • Please be punctual • Focused sessions (avoid multi-tasking, divert phone, turn off other computer applications) • Quiet space (no discussion i.e. all discussion outside) • Back-up your work on thumb drive • ….. however the distribution of writing expertise and pace is inevitably variable so…… CSIRO.Journal Writing

6. Behaviours • Respectful • Critical • Supportive CSIRO.Journal Writing

7. Trusted and distant reviewers • Idea of writing buddy • Getting papers written quickly • Benefits of continuous review • Wise heads • Do not hesitate to consult • Name in each column once CSIRO.Journal Writing

8. Concept planning and the original contribution • One contribution = one paper • Avoid multiple minor contributions • Identify the primary/main contribution in this particular paper and document material for other papers • Multi-part papers are complex – consult with the journal editor before committing • Concept planning is crucial • Use several versions/drafts • Often it is best to do this by hand and • Orally with Colleague 1 CSIRO.Journal Writing

9. Sample Template for Concept Mapping of Journal Paper Implication(s) and/or application(s) • Key Contribution(s) • Primary (i.e. “ the one”) contribution • Supporting/key findings Rationale, context & key previous work Emerging or new issues Method(s) How developed How tested or validated The journal paper will be written around the “key contribution” – the concept map provides an overview of the narrative that will be developed in the paper; review & revise this as many times as necessary until the narrative is really clear CSIRO.Journal Writing

10. Agenda Day 2 08:00 Revision of Concept Plan (cont.) 08:30 Selecting your Target Journal (Rob S) 09:00 Individual work on Target Journals 09:30 Reference Managers (Rob S) 10:00 Morning coffee/tea 10:20 Individual work on Target Journals/Reference Managers 11:00 Outlines (Chris B) 11:15 Individual work on Outlines 12:30 Lunch 13:15 Individual work on Outlines (cont.) 13:45 Review and Revision of Outlines/Target journal selection by Colleague1 using 5 Critical questions 14:30 Figures, Tables & Captions – their design to enhance the narrative (Peter W) 14:45 Individual work on Figures, Tables & Captions 15:15 Afternoon coffee/tea 15:30 Individual work on Figures, Tables & Captions (cont.) 16:00Review and Revision of Figures/Captions by Colleague 1 17:15 Appraisal and Feedback for Day 2 17:30 Finish CSIRO.Journal Writing

11. Selecting your target journal and related matters • More than 21,000 peer-reviewed academic journals • New journals published every year and new articles are published every day Where do you start?

12. Why does it matter which journal you choose? Enhanced search capabilities and indexing vastly expand immediate access to journals of interest The journal you choose to submit your paper to has major implications • Authors must consider • Audience • Type of paper • Journal scope • Cost • Impact factor

13. Why do you want to publish? “What is your goal?” • Different reasons for publishing • Sharing scientific knowledge • Project/institution requirements • Career advancement CSIRO.Journal Writing

14. Sharing scientific knowledge What do you want your readers to use the contents of your paper for? • Decision making • Designing their own experiments • Referencing/citation in their own research

15. Who is my audience? • Ask yourself “Who would be interested in reading my paper?”: • Research scientists v. policy makers • Specialists v. generalists • Who is my work important to?: • Everyone, of wide interest • Discipline specific • Locally relevant

16. Is the audience national or international? • NATIONAL • Local researchers, farmers,extension workers or policymakers • Data mainly of local or national interest? • If so, consider a journal whose audience is national or regional OR INTERNATIONAL • Topicrelevant to audiences all over the world? • If so, consider an international, easily accessible journal • English is the international language for publication

17. Writing for your audience Selecting your journal: what audience do you want to reach? An example: Core result: The exotic cattle tick Rhipicephalusmicroplushas displaced the endemic tick R. decoloratusover much of East Africa over the last two decades. It is likely to bring increased threats of disease transmission and pesticide resistance. International ecology / disease journal An example of the displacement of an endemic by an exotic species with implications for disease control. An (African) public policy journal A new and possibly very damaging threat that will require policy action.. A journal on African livestock production An emerging disease threat that farmers need to know about. For each of these options both the writing and supporting information will be different. Your success depends on recognising this.

