Untitled Manuscript

Manuscripts Team

About Manuscripts

Manuscripts is designed for a seamless writing process from start to finish of a large

writing project. We want to especially serve writing large scholarly documents:

literature reviews, Master's dissertations, PhD theses, journal articles, book chapters,

grant applications, patent applications, the list goes on.

What makes Manuscripts special?

Manuscripts helps a writer to focus on producing great work throughout a writing

project, from planning to publishing stage.

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 You can start writing using a manuscript template, by importing an existing
document, or by creating a new empty manuscript.
You can outline and plan your writing project using a powerful manuscript

outline that updates live as you write.

Editing has been tuned to needs of scholarly writing: clean, simple and built
for purpose.
Top of the range citing workflow and automated bibliography formatting
either using Magic Citations from Papers, or a built-in citation tool that imports
references from pretty much any common format: EndNote XML, RIS, BibTeX,
Citeproc JSON, MODS, and several more.
Cross-referencable multi-panel figures, tables and equations.

Import and export key file formats used for scholarly writing: MS Word,
LaTeX, or Markdown.
The manuscript file format is versioned.
For those writing peer reviewed literature, Manuscripts will allow you to
directly submit your work to thousands of different journals.

How to get started?

There are three ways to get started with Manuscripts.

1. Select one of our built-in templates. Manuscripts comes with over 1,100
verified templates, as well as unverified templates based on CSL styles.
We are building literally thousands of them for many types of documents,
including for journals across all sciences, university specific PhD theses,
grant applications etc.
2. Import an existing document. Manuscript supports multiple import
formats such as MS Word, LaTeX, Markdown and many more.
3. Create a new blank manuscript.

Selecting a built-in template

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Choose Create new manuscript from the welcome screen or if do not have the
welcome screen available, go to File > New > Manuscript with Template

Figure 1: Template selector

Browse or search for available templates. Manuscript-verified templates are indicated

by a badge icon as shown in Figure 1. Once you have found and selected the
template you need, click Choose and a manuscript template is opened for you.

Figure 2: New manuscript from template

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I cannot see a template for the document I would like to write, what should I
do?

In case you cannot find the template you are looking for, do not worry, you still have
several options to get started.

If you are looking to get started with a generic template that consists of an abstract,
introduction, methods, results and discussion, you can choose a different journal
template (e.g. Genome Biology Research Article) and modify the template to your
needs. Remember that the template is only there to help you get started and to
provide you with guidance. However, you are still the master of your own
manuscript.

If you rather get started with a blank canvas, choose Create Empty Manuscript
option from the bottom of the template selector and you are all set to write your first
document with Manuscripts.

You can contact us at support@manuscriptsapp.com with a link to the

journal/template style you would like Manuscripts to support and we will do our best
to add your requested template to Manuscripts.

I can find a template but it does not have the Manuscript verified badge next
to it.

We have added over 7,000 journal CSL styles that you can choose to get started from
to create a template of your own. If you find a journal template without a badge next
to the journal name it means that we have not verified the template for that journal
yet.

You can still choose the journal template as your starting point. When you select the
template a pop up window appears where you can see and edit basic template
metadata such as which sections it should contain, which font and font sizes will be
used, and so on. Once you are ready, click Create Manuscript.

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Import an existing document to Manuscripts

If you already have a draft in another document format and you would like to
continue writing it with Manuscripts, you can easily import the document to
Manuscripts and continue writing your draft with ease.

1. Create a new empty manuscript from File > New > Manuscript.
2. Go to File > Import > Content..
3. You can see all the supported document formats that can be imported to
Manuscripts by clicking Options in the file browser window.
4. Choose the document that you want to import to Manuscripts, click Open
and the document is opened as a new manuscripts file.

Figure 3: Import an existing document to Manuscripts

How to reorder manuscript sections

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The manuscript outline lets you not just see and navigate an outline of your
manuscript project, but also manipulate the structure of it in powerful ways. Simply
drag and drop to reorder sections or paragraphs to change the flow of your
document.

