FFLC Seminar: Place Position in the Publication Process Equipping yourself with the tools to succeed in the world of the peer-reviewed scientific journal - PowerPoint PPT Presentation

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Title: FFLC Seminar: Place Position in the Publication Process Equipping yourself with the tools to succeed in the world of the peer-reviewed scientific journal


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/S
4/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  • Preprint archive arxiv.org (not peer-reviewed)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/ga
nderso/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_figure
s.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/2
009/03/18/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/matplotl
ib/downloads
22
More matplotlib/python/scipy resources
  • LaTeX http//www.scipy.org/Cookbook/Matplotlib/La
    TeX_Examples
  • Matplotlib tutorial slideshow
  • https//safe.nrao.edu/wiki/pub/GB/Knowledge/GbtDat
    aAnalysisUsingPython/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//learnpythonthe
    hardway.org/book/

23
Publication-quality figures ImageMagick
  • Cross-platform image file format converter with
    many more features

For more information http//www.imagemagick.org/s
cript/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/Compariso
    n_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/art1
3.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/
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