Bookends for iOS User Guide


What is it?


Bookends for iOS (here called just Bookends unless a distinction with Bookends for Mac must be made) is reference management software for your iPad, iPhone, and iPad touch. You can use it as a standalone app, or pair it with Bookends for Mac, syncing the contents of your mobile and desktop devices via Apple’s iCloud Drive.

An unregistered version of Bookends for iOS is limited in the following ways: searches return a maximum of 20 references, only 50 references can be stored in your local database, PDFs that you annotate on the iOS device are watermarked, and you will see ads. To have full access without these restrictions and no ads you must purchase Full Version from within the app ("in-app purchase").

InAppPurchases

In addition, Bookends has an option for Pro Features Yearly, which at this time means Cloud Sync (details below). This can be bought with a in-app purchase as a yearly-renewable subscription. The subscription can be auto-renewable, and can be managed in iOS -> Settings > iTunes & App Store > Subscriptions. The subscription might renew if it isn’t canceled more than 24 hours before the renewal date.

A few terms…


Bookends creates a library on your iOS device that contains
references (or reference metadata, meaning details about the works such as the author, place of publication, etc.) and, optionally, attachments such as pdfs.

References can be entered added to your library in three ways:

• Manually.
• Internet search and import.
• Sync with Bookends on the Mac.

Each reference has a Type that identifies the kind of publication. The default Types are:
• Artwork
• Audiovisual material
• Book
• Book Chapter
• Conference proceedings
• Dissertation
• Edited book
• Editorial
• In press
• Journal article
• Letter
• Map
• Newspaper article
• Patent
• Personal communication
• Review
• Internet
• Unused (through Unused20)

Many of the fields in the Unused range will have other labels, depending on the Type, such as Edition, Translator, ISSN/ISBN, DOI, PMID, and others appropriate for particular Types.

The Types correspond to those in Bookends, and can be changed in Bookends only by syncing with Bookends. The factory default Type is Journal Article, but you can change this in Settings.

You can organize your references into
groups that you name and can quickly recall. Static groups contain references that you explicitly add. Smart groups contain references that meet criteria you specify (such as a word in the title, a keyword, a specific author, a date of publication, or all of the above), and the contents can change dynamically as references are added, deleted, or edited.

Each group must have a unique name.

Multi-library support


Tapping on the top right button ("…”) will show a menu with actions. "Switch Local Library” should be used to change your current library to any that already exist, to create a new local library, or to download a new library from the cloud.


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Multi-screen support for iPad


Here’s an example of Bookends displayed next to Safari

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Display of References


References are viewed in two ways: in a list or in abstract view. Note that for the iPad, if the orientation is horizontal you must tap the Library button at the top left to see the reference list. You can add additional fields to view in the abstract view in Settings.

List


group_all



A summary of the metadata for each reference is listed. A (tappable) small paper clip appears on the right if the reference has one or more attachments. If you sync your library with Bookends, labels (applied in Bookends) will appear as a vertical bar of color to the left of the reference.

Tap the Manage button to delete (no limit) or email (limited to 20 at a time) multiple selected references at once.

To see the abstract view, tap on the reference. To bypass the abstract display and see the attachment on the right, tap on the paper clip (if available).

Tap in the search field to find specific references in the list. You can limit searches to Title, Abstract, Author, or All (All means Bookends will search all of these fields). Searches are case-insensitive. If your library is very large, searches can take seconds, which makes the live search unwieldy. To disable live search, start the search text with a space. The search will not being until you tap the Search button. For example, search for

“ einstein”

(without the quote marks).

Author searches distinguish between first names and surname by the presence or absence of a comma: “E Jones” or “Jones, E”. Note that if you search for the initial of the first name, all authors with first names beginning with that letter will be found.

Abstract


iPhone/iPod touch

detailedreference

iPad

ipaddetailedreference



At the bottom of the abstract you may see tappable links to the reference on-line (e.g. a PMID or DOI).

