Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience

1. FFLC Seminar: Place Position in the Publication Process Equipping yourself with the tools to succeed in the world of the peer-reviewed scientific journal Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Member, Future Faculty Leadership Council of UAlbany December 3rd, 2012 Slides will be made available at www.abehmiel.net

2. Outline • Overview of Peer-Review Publication Process • Writing Style • Publication-quality figures • LaTeX for scientific journals • Responding to reviewer comments • Summary

3. Why Publish? • Publication of research in scientific journals is costly, slow, like a “lotttery,” biased, does not detect errors, and contains myriad other problems [1] • Allows your colleagues to find and cite your work • A “deliverable” in terms of scholarly grants • In the absence of a “killer app,” there is no real alternative • You need to do it repeatedly to graduate, get a job/keep your job (in academia) and obtain grants [1] http://breast-cancer-research.com/content/12/S4/S13

4. In which journal should you publish? • Your research is part of a scientific conversation, and that conversation is being confined to certain spaces • Example: Physical Review B, J. Phys. Chem B & C. • What is your research citing? • Research the editors of the journal to find their level background and expertise in your field • Impact factor: measure reflecting the average number of citations to recent articles published in the journal • Preprint archive: arxiv.org (not peer-reviewed) • Trust your PI

5. Journal format and submission guidelines • Each journal will have its own format and submission rules so that the editors can form it into a manuscript for publication • Some may require a .doc format, others .tex – figures may be required to be in .eps, .gif, or .tif format • Some journals will give you a nearly empty document as a template. If you've submitted to the same journal before, you may consider using a completed article as a template • Straying from journal guidelines could cost you time and referees' ire in the peer review process. This includes word count, figure count, caption format, abstract length, citation format and more For an example, see the REVTEX 4.1 Author's guide at https://authors.aps.org/revtex4/auguide4-1.pdf

6. Writing the paper Some text adapted from http://abacus.bates.edu/~ganderso/biology/resources/writing/HTWtoc.html

7. Writing the paper: where to begin? • What are the most important aspects of this research that would be of value to the existing scientific conversation?

8. Writing style: strategy for writing the paper • Before you write anything, synthesize your data “horizontally” • Develop an outline • Try writing the results section first • Order figures and tables in a sequence that is accessible to the readership and consistent with the flow of the paper • It's optimal to be as concise as possible • Proofread often, give to colleagues for their input

9. Writing style: title and abstract • Title: A majority of your readership will find your paper based on keywords in your title • The title should unambiguously and succinctly describe the contents of your paper • The abstract allows you to elaborate on the aspects of the paper that are implied by your title • The abstract will help a reader determine if they want to read a paper at all • A simple rule-of-thumb is to imagine that you are another researcher doing an study similar to the one you are reporting. If your abstract was the only part of the paper you could access, would you be happy with the information presented there?

10. Writing style: citations • Cite references whenever you use outside information • Use the journal's formatting guidelines • Introduction & methods sections usually carry the most citations of others' work • Cite recent data when benchmarking your results against others • Your scientist peers like being cited.

11. Writing style: methods • Your methods should be described in such a way that a subsequent investigator could repeat your work and know if they have arrived at the correct result, while still being succinct • Appropriate theoretical background should be given to your work as it relates to the current scientific conversation, more details are usually better

12. Writing style: results • Purpose of the results section is to state your findings objectively and without interpretation, organized clearly and logically • Use the past tense • Use the text of the results section to guide the reader through your illustrative materials (tables, figures) and explain what information each of them conveys. • Be sure to spend the most time describing the key findings that attempt to answer the original question you're investigating

13. Writing style: discussion • An interpretation of the results based on the previous literature should be presented in a way such that a reader with knowledge of the field could follow the argument and confirm that your conclusions have merit • Do your results provide answers to your testable hypotheses? If so, how do you interpret your findings? • Do your findings agree with what others have shown? • Given your conclusions, what is our new understanding of the problem you investigated and outlined in the Introduction? • If warranted, what would be the next step in your study, for example, what experiments would you do next?

14. Writing style: acknowledgements • Definitely divulge information as to which organization funded the study and, if applicable, under which grant • Acknowledge helpful conversations with, and assistance from collaborators (and state their affiliations) if their contribution is not enough to deserve a co-authorship • If you're doing a computational study, state where the computations were performed • Keep it very brief.

15. Figures

16. Publication-quality figures: basics • All figures and tables need captions • All figures need to tell their own story. That is, each should be understandable without referring to the text. • Figures should be drawn in vector graphics or uncompressed file formats for highest clarity and scalability.

17. Publication-quality figures: tools • Origin (current version: Origin 9, by Originlab) • MATLAB (current version: R2012B by Mathworks) • Python, with the Pyplot extension (Matplotlib library)

18. Publication-quality figures: guidelines • Add labels to all axes and make axis labels and any other labels in the figure sufficiently large • Minimize visual clutter by maximizing the amount of ink used to convey data relative to the total amount of ink. Remove any lines that don't convey any information. Make sure that the lines that represent data are thicker than the axis lines • Don't put a title on top of the figure. The title belongs into the figure caption • Be mindful of color usage. Many people are color blind and may not be able to distinguish some of the different colors you are using. In general, if at all possible, a figure should still convey all its information when printed black-and-white From: http://wilke.openwetware.org/Creating_figures.html

19. Publication-quality figures: guidelines • If possible, avoid overly busy line styles, such as dotted or dashed lines, in particular many different types of dotted or dashed lines. Always avoid patterned fill styles in bar graphs • Include error bars when necessary and trendlines when appropriate • In general, MS Excel cannot produce acceptable figures and should be avoided. MS Excel also makes it difficult to export figures into commonly used formats such as eps, pdf, or svg without using GIMP or Photoshop