How to use the focus mode in Manuscripts

Maintaining focus is essential to productive writing. One of the ways we help you
focus in your work is the so-called focus mode. You can activate the focus mode in
two ways.

A. Click View > Selected Sections in the main menu.

B. Click the focus button in the manuscript outline, visible when you hover on an
individual section in the outline on its right edge.

To toggle back to viewing the entire manuscript, simply

A. Click View > View All Sections in the main menu

or

B. Click the focus button again

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 1. Focus mode in action.

2. Focus mode icon

Figure 4:

1. The manuscript editing window when you have activated the focus mode. 2.
The focus mode icon, visible when you hover on a section item.

How to use the gutter menus

The Manuscripts editor includes so-called "gutter helpers", designated with the blue
+ and o symbols in the left margin for the currently active paragraph. These symbols

are buttons that lead you to shortcut actions for inserting (the+symbols) and
manipulating (the o) the document contents in a way that is contextual.

The gutter insertion helper (+ symbol)

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 Figure 5: How to create a new section

The gutter selection helper (o symbol)

The following example shows what the gutter selection helper tool presents in the

case of a paragraph.

Figure 6: The gutter selection helper for a paragraph.

The gutter helper is entirely optional and can be toggled on or off from the Editing
Preferences by choosing "Show smart gutter in the left margin when editing.

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 Figure 7: Smart gutter can be enabled or disabled in the Editing Preferences

Exporting a selected subset of a manuscript

It often comes handy to place material in your manuscript project which is never
intended to reach readers. For instance you may want to keep

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 1. Notes regarding your research or writing progress: material that helps
you organise your writing, but is never intended for publication or for

feedback.
2. Unfinished material that is not yet ready for feedback or publication.

Manuscripts supports this way of writing by allowing you to choose what is shared or

exported by first making an outline selection and then sharing or exporting.

Share the current selection

Select what you want to share in the manuscript outline (+click or +click
to select multiple sections).

Choose the applicable option from Publish > Share >. The export formats

made available for sharing are:

the manuscript file format (.manu, which is a compressed variant of the

file format).
MS Word (docx)

Your default markup format (which you can choose from Preferences >
Editing): one of Markdown, LaTeX or HTML at the time of writing.

PDF

Figure 8: Sharing the current selection

Note that if you have selected your bibliography as one of the items you want to
export, only the subset of it that is cited in the selected part of your manuscript is

included in the bibliography.

Export the current selection

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 Select what you want to export in the manuscript outline (+click or +click

to select multiple sections).

Click File > Export (K)

Choose Export selected content only.

As with sharing, if you have selected your bibliography as one of the items to export,
only the subset of citations in the selected part of your manuscript get included in the

bibliography.

Spell and grammar checking in Manuscripts

Manuscripts allows you to check your spelling and grammar as you type to avoid
disasters like the one shown in Figure 10. Grammar and spellchecking can be

accessed from Edit > Spelling and Grammar in the main menu.

Figure 9: Enable spell and grammar check

Check spelling and grammar manually

To check spelling and grammar manually, choose Edit >Spelling and Grammar >
Show Spelling and Grammar (:).

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 Figure 10: Check spelling and grammar manually

To update the spelling and grammar analysis of your document after you have made

some changes, choose Edit >Spelling and Grammar > Check Document Now
(;).

Check spelling and grammar as you type

Spelling and grammar can also be checked as you type, by toggling on Edit >
Spelling and Grammar > Check Spelling While Typing. Grammatical errors are

presented in the familiar green, and spelling errors in red.

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 Figure 11: Check spelling and grammar while typing

Correct spelling automatically

You can even make Manuscripts correct your spelling for you by choosing Edit >
Spelling and Grammar > Correct Spelling Automatically.

