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
1FFLC 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
2Outline
- Overview of Peer-Review Publication Process
- Writing Style
- Publication-quality figures
- LaTeX for scientific journals
- Responding to reviewer comments
- Summary
3Why 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
4In 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in the journal - Preprint archive arxiv.org (not peer-reviewed)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
5Journal 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
6Writing the paper
Some text adapted from http//abacus.bates.edu/ga
nderso/biology/resources/writing/HTWtoc.html
7Writing the paper where to begin?
- What are the most important aspects of this
research that would be of value to the existing
scientific conversation?
8Writing 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
9Writing 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?
10Writing 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.
11Writing 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
12Writing 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
13Writing 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?
14Writing 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.
15Figures
16Publication-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.
17Publication-quality figures tools
- Origin (current version Origin 9, by Originlab)
- MATLAB (current version R2012B by Mathworks)
- Python, with the Pyplot extension (Matplotlib
library)
18Publication-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
19Publication-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
20Publication-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/
21Publication-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
22More 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/
23Publication-quality figures ImageMagick
- Cross-platform image file format converter with
many more features
For more information http//www.imagemagick.org/s
cript/index.php
24LaTeX
25LaTeX 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.)
26LaTeX for scientific publishing example
27LaTeX 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
28Revisions
- 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
29Responding 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
30Responding 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?
31Responding 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.
32Responding 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.
33Summary 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!
34Supplemental 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/