18. Type of paper What type of paper is it? • Original article • Review paper • Commentary • Short communication or ‘Technical Note’ Make sure the journal you select publishes the type of paper you want to write. • Go to journal website • Consult with journal editor

19. When to choose the journal? • As soon as possible! • Definitely before you start to write as this will determine the: • Format; • Style; and • Scope of your paper

20. Strategy for choosing journal (1) Paper Journal Audience CSIRO.Journal Writing

21. Strategy for choosing journal (2) • What is the scientific level of the journal? Is my work as good as, or better than, the material the journal is publishing? Who is the editor? Which authors/competitors publish in the journal? Does the journal have an international audience? • What are the scope and aims of the journal? Read the “Aims and scope” statements to find out exactly which area of your discipline the journal is interested in. Contact the editor. See Scope on journal site: http://www.ploswntds.org/static/scope.action • What types of article does the journal publish? Will yours fit this pattern? Many journals have a specific format for the articles they publish. If your article does not fit, the paper may be rejected. CSIRO.Journal Writing

22. Strategy for choosing journal (3) • How often is the journal published? Scientific publishing is usually a slow process. You have to ask yourself “Will publication time affect the relevance of my article?”. • Are there any conditions to submitting to the journal? E.g. one author must be a member of the society that publishes the journal. E.g. certain types of statistical analysis that must be used, experiments must have been repeated a certain number of times. E.g. Restrictions on the number of words and figures CSIRO.Journal Writing

23. Additional considerations • Cost of publication • Submission fees/author fees (Open Access model) • Many journals have page charges, especially for colour images. However, some journals will not charge authors from certain countries. • Availability of journal • Print / online / both? • Available through Agora/ Google Scholar / citation databases e.g. AGORA? • Is the journal in your library? • Other criteria • Is it indexed by Thomson Reuters Journal Citation Reports? • Does it have and how high is the Impact Factor?

24. http://www.aginternetwork.org/en/ • Set up by FAO with major publishers • Enables developing countries to access a digital library collection (3500+ journals) • Food • Agriculture • Environmental science • Related social sciences • Institutions in 116 countries

25. Vietnam is eligible to access AGORA • Go to this address to find out if your institution is registered. aginternetwork.org/en/journals/registered_institutions.jsp

26. http://www.who.int/hinari/en/ • Set up by WHO with major publishers • Enables developing countries to gain access to one of the world's largest collections of biomedical and health literature • More than 8,000 digital information resources (in 30 different languages)

28. Impact factor (IF) • Used as a proxy for the relative importance of a journal within its field • Is a measure reflecting the average number of citations to articles published • Impact Factor (IF) is the number of current citations a journal receives divided by the number of articles published in the two preceding years • Impact factors are calculated yearly for those journals that are indexed in Thomson Reuters Journal Citation Reports • Calculated yearly for those journals that are indexed in Thomson Reuters Journal Citation Reports(6166 science journals) See Master Journal List at Thomson Reuters http://science.thomsonreuters.com/mjl/

29. How do I find the impact factor for a journal? • Current IFs: Web of Knowledge (Thomson Reuters) http://wokinfo.com/payment required! • Journal home page if indexed on Thomson Reuters Journal Citation Reports • 2008 IFs can be found at http://abhayjere.com/Documents/Impact%20factor%202008_PDF.pdf

30. How are IF’s used? • To evaluate the scholarly worth of a journal (ranks journals) • To judge a publication’s quality or prestige • To assess academic productivity • To help you decide where to publish your article for maximum impact • Evaluates an author or journal editor • Libraries use as an evaluation source during journal cancellations or new purchases