Choosing a citation style

You can change the manuscript's citation style in the inspector available on the right
hand side of the main window by clicking the Toggle Inspector button available in

the lower right corner of the application window.

Figure 12: Inspector toggle button icon

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This reveals the inspector which includes two tabs, second of which is the style
inspector. At the bottom it includes the Manuscript Styles inspector palette (where
you see the keyboard focus in the screenshot below). This inspector palette is where

you can change the citation style.

Figure 13: Changing the citation style in the Inspector

How to change the font family and size?

You can change the font family and size and edit other properties of paragraph styles
in the inspector on the right hand side of the main window by clicking the Toggle
Inspector button (available in the lower right corner of the application window).

Figure 14: Inspector toggle button icon

This reveals the inspector which has two tabs, second of which is the style inspector

that includes the Paragraph Styles palette that let you choose font sizes, etc.

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 Figure 15:

Change font and font size in the Paragraph Styles section of the Inspector

How to create a figure panel

The basic workflow for adding figure panels into your Manuscripts document
involves first placing a figure placeholder into your document (which you can

caption at this stage), and then adding an image as a second step.

Importing manuscript content that includes images is another option, i.e. File >

Import > Content. This is not further discussed separately here.

Creating an empty figure panel

There are three different ways to create an empty figure. Each one of them requires
you to first place the text insertion cursor next to the spot where you want to insert

the figure. After that, you can either:

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 Click the figure symbol in the toolbar.

Use the menu item Insert > Figure in the main menu.
Use the smart gutter menu to the left of the paragraph that is in focus, before
or after which you intend to add the figure. Click the blue + symbol in it, and
choose Insert Figure.

1. Figure panel icon

2.

Figure 16: How to create a figure panel

The figure placeholder you create will look something like the following:

Figure 17: New empty figure panel

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Adding images to a figure panel

You can add images to a figure panel in three ways, starting from an empty
placeholder image.

1. By dragging and dropping into the figure + symbol.

2. By clicking the figure + symbol and choosing Choose File to Import
3. By clicking the figure + symbol and choosing amongst orphaned figures
in the manuscript in case you have previously added and then removed

figures (orphaned figure images can be removed permanently by right

clicking the figure in the list of orphaned figures, and choosing Delete).

To replace a figure, simply either:

1. Drag an image on top of the image you wish to replace.

2. Alternatively, click on the image and drag in the popover that opens, or
again Choose File to Import

Creating a multi-panel figure

You can create a multi-panel figure in Manuscripts simply by:

Figure 18: Creating a multi-panel figure

Figure file formats

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Manuscripts always deals with image data in a non-destructive way. For instance
figure panel images all internally still store the original full sized image even if any
panel members need to be scaled. Similarly, Manuscripts keep vector formatted

graphics in their original form and only rasterises them to bitmap images on export if
required (see below).

Some manuscript export formats have specific restrictions on the format in which you

need to store your images. You should not have to worry about any aspect of image
data other than where the images reside on your disk. Manuscripts handles the rest
for you transparently: the export format, and manuscript templates even define rules

for formatting and exporting of figures that are automatically followed on export.

How to create a table

Manuscripts allows the users to create tables that are easy to fill in, and simple to
edit by adding or removing columns and rows.

There are three different ways to create an empty table. Each one of them requires
you to first place the text insertion cursor next to the spot where you want to insert

the table. After that, you can either:

Click the table figure in the toolbar.

Use the menu item Insert > Table.

User the smart gutter menu to the left of the paragraph that is in focus, before
or after which you intend to add the table. Click on the blue + symbol in it,
and choose Insert Table.

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 1. Table icon

2.

Figure 19: How to create a table in Manuscripts

The table that is created looks like this:

Figure 20: New table

To add or remove rows or columns, right-click any of the columns or rows and

choose the relevant option from the context menu.