The abstract view lets you quickly access ratings, thumbnails of attached pdfs, and notes (notecards, shown in a note stream). Tap on the rating bullets/stars to add/edit the rating.

Notecards are shown in yellow, and sync with Bookends notecards. Tap and hold on any note to enter the editing mode for all notes at once. Note text separated with 2 new lines will be split into separate notes.

Tap on the pdf thumbnail to show the enlarged (normal) view of the pdf.

If you tap on the attachment icon (the paper clip), you will be able to annotate the pdf, show the table of contents, and search for text in the pdf. Here is an example of the options you have when annotating: highlight, strikethrough, underline, add text, comment, draw):

ipadannotateattachment


attachment annotatons


Annotations made in Bookends will be shown in Bookends if “Use WebKit to display pdfs” is checked (in Bookends).


Citations



Citations can be created from the reference view via ‘Citation’ link or Open In menu (marked red in the screenshot). Tap on the kind of citation you want: temporary citation (to be used by Bookends for Mac when scanning) or the final citation. You can paste the the copied citation into other apps, such as Pages or Mellel.

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You can selection the citation format you want to use, and the delimiter for temporary citations in Settings


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You can choose a default citation style from the styles list . Tap on the “+” button to add more citation styles to the list.


CitationsInternalImportZoteroSource

The Zotero Style Repository web page will be shown where you can tap on any style. The first tap on the style name will show a formatted example. Tap on the style name again and Bookends will ask you if you want to import this style.

CitationsInternalImport

Note: CSL files, which contain the formatting instructions, can be imported from external sources like Safari or an email. You can email a CSL file to yourself and after tapping on it, iOS will offer to open it in Bookends.


CitationsExternalImport




Library Toolbar


Regardless of which iOS device you are using, there will be a toolbar that lets you work with the reference.

toolbar-buttons-description


If the reference has a link to the article on the Web, tap this icon to open the browser view and access the Internet content (tap the Abstract icon to return to that view in Bookends). If you have access privileges, navigate to the pdf of the article (if available) and the paper clip icon (Download PDF) will become enabled. Note: neither the pdf nor the reference metadata will be imported to your library unless you tap the Import icon. Tap the Import icon to import the reference (and pdf, if you downloaded it) into your personal library. You can import to a specific group by tapping and
holding the Import button. A list of static groups will appear, and you can choose the one to which the new reference will be added.

Tap Attachments to see the contents of attached files (typically pdfs). The image is disabled if the reference has no attachments. The pdf will open in full screen.
Organize Groups lets you add or remove the reference from you static groups (including Trash). You cannot remove a reference from the group All (except by moving it to the Trash).

Tap the Share button to send the reference to one of several destinations.

reference share option

Tap Mail to send the reference to yourself or others. Note that the emailed text can be formatted for readability (formatted display) or tagged for importing into reference management applications like Bookends or EndNote (modified RIS)—configure this in Bookends Settings. If you have downloaded the pdf, you’ll have the option of sending that as well.

You can send a tweet containing the title of the paper, prefixed with the text you entered in the Bookends Settings under Other (see section on Settings below).

social section twitter and facebook


The Share button will also appear above a pdf you’re reading in Bookends.

attachment-oprn-in

With it you can export pdfs to other apps for reading or markup, then import them back into Bookends. When you tap on the Share icon on the right above the pdf you will be given the opportunity to email the pdf, open it in another app that handles pdfs, or print it.


If you send the pdf back to Bookends, you will be asked if you want to attach the named pdf and be offered the best matching reference. Usually, that will be a reference with a pdf of the same name. However, the pdf may have been renamed by the annotation software, or it could be a pdf that had never been in a Bookends library. You will be offered these choices:

find-reference-to-attach-320


If Bookends has identified the correct reference, click OK to replace the older pdf with the newer one. If the annotation app changed the name of the pdf, you can rename it to the original and Bookends will replace the old with the new. You can also attach the pdf to another reference or a new reference. Here is a short walkthrough using iAnnotate as an
example.