31. Journal impact factor (IF) • Discipline-dependent • Size of field, pace of citation • Medicine has high level of networking, so high impact (e.g. New England Journal of Medicine = 45) • Social Science has low level of networking, so low impact • Work out impact threshold you want to achieve • Euphytica (International Journal of Plant Breeding) IF = 1.597 • 70% of journals have IF of less than 1

33. Calculating journal impact factor What is the journal impact factor: • A rough measure of a journal’s impact within its discipline • A ratio between citations and recent citable items published. • Other measures – h-index, SCOPUS SNIP, 5-year impact factor, editorial and publication times Current year citations Items published in the past 2 years Impact factor =

34. Finding and using journal impact factor Where to find the journal impact factor: • Journal website • Published yearly in Thomson Reuters’ Journal Citation Reports Criticisms • Limited subset of journals, biased towards English language • Short time frame for calculation - two years • Does not discriminate between paper types e.g.research/review • Maybe a paper is cited because it is poor quality?

35. Picking the right journal • Your goal should be to publish in the best journal for your work • Picking the right journal: • Increases your chance of getting accepted the first time • Increases your chance of having your work read/cited • Increases chances that your research will have impact • Advances your career

36. Journal home page and journal selection e.g. Euphytica http://www.springer.com/life+sciences/plant+sciences/journal/10681 • Recent examples of papers • Scope • Instructions to authors • Editorial and publication times, impact factors ONCE YOU HAVE SELECTED YOUR JOURNAL, GET THE “INSTRUCTIONS FOR AUTHORS” FROM THE JOURNAL HOME PAGE AND USE IT IN THIS WORKSHOP

37. Outlines   An outline will be between 3 and 6 pages (no Figures/Tables yet) • Use the outlining tool in MS Word (or similar) OR • EndNote/Tools/Manuscript templates • Set out the sections • Fill in the sub-headings Content of each sub-heading as 2-to-5 dot points • e.g. 1. “ a paragraph on who has used what methods of analyses; come up with particular findings, in the last five years. Emphasise major groups. • Include important references (e.g. major review) and other prompts (e.g. reminders for Acknowledgments) • This is an opportunity to get the logic of the paper right • Getting the logic right at the start avoids multiple versions CSIRO.Journal Writing

38. Outlines – an example of first level headers • Abstract (Summary) • Introduction (Background) • Methodology • Results • Discussion • Conclusion • Acknowledgments • References • Tables • Figures Specific outline & headers actually depend on the ‘type of paper’ and nature of the work CSIRO.Journal Writing

39. Example outline for Background/Introduction Start with a statement about how your area of interest is rich in relevant observations. Then identify the specific area that still requires attention, that is the issue that defines the reason for your study. Scope • Define the scope of your paper Previous studies • Briefly review the main studies to date. Refer to particularly important review papers (name reference). Mention specific studies that need to be included (name references to be used). Existing relationships/findings/uncertainties • Debate particular issues and define all terms Statement of contribution of this paper • This paper proposes a new relationship, tests the following hypotheses, examines………., context of discussion CSIRO.Journal Writing

40. Critical Questions: • Is the paper a self-contained narrative? (a story with the appropriate level of complexity) • Does the paper build on previous key work? • Have the current trends in this field been identified and contrasted? • Is the original contribution clear? • Are the target journal and paper type e.g. original research paper, review, short communication good choices? CSIRO.Journal Writing

41. Figures, tables and captions • Simple and structured; follow the journal format • Reduce the number of Figures and Tables if possible, or move extras to Appendices or Data Repositories • Innovative Figures are welcome but they must be readily understood (or sufficiently explained ) • Captions and Legends must be clear; reader must understand content. Use keys within Figure if advantageous. • If you are to use colour, check with the journal first • Ensure the essentials are in place (north arrow and scale on maps, units on axes) CSIRO.Journal Writing

42. When to use Figures and Tables TableFigure Most useful Number Shape When working with Individual data Overall pattern When accuracy/precision More important Less important CSIRO.Journal Writing