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 Figure 21: Editing a table in Manuscripts

How to edit the table format in Manuscripts

You can change and edit the table format with the table styles inspector available on

the right hand side of the main window by clicking the Toggle Inspector button
(located in the lower right corner of the application window):

1. Inspector Toggle icon

2. Table Styles in the Inspector

Figure 22: Edit and change table styles in the Inspector

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How to create an equation

Manuscript includes a powerful equation editor that allows you to insert beautiful

equations using LaTeX.

Creating an empty equation

There are three different ways to create an empty figure. Each one of them requires

you to first place the text insertion cursor next to the spot where you want to insert
the figure. After that, you can either:

Click the equation symbol in the toolbar.

Use the menu item Insert > Equation in the main menu.
Use the smart gutter menu to the left of the paragraph that is in focus, before
or after which you intend to add the figure. Click on the blue + symbol in it,
and choose Insert Equation.

1. Equation icon

2.

Figure 23: Creating an equation

The equation placeholder that is inserted to the manuscript looks like this:

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 Figure 24: Equation placeholder

How to edit an equation

To edit an equation, click on the equation so that the equation editor pops up. Now

you can type or paste your equation using LaTeX, the equation will be rendered in
real time. If you are not familiar yet with the LaTeX syntax for equations you can find
out more here: https://en.wikibooks.org/wiki/LaTeX/Mathematics#Symbols

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 1.

2.

Figure 25: Editing an equation in Manuscripts

Manuscript file versioning: backups & change tracking

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In short, your Manuscripts documents are versioned for backup and rollback
purposes right now. It will also form the basis for change tracking features we intend

to build after 1.0.

The Manuscripts file format is fully version controlled and provides an "infinite"
history (all the way back to its beginning), at the level of each edit you make.

All edits you make to the manuscript go into an infinite version history already.
There is no user interface in the app yet to present this embedded version

history.
We intend to build some exciting features based on this version history after the

1.0 version: change tracking and snapshotting named versions of your

document.

Manuscripts also stores versions of the document that you edit on each device in a

separate, redundant backup and rollback intended version history.

You can view this version history with File > Versions > Browse Earlier
Versions.

With this file versioning feature you can roll back to earlier revision stored on

the device where you made that version.

This version history is a redundant backup mechanism for your data intended

to protect your data and allow going further back in time than what the undo

history of each app session allows.

However, you can never be too careful and we still recommend you to keep a regular
Time machine backup of your work.

Citing with and without the Papers reference manager

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Our recommended reference manager to use together with Manuscripts is Papers .

Papers includes a citation tool Magic Citations , which works beautifully with our
app.

However, Papers is just one option available to you amongst other reference

management tools like Zotero, Mendeley, EndNote, etc. You can use any of these
tools together with Manuscripts because it includes a super easy to use citation tool

that allows you to cite papers without directly requiring to interact with an external
reference manager. This is what the Manuscripts citation tool looks like:

Figure 26: Using the citation tool within Manuscripts

Importing bibliography data into Manuscripts

We support importing references from all the major reference file formats (Endnote
XML, RIS, BibTeX and more). All popular reference managers can export to at least

one of these formats. To insert references, either:

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 1. Choose File > Open in the main menu to open a bibliography file that

you exported from your favorite reference manager.

2. Choose File > Import in the main menu to import bibliography data into

your currently open manuscript.

3. Drag a bibliography file into the Manuscripts dock icon.

Configuring a citation keyboard shortcut

You can configure the keyboard shortcut to use for the internal citation tool with the
option available at Preferences > Editing > Citation Shortcut:

Figure 27: Configuring a citation tool shortcut in Editing Preferences

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Enjoy writing your next best work with Manuscripts

We hope you really enjoy writing with Manuscripts. Visit our forums for more
information and up-to-date answers to questions you may have:

http://support.manuscriptsapp.com. Please contact us via

support@manuscriptsapp.com if you would like to talk to us or hit issues with the

app. We would love to hear what you think of Manuscripts and how we can make it

even better. Enjoy!

The Manuscripts team

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