December 2010 Archives

Desktop Sente, on the other hand, is easier to update, so we have just released Sente 6.2.4 with a number of import changes:

-- We fixed a problem with PDF annotation when a reference had more than one PDF attachment.  The previous version made it appear that the annotation was sometimes being applied to all attached PDFs, rather than just the appropriate one.

-- We fixed a bug that sometimes caused updated references to disappear from smart collections in synced libraries.  The disappearance was temporary (they returned under several conditions, including relaunching the app) but disconcerting.

-- We fixed a problem with the note editor not accepting input sometimes after the deletion of a note.

-- We fixed a problem where tapping on comment, after selecting a previously highlighted passage, would not do anything.  Now it creates a comment, as expected.

-- We have made the PDF highlighting colors a bit darker, especially when exporting PDF with attachments to be read in Preview.

We have a number of other high priority issues that we will be looking at in the coming days, but we wanted to get these changes out to users.

Michael

For people who are interested in reading a bit about the application, but who may have missed some of my recent blog posts on the subject, here is list of short articles highlighting some of the important features of the new app:

Sente for iPad is $19.95 in the app store.

We have just released Sente 6.2 with a number of important changes.  I wrote another post about changes to the PDF view.  This post is about the new ability to directly import libraries from:

In essence, the process is the same for handling libraries from each of the above programs.

{your home folder}/Library/Application Support/Firefox/Profiles/{some folder}/zotero

For Mendeley, the folder is typically:

{your home folder}/Library/Application Support/Mendeley Desktop

And for Papers:

{your home folder}/Documents/Papers

In each case, you are selecting the folder that contains both the database file and the sub-folders with the attachments.

After you select the appropriate folder, the entire contents of the library, including attachments will be imported into the current Sente library.  The original library will not be modified in any way.

Once you have the library imported into Sente on the desktop, you can easily install it onto the iPad using iTunes, for use with either Sente Viewer or the full version of Sente for iPad. (The instructions for this can be found in the Help material in both versions of the iPad application.)

If you make a synchronized copy of the library before installing it on the iPad, then the desktop and iPad copies will stay in sync with one another automatically.  Obviously, the Sente versions of these libraries will not stay in sync with the original library (in Mendeley, Zotero or Papers).

Note that this entire process can be done using desktop Sente in Demo mode, so if you are not currently a Sente user but you want to try out the new iPad apps, you can install desktop Sente as a demo and install Sente Viewer for iPad for free.  You will not be able to sync a library with more than 50 references in demo mode, but other than that, everything will work.

In Sente 6.2, the attachment view has been completely rewritten using the same technology that we use on the iPad app.  The user interface is new, as is the way in which everything works under the hood.

In terms of the interface, we have taken a cue from the iPad and removed some of the controls from the toolbar above the attachment view.  The attachment and autolink buttons remain, but some of the annotation controls have been removed.  All that remains are the Text vs Region selection buttons.

One improvement is that it is no longer necessary to open a single reference tab to highlight a PDF.  

To highlight a passage, simply click-and-drag to select the text.  A popover window (à la the iPad) will appear with the commands used to apply highlighting and create notes.

To highlight the text, select the desired color and click on Highlight.  To create a note with a comment, select the color for highlighting (or the "no color" option for no highlighting) and click on Comment.  To create a note with the selected text as the quotation, do the same, but click on Quote.

One difference between the iPad and desktop apps right now is that in the desktop app, all notes appear in the notes editor, whereas on the iPad you can set any individual note to be shown only in the PDF.  We will bring this option to the desktop in a future release.

Another difference is that it is only possible to create notes that include images on the desktop -- this is not yet supported on the iPad.  Notes creates with images will display correctly on the iPad, but they cannot be created there (yet).

To change the color of highlighting, just click on the passage, select the desired color from the popover, and click Highlight.

Region annotation works similarly.  Click-and-drag to select a region, choose the color and click Highlight (or one of the other buttons).

If you have been using Sente to annotate your PDFs for some time, it is important to understand that the underlying model has changed completely in Sente 6.2.  Annotation created in prior versions of Sente, or in other PDF tools, will be displayed, but not editable, in Sente 6.2.

Highlighting created in Sente 6.2 is not stored in the PDF itself -- it is stored in the library database.  This change has several very positive effects, notably on syncing.

There is a new command in the attachment view for exporting a PDF.  If you click on the title of the PDF, a menu appears with the Export option and two sub-options: With Annotations and WIthout Annotations.  (As should be obvious, if you use the Reveal in Finder option to get to the PDF file itself, and open it in some other PDF viewer, it will not include the highlighting added in Sente 6.2 or later.)

This is a big update to a critical component of desktop Sente.  We know that we have left a few loose ends, but we think that 6.2.0 is solid enough for regular use and we did not want to delay any longer (given that the iPad app requires Sente 6.2).  If you have any specific suggestions for improvements in this area, please let us know because we are likely to be spending more time on this part of the app in the coming weeks.

Like all recent versions of Sente, Sente for iPad supports multiple notes per reference.  This makes it easy to create "atomic" notes, or notes that make a single point, as opposed to one long note on each reference.

In Sente for iPad (and Sente 6.2, which is about to be released), this is taken a step further.  In these new versions, each note can appear either only within a PDF, or also in your list of notes for a reference.  Which of these options you will want will depend on your intentions.

Suppose, for example that you are simply reading a paper, highlighting some passages of interest, and you want to record some questions you have as you are reading.  These may be best handled as PDF-only notes.  They will show up in your PDF as little yellow sticky icons, which can be tapped to pop open a larger note display containing your questions.  This kind of note will not show up in the list of notes for the reference and cannot be seen anywhere other than within the PDF itself.