You can import RIS files (containing reference information) exported from any other app (e.g. Safari, Mail, etc.). Here’s an example of an RIS file being exported from Safari:

ris-export-from-safari


and imported into Bookends:

ris-import



Tap the edit icon to allow manual editing of the reference’s contents. This is covered in the section Adding References and Groups Manually.


Adding References and Groups Manually


This is the top portion home screen (items will change when groups are added)

library-view

To add items on the iOS device, use the + button. You can also add items by syncing with Bookends (see below).

The + Button


Tap this button to manually add references or groups to your Bookends library.

on the plus button

Reference


new reference


You can assign a rating of 1-5 stars, set the reference Type, and add information to the fields that constitute a reference. Note that name fields (e.g. Authors) ask you to enter each name one at a time. To ensure that the names sort correctly, they must be entered surname first, separated with a comma:

Hutchinson, RJ
Edgars, Susan Wright
Simons, MM, Jr.

If you sync with Bookends, you may find that institutional names end in a comma:

The American Council on Diet, Health, and Fitness,

This ensures that Bookends will not try to parse the name when it creates a bibliography.

You can manage attachments, typically pdfs, here. Tap on the name of an attachment and you’ll see an option to Rename or Delete it from your library.

attachment rename


Static Group


You will be prompted for the name of a static group. Adding and removing references from static groups is discussed below.

You can edit the name of the static group by pressing the name for 1 second.


Smart Group

new smart group


Once you have entered a name for the new smart group, you must enter the criteria that Bookends will use to search for members of the group. Fill in the search options (field name, conditional operator, and the text). The conditional operators are

contains
does not contain
is
is not
starts with
ends with

Here is an example entry:

new smart group example


You can edit the name of the smart group and change search criteria by pressing the name for 1 second.

Removing references from the library


You can delete references from the list in two ways:

Swipe to the left and press the Delete button.

delete reference


Tap Manage, select the references you want to delete, and tap Delete.

delete a few references


Note that when you delete a reference it is not actually removed from the library, it is placed in the Trash. You can tap on the Trash icon at any time and rescue or permanently delete any references it contains.


Using Static Groups


There are two built-in static groups that you cannot alter: All and Trash.

Tap on All to see a list of all references in your library.

Tap on Trash to see any references you deleted. You can remove the reference from the Trash or permanently remove it from your library.

Any static groups that you have created (or imported from Bookends) will appear in this list.


Using Smart Groups


There are three built-in smart groups: Authors, Attachments, and Last Modified.

Tap on Authors to see a sorted list of each author found in the library. Tap on a name to see a list of all references authored by that person.

Tap Attachments to see a list of all references that have one or more attachments.

Any smart groups that you have created (or imported from Bookends) will appear in this list.
Note: The smart groups created in Bookends for iOS are not recognized by such in Bookends for Mac and vice versa. As a result, when smart groups are imported from Bookends they become static groups in Bookends. However, the group members may change when next synced with Bookends if the members have changed in Bookends. A small picture of the Bookends icon will be displayed next to smart groups imported from Bookends, as shown in this example:



Last Modified shows the last 25 references that have been added or edited. This includes references added or changed because of a sync with Bookends.

Sorting Group Contents


You can sort the contents of a group by clicking on the Group name, then Edit. At the top of the screen is the field the groups are sorted by (in the example, Date Added).

sorting group contents


You can change the sorted field by tapping on it:

sort by fields



The direction of the sort (ascending or descending) is shown next to the name of the field, and you can change from one to the other by tapping.