20. Publication-quality figures: Excel (DON'T) “The flaccid staff of the Chart Wizard” Adapted from: http://scienceblogs.com/principles/2009/03/18/why-does-excel-suck-so-much/

21. Publication-quality figures: matplotlib/pyplot • pyplot.matplotlib is a collection of command style functions that make matplotlib work like MATLAB • You need a working distribution of python (python 3.3 is available, but I recommend 2.7) and numpy (numerical python, has numerical array utilities) • Pylab is also recommended (creates python commands that work just like MATLAB commands) • Python is a contextual, multi-purpose high-level language with a large developer community • FREE! • Downside: no 'clickable' axes, series editor To download python: http://www.python.org/ For matplotlib: https://github.com/matplotlib/matplotlib/downloads

22. More matplotlib/python/scipy resources LaTeX: http://www.scipy.org/Cookbook/Matplotlib/LaTeX_Examples Matplotlib tutorial slideshow: https://safe.nrao.edu/wiki/pub/GB/Knowledge/GbtDataAnalysisUsingPython/matplotlib.pdf More general examples of some of matplotlib functionality: http://www.scipy.org/Cookbook/Matplotlib SciPy: http://www.scipy.org/ Learn python “the hard way”: http://learnpythonthehardway.org/book/

23. Publication-quality figures: ImageMagick Cross-platform image file format converter with many more features For more information: http://www.imagemagick.org/script/index.php

24. LaTeX

25. LaTeX for scientific publishing: basics • LaTeX is a comprehensive primary document preparation and markup language • TeX is the low-level language used for creating visuals out of document markup, LaTeX is a set of macros used to access the powers of TeX • The perks of using LaTeX for journal publication is to get nice-looking pdf's with crisp figures and tables, hyperlinked references, and sharp text presentation • LaTeX templates and guides exist for many scientific journals • LaTeX can import/supports several reference managers (Zotero, Mendeley, etc.)

26. LaTeX for scientific publishing: example

27. LaTeX for scientific publishing: distributions Linux: TeX already installed Windows: MikTex http://www.miktex.org/ Mac: MacTeX http://guides.macrumors.com/LaTeX Some cross-platform editors for easy LaTeX project management: TeXmaker Kile Notepad++ (Windows) TeXworks More here: https://en.wikipedia.org/wiki/Comparison_of_TeX_editors

28. Revisions • Often, your paper will not be accepted by an editor on the first submission and revise it, responding to reviewer comments in the process • When re-submitting, you must include a summary of your revisions and reference those revisions • Generally it is ok to delete figures/tables (or introduce new ones), and make changes to the organization of the paper if it is warranted

29. Responding to reviewer comments • Read the comments carefully • Give point-by-point comments, respond completely • Provide well-reasoned arguments with details • Make it easy for the reviewer/editor • Carry a polite tone • Appreciate the reviewers' work Adapted from http://www.editage.com/resources/art13.html

30. Responding to reviewer comments: example In order to motivate the methodology used, the authors state that: “Despite this well known under-estimation of band gap in the current DFT- GGA functionals recent quasiparticle calculation on bulk rutile TiO2 using the GW approximation [35] which is computationally expensive indicates that the general trend of band dispersion close to the gap region can be well reproduced by the DFT calculations. This makes possible investigation on the indirect and direct character of the band structure in TiO2 nanowires with moderate computational costs.” This consideration is, in my opinion, totally objectionable. Results reported in Ref. 35 does not prove, in fact, that DFT-GGA can be used, as a good approximation, to investigate structural and electronic properties of TiO2 NWs and in particular to analyze indirect or direct character of the band gap in case of TiO2 low-dimensional nanosystems. How can the authors be sure that the inclusion of quasiparticle corrections (and in general of Many Body effects) leads to the same trends reported in the manuscript?

31. Responding to reviewer comments: example response We thank the reviewer for catching this obvious error. We agree with the reviewer that we cannot be sure that the inclusion of quasi particle correction will lead to the same trends reported here. A survey of recent literature shows that no systematic quasi particle calculation on TiO2 nanowires has been reported to support fully this statement. Therefore the above rather misleading statement has been removed in the revised manuscript. In addition, we have performed a new set of bandstructure calculation using spin-polarized LDA with the corresponding pseudopotentials. The results (Fig. 4 in the revised manuscript) show that for the nanowires studied here, the trend in the bandstructure character was not affected by the choice of PBE and LDA functionals. Since LDA bandstructure ofter serves as the starting point for the more rigorous GW calculations, we hope the results reported here will serve as a useful qualitative guide to future quasi-particle calculations, which could be computationally expensive given the rather complex atomic structure and hard pseudopotentials of TiO2 nanowires.

32. Responding to reviewer comments: example • Reviewer comment: • 2) In the caption of figure 2, explain the meaning of open and closed symbols. • Our response: • This may have just escaped the reviewer's attention. In the captions of both Fig. 2 and Fig. 3, we have explained that the filled markers denote a direct band gap at the Gamma point and empty markers denote an indirect gap.

33. Summary and concluding remarks • Peer review isn't perfect, but it's what we've got for now • Follow submission guidelines, use templates, and use good literature in your field as a model for your paper's flow • Use a professional plotting suite or Pyplot to create figures for publication, save in vector graphics formats when possible • LaTeX: a good skill to learn, could be very useful for writing long documents and organizing references • Be gracious, organized, and complete when responding to reviewer comments • WRITE OFTEN!

34. Supplemental slide: reference management Mendeley is a free, cross-platform reference manager and academic social network. It contains an interface to export references to LaTeX .bib format For more information: http://www.mendeley.com/ http://blog.mendeley.com/tag/latex/