Authoring a manuscript for BioMed Central using Publicon

Introduction
Publicon allows authors to preformat manuscripts using a style that is fully compatible with the BioMed Central submission system and can be converted into XML, therefore allowing faster publication.

Using the Publicon interface
Publicon manuscripts are composed in notebooks (indicated by the file extension .nb) which, once complete, can be submitted to BioMed Central journals (along with the relevant figures and additional files). Notebooks are structured files that consist of elements called cells. Styles can be applied to cells so that they can be formatted appropriately and so that the manuscript's hierarchy is correctly organized. The extent of each cell is indicated by a bracket to its right and so the hierarchical structure of a manuscript is indicated by the overall grouping of brackets.

Notebook and cell contents can be edited using palettes - organized toolbars that are displayed in the Publicon interface. The document palette, of which there are several customized types, contains the commands necessary for structuring a manuscript, and is organized into Tabs that control different aspects of the manuscript. The typesetting palette is used to format font styles, add special characters and to construct any mathematical formulae required.

To insert a new cell, position the cursor at the required point in the document and when the pointer becomes horizontal, click to indicate the position then choose the desired cell type from the selection in the document palette. The default cell type is text. To change the style of a cell, click the cell bracket so that it is highlighted then choose the required style from the document palette.

Creating a new BioMed Central notebook file
Chose FILE ⇒ New ⇒ 3. BioMed_Central_Article. A new file is opened based on a BioMed Central template containing examples of the sections required in a manuscript. A new document palette (BioMed Central) is also opened, which contains the Tabs that refer to different sections of the manuscript with appropriate command buttons that allow you to add and edit these. The palette has a top tool bar with buttons that function as follows: ? = opens help file; S = opens sample notebook; << < > >> change the position of the palette within the Publicon window; - = minimizes the palette (can be maximized by clicking on minimized version).

If the BioMed Central palette is already open a new file can be created by clicking the 'New document' button in the palette to create a new notebook in BioMed Central style with required elements laid out in template form.

BioMed Central template contents
FRONT MATTER
Definition
This section contains the title, author details, abstract and other initial information about the manuscript.

Required elements
Title
The title of the manuscript

Authors
The names, e-mail addresses and affiliations of all authors of the article.

Abstract
The abstract of the article. This should be structured according to the BioMed Central instructions for authors.

Abbreviations
A list of abbreviations used (if appropriate)

Entering information
Title
Replace the dummy text for Title with your own text (either by entering the text directly or by cutting and pasting from your own manuscript document). Please note that when you copy and paste into Publicon, the template's font and style may be overridden by the formatting of your own material. BioMed Central will reformat the text , so you can ignore irregularities in spacing and sizing (e.g., of superscripts).

Authors
Click on AuthorName in the template document to open the wizard for adding author names. The wizard allows specification of each author's first, middle and last name, name suffix, e-mail address and institutional affiliation. More than one institution can be assigned to each author using the + - and ⇒ key in the box functions as follows: + adds an institution; - removes the institute in which the cursor is positioned; ⇒ gives a list of institutions already used in the manuscript to allow the same address details to be assigned to different authors. A manuscript must have at least one author and each author must have at least one institution. Indicate the corresponding author and any authors who contributed equally. If you have used Publicon to produce a manuscript previously, a list of the authors you used is stored and can be reused - to select from this list click 'load' and choose the required author.

Abstract
Replace the dummy text for the abstract with your own text (either by entering the text directly or by cutting and pasting from your own manuscript document). This should be structured according to the BioMed Central instructions for authors. To add sections and text to the abstract, click the Abstract section and Abstract text buttons in the palette.

Abbreviations
A list of abbreviations used (if appropriate)

BODY
Definition
The main body of the article including all text sections.

Required elements
Refer to the BioMed Central instructions for authors for the sections that are required for different article types.

Entering information
The BioMed Central template notebook includes sample section headings and subsection headings with text sections. To add new sections and text cells, use the buttons in the Main Elements tab of the BioMed Central document palette. Section Level 1 inserts a top level heading (such as Background, Results, Conclusions etc.), Section Level 2 and 3 can be used if subdivisions within main sections are required. Each paragraph of text should be entered in a separate text cell (by clicking on the text button in the Main Elements tab), bear this in mind if you are pasting in a large section with multiple paragraphs,

Importing existing text
Text can be imported from text files (.txt)

Inserting figure legends, figure captions, and figure links
The template contains an example figure reference with sections to include the caption and legend of the figure. To insert the details of a further figure (number, figure caption and figure legend text), click the Figure button in the Main Elements tab. To insert a figure link in the main text, position the cursor where you want to insert the reference to the figure and click 'Insert Figure XRef' in the main elements tab. This opens a small window with the numbers of figures available. To insert the reference click on the number of the required figure in the new small window. The words Figure x will then be inserted into the manuscript.

Inserting tables
To insert a table choose the position in manuscript, expand the tables tab on the palette and click the appropriate button. Insert table allows you to choose how many rows and columns the table has. Import table allows the inclusion of tables formatted as CSV files (in which case, you do not have to specify the number of rows and columns). Table structures can be edited once created using the commands in the Adjustments menu. New columns and rows can be added using the Add Column or Add Row buttons.

To insert a table link in the main text, position the cursor where you want to insert the reference and click 'Insert Table XRef' in the tables tab. This opens a small window with the number of a table. To insert the reference click on the number in the new small window. The words Table x will then be inserted into the manuscript.

Inserting equations
The Math tab on the palette contains the commands necessary to create equations within the manuscript text. The typesetting palette is used to include mathematical symbols and characters. If you want your formula to appear on its own line, be sure to start a new paragraph cell before inserting the formula. Otherwise, merely place the cursor precisely in the text where you want the formula to appear within a paragraph.

Inserting additional data files
Additional data files are added and referenced in the same way as figures.

Inserting reference links
If you have a Publicon reference library already set up click at the point in the text where you wish to insert a reference to a bibliographic record. Click Insert Reference from the References tab. This brings up a window allowing you to search for your reference by key, author name or title. Once the desired record is found, click on it then click 'Insert' to add the citation reference. New references can be added by hand to the Publicon database at any stage and can be imported from EndNote BibTeX files.

To make new references in the Publicon database. You will encounter a place to enter either a Keyword description, an Author name or a Title, which will be used to identify each item in the database. You cannot enter a new reference until you have filled out at least one of these fields. Once you do, you can click on the New button, which takes you to a place where you can fill out all the required fields to describe your reference adequately.

BACK MATTER
Definition
Contains the acknowledgements and reference section.

Entering information
Acknowledgements
Replace the dummy text with your own text.

References
Once all reference have been entered in the main text of the manuscript a bibliography is created by clicking Gather References.