Online Search


You can search for references in PubMed, Google Scholar, JSTOR, Web of Science (requires ip authentication), arXiv, and the Library of Congress. All searches provide a simple search option

online search



and a Recent Searches option




PubMed Advanced Searches



Tap on Advanced Search to construct a boolean (and, or, not) search and restrict the results by date of publication, publication type, the availability of full text, etc.

advanced-search


The maximum number of results returned for each search is configurable in Settings (10, 20, 40 or 60). If there are more hits than that, you’ll see a message at the bottom of the found references like this



This is an example of a reference found on PubMed with an iPad

ipad-pubmed-searcg-results


The full reference view is displayed on the right. If you find a reference that you have already imported into your own library, it will be displayed in yellow.
Bookends will display a badge that tells you if the article on PubMed is linked to the full text (HTML or a pdf), and if the full text is available for viewing at no cost (Free Full Text). Note that this information is supplied by PubMed and in some cases is incorrect.

full text indicator


arXiv Searches

Use the fast typing bar to create advanced search queries that include boolean operators (AND, OR, NOT), specific arXiv searchable fields tags (ti, au, abs, co, etc.), and/or limit your searches by subject by choosing any from the list of available subjects by tapping on “cat:all”.

arxiv subjects

Use parentheses ‘( )’ to group boolean expressions and quote marks to search for an exact phrase.

Here is an example of advanced search for an article with the words atom and physics in the Title, and authored by Friedman:

arxiv advanced search


Note: it’s not necessary to add ‘AND’ between tags, the previous example returns the same result as: ti:atom physics AND au:Friedman

Google Scholar Advanced Search

BOTGSAdvancedSearch1s

BOTGSAdvancedSearch2s



Cloud Sync


You can sync the contents of Bookends for iOS with the cloud, from where they can sync with other iOS devices or with Bookends for Mac.

Start Cloud Sync by tapping on the top right button ("…”) or tapping “Sync” under the “Bookends” section on the main screen.

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After the first successful sync the library will be synced automatically every time the app is launched and closed. In addition, you can sync manually any time by tapping the … button and selecting Sync Now.

After every successful sync of references, Bookends will start syncing attached files, usually PDFs.

Sync of attachments is based on iCloud Drive. All files must be located in the iCloud Drive -> Bookends folder. Note that if on the Mac you store your attachments outside of the iOS sync folder, for example in a Dropbox folder, Bookends for iOS won’t be able to see them. Therefore, if you intend to sync with Bookends for Mac you must enable iCloud Drive on your Mac in System Preferences. It will appear in the Finder window, like this

Pasted Graphic 1


To create the Bookends iOS sync folder on your Mac, you must perform a few extra steps.

In Bookends for iOS:
• The Bookends for iOS library should be synced with cloud.
• Download any reference with attachments from any online source you have privileges for (e.g. PubMed or PubMed Central) in Bookends for iOS. Import this reference to your library. 
• The Bookends folder with this new attachment should be created by macOS on every one of your Macs.

In Bookends for Mac:
• In preferences, set your default attachment folder to iCloud Drive.

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Note that the Bookends iCloud Sync folder will become visible only when it has content. So it is important that you import a PDF into your Bookends for iOS library or attach one to your Bookends for Mac library. The folder, once it has content, will have the Bookends logo on it:

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Important note: Do NOT create the iCloud Drive Bookends folder yourself in the Finder. If you do it will not have the Bookends icon and it will not be recognized by Bookends for iOS. You must let Bookends create the folder for you as described above.

If you have pre-existing attachments on the Mac, you must go to the Finder and move them from their current location to the Bookends iCloud sync folder (the one with the Bookends icon).

Troubleshooting tip: Sometimes the Bookends sync folder will not appear in the Mac iCloud Drive even after completing the above steps. You may be able to fix this by taking these steps:

1. Turn off iCloud Drive in iOS Settings.
2. Close Settings.
3. Open Settings and turn iCloud Drive on.
4. Let Bookends sync.

Currently, Bookends for iOS will download files from iCloud Drive -> Bookends folder if they are 50 MB or smaller.

