2010 edition

I. Steps

A.  Assemble the data, and for supporting material that is not original, obtain permission from copyright owners

B.  Decide on a journal.

C. Choose the type of paper, usually either an original article or report, or a short communication.

D. Obtain the Instructions for Authors for that journal.

E.  Write several drafts until all co-authors agree the manuscript is ready to submit.

F.  Obtain a copy of the cover letter instructions from the journal website and include all required statements in your cover letter.

G.  Submit the manuscript electronically at the journal website.

H.  Suggest several potential reviewers and list for the editor any names that you wish to exclude as reviewers, usually competitors with conflicts of interest.

I.  This brings up the topic of publishing ethics, which is a class period in itself, but it is useful to go over the author ethics part here.  Scroll down to Part 2 for the complete treatment of publishing ethics.

II.  The writing process – use the Instructions for Authors (IFA) as a guide.  IFAs are journal-specific, but there are common elements.  Springer has adopted a uniform IFA for all of its journals and then lists separately the elements unique to each of its journals.  We will refer to the Springer IFA as an example.

A  Getting started.  Some writers just need to start with a title.  Consider it a working title at best, to be revisited at the end of the process.  I like to start with the Results Section.

B.  Results Section.  Think of this section as the tables, the figures, the figure legends and the text of the results.

1.  First, make the figures.  Refer to the IFA to determine the correct font sizes.  Include the statistics in the figure.  This is when you decide on the data best put into tables, bar graphs, line plots, etc.

2.  Lay the figures out in a logical order.  This will rarely be the chronological order in which the experiments were done in the lab.  Sometimes, it is at this point that it first becomes clear that there is a gap in the logical progression and an additional experiment is needed.  It may or may not be possible to continue the writing without the results of this experiment.

3.  Write the figure legends.  Give each legend a title that concisely describes the figure.  The text of the legend should include the name of the method used and enough information on the experimental set-up or protocol to allow the figure to be understood without reference to other sections of the paper.  It should not duplicate the Methods Section.  All abbreviations and statistical symbols in the figure must be identified.

4.  Some reviewers, i.e. “the purists”, start with the figures and the figure legends.  If they do not like what they see, they will reject a manuscript on them alone.  If they like what they see there, these reviewers will read the rest of the manuscript to decide among the following possible recommendations:  accept as is, minor revision, major revision.

5.  Now write the text of the Results.  Describe the outcome of the experiments shown in the figures and tables or as data not shown, if appropriate.  All key experiments must be shown as figures or tables.  It is OK to state the methods used but do not duplicate the Methods Section.  Describe each individual panel of a figure.  State the conclusions of each experiment but do not discuss them.  Most of the overlap and duplication in the Results Section is with the Discussion Section.  Sometimes a result can be discussed in one or two additional sentences and will not be expanded upon or linked to other results in the Discussion.  It is OK to leave those sentences in the Results.

C.  Methods Section

1.  Now the writer is perfectly set up for the methods section.  List the methods and reagents used in the chosen figures and tables.  Present each one in a section of the methods along with appropriate references and identified abbreviations.  Journals often have an approved list of abbreviations of commonly used terms and chemicals that can be used without identification.  These are either part of the IFA or their location is listed there.  The cities and countries in which are located the companies from which reagents were purchased are still required by most journals.  Purchased antigens and antibodies need to be identified by company product number to avoid confusion.  The same is true of commercial kits.

2.  If humans and/or animals are used, the methods must include a statement regarding permission or humane treatment according to national or international guidelines, identified by name or document number.  Also, the institutional committees from which approval was obtained must be listed.

3.  Experimental methods that have been described in detail in previous publications can be briefly named and/or described along with the appropriate reference.

4.  One of the most frequently misused sentence structures is in this example:  5 mg/ml of NaCl was used.  This literally means 5 mg of an unidentified substance per ml of salt.  So, it should be NaCl at a concentration of 5 mg/ml of solution or NaCl (5 mg/ml) was used.  We all have our pet peeves when it comes to methods.  The point is to read what you have written and don’t make short cuts that do not make sense in order to “concise” the methods.  Yes, I once had a reviewer write that a section I wrote needed to be “concised”.  Obviously, this reviewer was a master of the craft!

D. Discussion Section

1.  Some writers like to write this section immediately after the Results, which is reasonable too, because the Results Section text-writing primes the mind for discussion of the results.  So it is your choice.  The biggest mistake in writing the Discussion is to make it too speculative and too long.  It is the place to link experimental results into a larger coherent model or theory and to bring in links to the published literature that your data either supports or contradicts.  If the latter, try to suggest reasons why the results might be different, such as different animals, some differences in reagents, or a slightly different protocol.  It’s fine to add a little speculation and perhaps a diagram of a pathway or cellular process, but it is not necessary to claim ownership of every possibility you can think of.

E.  Introduction – This section only has two goals.  One is to state the purpose of the study and the second goal is to provide sufficient information from the published literature to allow the reader to follow the new work presented.  I also like to clearly state how the present work goes beyond the published literature.  It should be brief, one or two double-spaced pages.  Resist the temptation to present results and discuss them in the introduction.  You have sections in which to do that well.

F.  A note on the Title, Abstract and Keywords – These items all share two characteristics: First, they are often thrown together as an afterthought almost, and second, they are the source of terms used to cross-reference and index your published paper in databases.   In the case of articles that are not open access, that is, not freely available to the public immediately, these three items are still freely available and serve to advertise your article.  An interesting title or abstract may determine whether or not a reader bothers to buy your article on-line or search it out at a library website.

1.  The title should be a clear and concise representation of the major thrust of the paper.

2.  The abstract should include a statement of the purpose of the work, the major methods used, and the major conclusions reached. It should end with a statement of the significance of the work.

G.  References and in-text citations – One of the best products of the computer age is bibliographic software.  Start making your library using EndNote, RefManager, or whatever you prefer, the day you start working in the laboratory. Major word processing programs like Word have plug-ins that allow writers to create in-text citations and a reference list as they write the manuscript.  Virtually all journal styles, and there are many hundreds of them, are now available as small files as part of the major bibliographic software packages.  They also make it easy to download citations for journal sites and on-line databases directly into your custom library.

H.  Acknowledgments – mention colleagues who provided key reagents and helped in various ways such as reading a commenting on the manuscript.  List and thank the granting agencies.  No need to thank mentor and co-authors.

I.  Odds and ends

1.  Verb tense.  Refer to previously published studies and results in the present tense.  Refer to work not yet published in the past tense, including the new work in the manuscript you are writing.

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