43. Constructing Figures  Artwork Often journal specific Refer to journal style sheet Colour can be expensive; convert to grey-scale Editing Do the figures match the legends? Are the axis labels properly explained in the legend? For reduction in publication: – what reduction is appropriate for figure? – does it fit column width of journal? Use keys within Figure if advantageous Add a), b) etc if using multiple Figures CSIRO.Journal Writing

44. Example: A figure dealing with lots of data FIGURE 1. The orbital and size distribution of the observed Baptistina asteroid family. From the following article: An asteroid breakup 160 Myr ago as the probable source of the K/T impactor William F. Bottke, David Vokrouhlický & David Nesvorný Nature 449, 48-53 (6 September 2007) CSIRO.Journal Writing

45. “Nature” legend – note need for fine detail William F. Bottke et al. (Nature 449, 48-53) The family has been projected onto a plane of proper semimajor axis a versus absolute magnitude H. On the right ordinate, we show asteroid diameters for a typical C-type asteroid albedo of 0.04. The central and largest body of the family, C-type asteroid (298) Baptistina19, has proper semimajor axis a = 2.264 au, eccentricity e = 0.15, and sine of inclination sin i = 0.10 (ref. 18). The BAF was identified using the hierarchical clustering method (HCM) applied to the proper orbital element database found in the AstDyS database18 (see Supplementary Discussion). The HCM locates bodies in the neighbourhood of (298) Baptistina with mutual velocities less than a threshold limit Vcutoff. The filled and open circles show 3,042 linked objects with Vcutoff = 53 m s-1. The family is also noticeably depleted near the adjacent J7:2 and M5:9 resonances20 (grey bar at a  2.2545 au). The two-lobed structure with an evacuated centre is diagnostic of families that have spread in a for an extended time under the influence of Yarkovsky/YORP thermal forces21, 22. The dark grey lines that bracket the outside of each lobe represent our best estimate of how far the majority of family members could have spread in 160 Myr. Objects outside these curves, shown as open circles, are assumed to be predominantly interlopers. Most come from the nearby Flora or Vesta families, whose spectroscopic signatures are similar to space-weathered ordinary chondrites (that is, S-type asteroids; Flora family) or basaltic achondrites (HED) meteorites (that is, V-type asteroids; Vesta family)19, 43, 45. Their number density near a H of 16, at which the SDSS is sensitive to asteroids, indicates that interlopers between the grey curves only contribute 10–20% to the overall BAF. CSIRO.Journal Writing

46. Example Legend #1(Figure) Legend Figure 1. Mean light-saturated photosynthetic rate (Amax) of apical (A), mature (B) and old foliage (C) in the crowns of trees in thinned and unthinned treatments at Creekton from October 1998 to May 1999. Error bars show mean standard errors. Old foliage was measured in the lower and middle crown zones only. Old foliage in the middle zone of the unthinned treatment was not measured in the third measurement period. Medhurst JL and Beadle CL (Tree Physiol. 25, 981-991) CSIRO.Journal Writing

47. Example Legend #2 (Table) Glen et al. (2009) Aust. Plant Path. 38, 345-356 CSIRO.Journal Writing

48. Example Legend #3 (Colour plate) Fig. 1 a. Sporocarps of Ganoderma philippii (collector’s number E7108) growing on the trunk of a dead Acacia mangium. b. Underside of Ganoderma philippii sporocarps. Glen et al. (2009) Aust. Plant Path. 38, 345-356 CSIRO.Journal Writing

49. Constructing Tables  Formatting Align column headings with entries Capitalise first word of an entry Use spacing to reduce complexity Editing Use the Table legend as a title that describes its content Place details about methods, statistics and specifics in footnotes Define abbreviations in footnotes Put units into column headings Make sure that the hierarchical structure is correct and all necessary information is in Table, not just legend CSIRO.Journal Writing

50. Example: How to improve a Table “After…..” “Before…..” CSIRO.Journal Writing