As files are downloaded in the background by iOS, it may take some time until you see the attachments in Bookends for iOS.

Wi-Fi Sync References and Attachments With Bookends For Mac

Note: We recommend that most users use Cloud Sync to share data between iOS devices and Bookends. Wi-Fi sync is useful for a subset of users, however, because it lets you manage large PDF collections and selectively sync only certain groups.

You can wirelessly sync the contents of your Bookends for iOS libraries with libraries used by Bookends for Mac. The sync is bidirectional, meaning that changes made in either library will be communicated to the other, the dates of modification being used to determine the sending and receipt of references and attachments.

Bookends uses Bonjour technology to detect Bookends running on devices on the same local network.

Below are steps that you take to sync Bookends for Mac with Bookends for iOS.

1. In Bookends for Mac Preferences, iOS tab, “Look for Bookends/PubMed On Tap on iOS devices” should be checked.

2. Launch Bookends for Mac and open a library.

3. Launch Bookends on your remote iOS device. You must be connected to the same local network as Bookends on the Mac. If you are not there can be no communication between the two.

4. In the Bookends for iOS home screen you will see an option to Sync.

LibrarySyncCell

5. When you tap on Sync for the first time you will be asked to add a (Bookends) library.

Screen Shot 2013-10-18 at 11.25.42 AM


When you tap Add Library, look at your Mac and you should see that Bookends is displaying the name of the iOS device at the bottom of the Groups pane (My iPad in this example).


If you do not see the Devices list in your Bookends library window at this point, it means that your iOS device and Mac are not on the same subnetwork. Please see the troubleshooting section for help.

6. A passcode screen will appear on the iOS device screen:

bot sync passcode



7. In Bookends, select the device in the Devices list (My iPad in the example) and a dialog will ask you to enter the passcode showing on your iOS device.



8. When you click Link, the Bookends display will update:

BookendsWiFiSync


Note: you can change the Bookends library you are connected to at any time by tapping the Change Library button. If you want Bookends to “forget” that the library was linked to a particular Bookends for iOS library, in Bookends go to File -> Synced iOS Device Info, select the device from the subsequent dialog, and delete it with the - button.

In Bookends for Mac you will see the confirm dialog, something like this:

syncdialog


Sync all references or just selected groups

If you have a very large Bookends library, you may want to limit the number of references transferred to the iOS device to just those you want to take with you. You can choose to select static and/or smart groups.



The contents of both group types will be transferred, but they are handled a bit differently on the iOS device. Static groups fully sync and changes to members of the group on your Mac or on the device will be bilaterally synced. Static groups will sync between Bookends for iOS and Bookends for Mac even if you sync All references.
Smart groups are different, because the searches used to generate them differ between Bookends and Bookends for iOS. Therefore, when syncing a smart group, Bookends will send the contents to Bookends for iOS, but there will be no corresponding transfer of references from Bookends for iOS to Bookends. Smart groups transferred from Bookends to Bookends for iOS will be updated on the device if the members change in Bookends (i.e. if references are added or removed from the smart group). Smart groups will be transferred to Bookends for iOS only if you have selected “Selected groups” and have checked one or more smart groups. The more smart groups you check, the longer the sync will take.

Attachments
Check this checkbox if you want attachments (typically pdfs) synced between devices. To prevent the transfer of very large documents that may take a lot of time, you can limit the attachment size:

Pasted Graphic 2


• If a sync is interrupted, don’t worry. It will resume at that point the next time you sync.
• Only direct attachments will be synced. This means that if you have attached a folder to a reference Bookends, its contents will not be synced between Bookends and Bookends for iOS.


9. Tap Sync to begin the process. A dialog in both Bookends for iOS and Bookends for Mac will inform you of the progress, and there is a Cancel button if you want to stop.

Note: Bookends and Bookends for iOS keep track of libraries by an internal unique identifier, not the library name. Therefore, if you change the name of the library (for example, after a Rebuild or Repair), do not perform a Change Library the next time you sync with Bookends for iOS, sync as you normally would. If you do a Change Library, references in Bookends for iOS and/or Bookends will be duplicated.

