Introduction:  While many peer-reviewed journals and granting agencies may vary in their rules of submission format, following the basic guidelines below will greatly smooth the initial preparation stages of a final manuscript or report, saving a great deal of time for the authors, corresponding author/PI, and the secretary finalizing the formatting.  Dr. McCouch encourages the use of these guidelines.

 

Please note: The formatting of a Thesis at Cornell is handled very differently than the guidelines below.  Please do not use thesis preparation guidelines for journal or report preparation.

 

Manuscript or Report Text:

Use MS Word and save as an MS Word document (.doc).  Use Times New Roman or Times for the font throughout, font size: 12 point.  Use 1 inch margins.  Find the journal 'instructions to authors' online and follow their suggested order of appearance/word limits. Look at the most recent issue of your chosen journal (or last year's finished report) for examples of how the paragraphs are indented, hierarchy of headings, and reference format. Note that reference format is DIFFERENT for each scientific journal.

               MOST IMPORTANT: DO NOT embed your tables or figures within your MS Word file (see info below on Tables and Figures)* .  When it is necessary to refer to a table or figure, indicate which one (see numbering conventions below in Tables and Figures.) 

When indenting paragraphs, tables or bullets do NOT use the space bar.  The tab key or paragraph indent feature must be used.

References:  use Endnote (or Refworks), if at all possible, for references-especially if your list is more than two pages long.  Send your Endnote file along with your manuscript.  If we have to combine reference lists or reformat for another journal/report style, this saves a great deal of time.  It also assists the author/corresponding author in checking references and citations before submission.  When using Endnote, please download citations rather than hand-typing them.  If you must hand-type a citation, do NOT truncate the author list to 'et al.' - not every publication allows this!

 

TABLES (return)

• All Tables must have a title.
• Do NOT embed tables in the manuscript/report file.*
• Tables must be numbered in order of appearance and submitter, especially if there are several authors:  i.e. Table 1_Smith; Table 1_Williams, Table 2_Williams. Save Table files using the above naming rules.
• Please provide an index of numbered tables at the end of your report/manuscript. If known, indicate whether they are to be included in the published manuscript (hard copy) or if they are Supplemental Files.  Supplemental files have different formatting rules:  for instance, they do not have to fit into a journal-sized page, since they are available only by download from a website. If your tables will be in a report section, indicate which one (i.e.: Activities or Findings).
• Tables can be made in either MS Word (.doc) or MS Excel (.xls).  Tables are not acceptable as 'images' or as tables made with Powerpoint.  If you insert a table that becomes converted to an image using another software program, please send the original table generated with that software along with your report.
• Be sure to include footnote(s) for unusual symbols used.
• Font size: for larger Tables that appear on letter-sized paper, do not drop the font size below 10 point, using Times New Roman or Times.
• Tables should fit on standard letter size paper to appear in the hard copy manuscript or report.  If they exceed standard paper sizes, they must be handled as supplemental files.

 

FIGURES (return)

• All Figures must have a title and a legend (especially needed if symbols/colors/greys have to be identified).
• Do NOT embed figures in the manuscript/report file.*
• Figures must be numbered in order of appearance and submitter:  i.e. Figure 1_Smythe; Figure 1_Jones, Figure 2_Jones. 'Order of appearance' is calculated from within individual reports from submitters. Save Figure files using the above naming rules.
• Please provide an index of numbered figures at the end of your manuscript/report, along with their Legends and Titles. If known, indicate whether they are to be included in the published manuscript (hard copy) or if they are Supplemental Files.  Supplemental files have different formatting rules:  for instance, they do not have to fit into a journal-sized page, since they are available only by download from a website.
• Color in Figures:  the cost to publish in color varies from journal to journal and can be very significant.  Check with the corresponding author on color versus greyscale before spending many hours on a Figure.  Do not use color if grey scale options are sufficient to understand the Figure.
• Font sizes:  Please size your figures 'actual' size - i.e. the size you want them to appear in the finished document.  This will help you size the fonts to their finished, readable, size, which can be no less than 6 point, though larger is preferred. Do not combine much larger text with very small text - the spread should not be more than 3 points. 
• CHARTS made in Excel MUST be submitted with original excel files used to create them: include the original data file worksheets or linked files.  Charts embedded in MS Word from Powerpoint are not acceptable: submit the original Powerpoint files.
• All Charts must have the X and Y axis identified.
• X and Y axis must have measurements included.  Use minimum number of 'tick' marks possible. 
• Do not put names or numbers on an angle - use text either vertical or horizontal.
• Indicate chart title separately, using index of figures, above.
• Use grey scale wherever possible.  Do not exceed 3 shades of grey.
• Include Legend within Chart.
• Figures should have 'moveable parts' whenever possible.** Figure files are preferred in Adobe Illustrator .eps format, if available.  If made in Powerpoint, do NOT submit as MS Word insertions, but provide the original Powerpoint files. A figure submitted as an 'unalterable' jpg is not acceptable, unless there is no alterative.
• If you used analysis software in creating your figure and it converted to a partial or complete image, please indicate the original software used in your Index of Figures.
• PDFs are not acceptable unless you created them in Adobe Illustrator.

 

 

*For some reports, tables and figures can be embedding in MS Word. However, do not submit your MS Word document without ALSO sending us the original source files for tables and figures, as outlined above. (return)

 

**Notes on moving a figure created in the originating software program to Adobe Illustrator: (return)

               Originating software (program where the figure was created-this could be MS Powerpoint, MS Excel, special data-analysis software, etc..  First: find out what the figure can be saved as in the originating software. If you can save as an .eps file, choose that and you should be done. 

If you can only save as a jpg or other 'image' choices, try the following, to see if you can improve the 'moveable bits' when transferred into Adobe Illustrator***:

 

Open both the originating software and Illustrator at the same time.

1.       Pull up the Figure in the Originating software and select it.  Drag and drop to a new Illustrator page.

2.      Pull up the Figure in the Originating software and copy it. Paste it into a new page in Illustrator.

3.      From Illustrator, select the Place command and find the originating software figure file.  Place it on a new Illustrator page.

 

IN ALL THREE CASES ABOVE:
From Illustrator, select all and check to see if your figure will ungroup, and whether text in your figure is clustered in word groups (good) or individual letters (bad). Some figure elements may ungroup, some may not.

 

When you only have an image (jpg) and need to alter it, or create a new figure in .eps format based on some elements of the image:  place the image into Illustrator.  Select transparency and make the image very pale.  Draw over it to recreate new elements that are the same size/location as the old, unchangeable ones.  When finished with the new elements, delete the transparent image and save the file as an .eps. Of course, the original figure image could be blocked out with white rectangles to cover up unwanted areas of the image as well; in that case you would not remove it or make it transparent.

 

*** Why Adobe Illustrator (return): This software will save as either .eps files or .pdf files.  These are heavily preferred by publishers, as they are very compatible with their printing software programs.  Also, Illustrator easily resizes text and figures, without distorting font and line sizes.  It has superior drawing /text adding capabilities as well.  If you are sending Illustrator files to collaborators who do not have this software, the option to save as a pdf is invaluable, since most computers can 'see' a pdf.