Troubleshooting Wi-Fi sync



The iOS device does not appear in Bookends when you first sync with a Bookends library (Add Library).

If you do not see the Devices list in your Bookends library window at this point, it means that your iOS device and Mac are not on the same network. If for some reason you cannot have both running on the same subnetwork, you can create a computer-to-computer network on your Mac:

1. Click on the Airport icon at the top of the Mac screen.
2. Select "Create Network" and give it any name.
3. Connect your iOS device to this network. Go to Settings > Wi-Fi, select the network and enter the password you selected on the Mac.
4. Now try to Add Library again.

The iOS device can be connected to Bookends, but no files are transferred on Sync.

This may occur if you use a firewall on your Mac. You can circumvent this problem by adding Bookends to the list of apps allowed to make an incoming connection, or turning off the firewall, in System Preferences.

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Settings



BOTSettingsScreen



Reference Options

Set the default reference Type for manually-created references or imported references whose Type cannot be determined.

If “Delete moves to Trash” is off, a deleted reference will be removed from the library immediately. If it is on, the reference will be moved to the Trash, from which it can be later recovered or permanently deleted.

You can add fields that are shown in the abstract view:

Pasted Graphic 1


Tap + to add a field. Tap - to remove a field. You cannot remove the default fields Source, Title, Authors, or Abstract.

Drag the three-bar icon on the right to change the order in which the addition fields are shown.

Search Engines


Searchable sites shows a list of all the search engines Bookends supports, and you can choose which ones you want shown (for example, if you work in the humanities, there may be no need to show PubMed). You can also reorder the list shown in Bookends by tapping the Edit button and dragging the three-bar icon on the right.

bot searchable sites


In the PubMed settings, indicate if Bookends should check for full text, and how the returned list of references should be sorted (by date of addition to PubMed or date of publication).
The number of references to retrieve with each pass (10, 20, 40, or 60).

Export Options


You can enter a default address for sending email. You can also tell Bookends to arrange the text in the email in a human readable form, or modified RIS (which can be imported into other reference management apps using their RIS filters).

University Library Proxy


Bookends supports the popular EZProxy web proxy server used by many university libraries. If yours is one of them, you can enter the URL of the proxy server (you may need to contact IT support to supply this). The URL is entered like this example:

http://ezproxy.princeton.edu/login?url=%@

Bookends will replace the %@ with the URL of the web sites you use.

Local Library


If your library is very large, you may want to disable Live Search to avoid the delay that occurs whenever you enter a letter. If you disable Live Search, the search will only be performed when you press the Return key.Empty Library will remove all references, groups, and attachments from your library. This should be used with caution and cannot be undone.

Autosync applies to Wi-Fi sync, not cloud sync. When Autosync is ON, Bookends for iOS syncs to Bookends for Mac without waiting for the confirm dialog in Bookends. If you have Autosync enabled and want to change options in the confirm dialog (e.g. to sync particular groups rather than all references), turn Autosync OFF. After changing the settings in the Bookends confirm dialog and performing a sync, you can enable Autosync again in Bookends for iOS.

Do Not Backup Attachments is used only for attachments stored locally, not for attachments that are synced to the iCloud folder during Cloud Sync. If you have a large number of attachments and don't want them being backed up by the system, turn this setting ON. Note that if you choose Do Not Back Up Attachments, on restoring your device from backup your attachments will be missing and should be downloaded from Bookends for Mac.

Empty Library removes all data and attachments from the library in use and removes the attachments from the device. Attachments in the iCloud Drive folder (synced) will be undisturbed.

Other


The Twitter setting lets you tell Bookends what text should be used to prefix a tweet (e.g. “Interesting article”, “Look at this”, etc.). Note that these characters count towards the 140 limit.