On the other hand, suppose that you are gathering background material for your own work, and you find something in a paper that you may want to refer to later in your own writing.  In this case you would probably want to create a full note (possibly including a quotation) instead of a PDF-only note.  When you do this, you will see the same display in the PDF view as in the first case, but when you are looking at the single reference view, you would see the complete note, including any quotation and your comments.  You will also see these notes when you format a citation using any bibliography format that includes notes, for example for printing or exporting.

In the Sente for iPad interface, when you highlight a passage and select Quote, it assumes you are creating a full note that you want to see in your list of notes for the reference.  If you select Comment, Sente will choose the option that you used the last time you selected the Comment command.  You can change the setting on any note at any time using the button in the top-right corner of the note editor.

In the Sente database, each note includes a title, page number, quotation, and comment.  When you specify a note as PDF-only, all of these fields are hidden other than the comment field.  The screen shot below shows a note set to display in "PDF and Notes."

In upcoming releases, we will be adding the ability to jump from a note in your note list directly to the spot in the PDF where the note was created. The support for this is already in the database, but the interface did not make the cut-off for the first release.  And there will be a number of other, note-related additions in the coming months; we think this is an important area for the future.

Finally, the same options that you see here will be present in desktop Sente 6.2, which will be available shortly.

The command is accessible from the single reference view in the top tool bar.  When you tap on the Compose button an email sheet slides up containing the draft message.  Enter an email address, adjust the contents as desired, and press Send.  (The attachments appear at the bottom of the message and can be deleted if you do not want to send them.)

And, yes, this feature will be added to desktop Sente in the near future!

As most of you will know, when you create a synchronized copy of a library, you have to specify when attachments should be downloaded from the sync servers in the new copy.  You choices are (a) as soon as they are available, or (b) on demand. 

If you select "as soon as available" the synchronized copy will attempt to download every PDF from our server as soon as they are available.  If you select "download on demand" the synchronized copy is told about each attachment, and a placeholder is added to the appropriate reference, but the file itself is not actually downloaded until the user requests it.

Here are three important reasons why you should consider using Download on Demand for iPad libraries:

What does Download on Demand look like?  Below is a screen shot of a single reference view with an attachment that has not yet been downloaded.  The "No Local Copy" box is telling you that there is an attachment available, but it has not yet been downloaded into this copy of the library.  To download the attachment, just tap on the placeholder icon; a short while later the placeholder will be replaced with the thumbnail of the PDF, indicating that the file is present locally.

I should note that regardless of the settings for when attachments should be downloaded, you can always press-and-hold on the attachment icon to get a menu with options for deleting the attachment from the library entirely, or for just removing the local copy.  If you remove the local copy, the placeholder returns, letting you download the file again from our server, should you ever need it.

So, what is the downside of using Download on Demand?  There are really only two that I can think of.  First, you will not be able to download a new attachment onto your iPad without an Internet connection.  All your previously downloaded attachments will be there, but new ones must be requested.  (You do not need to be able to contact any other copy of your library -- just our servers.)  Second, there is a brief delay for the download before you can begin reading.  In most cases this delay will be pretty brief, but large files on slow network connections can be more of a problem.

Here is what I would recommend.  Think about your likely usage pattern.  Are you likely to use Sente for iPad several times a day (so it is always up-to-date) or do you often need access to random PDFs in your library when you are in locations without network access?  If so, then you may need to set the library to download attachments as soon as they are available.

On the other hand, if you expect to use Sente for iPad only every few days, and you expect many PDFs to first enter your library on your desktop copy of Sente, then you should strongly consider setting up your library to download attachments only as needed.  Otherwise, every time you launch it, it will start downloading a lot of data that you may never need, and this will slow everything down that you are trying to do.

We were trying to achieve several goals in our design for PDF annotation.

First, we wanted the interface to be clean and unobtrusive.  There are some seriously ugly PDF annotation tools out there, and we did not want to be one of them.

Second, we wanted it to be easy to learn and easy to use (of course!).  

Third, as in desktop Sente, we wanted PDF annotation to be tightly connected with note taking. Of course, this means including the ability to add notes to a PDF, but it also means (optionally) adding notes to your Sente notes, which are visible outside of the PDF view.  This is not something that other PDF tools support.

Fourth, we wanted it to support a number of common usage patterns. This is where the UI design got tricky.  Some people like to highlight passages in documents but they are not interested in adding comments or saving quotations for later use.  Some like to add comments inside the PDF as an aid to remembering their thoughts on specific passages.  And some take copious notes, often with quotations, for use in their own writing.  We wanted Sente for iPad to support each of these common patterns in such a way that the user never feels as though they are fighting with the software.

Here is a brief overview of what the PDF annotation and note-taking interface looks like in Sente for iPad, starting with the PDF view showing some text highlighted and a comment marker.

To initiate highlighting, you can either press-and-hold somewhere in the text, or tap on the highlighter icon at the top of the screen and swipe your finger to select some text.  Either action places you into Annotation Mode.  

When you have text selected in Annotation Mode, you will see an edit menu that includes:

The Comment and Quote options both bring up a note editor.  Notes created here can be either internal to the PDF, or they can also appear in your list of Sente notes for the reference.  If you select the Quote command, Sente assumes that you are creating a full Sente note and it automatically adds the selected text to the note as the quotation.  If you select Comment, Sente creates either a PDF-only note or a full Sente note, depending on which you created the last time you used this command.  You can change the type of any note at any time.

Here is the note editor for a full Sente note (when editing a PDF-only note, the body of the editor is replaced with a single text field for the comment):

When the note editor is closed, the PDF is then displayed with the text highlighted (if a color had been selected in the note editor) and either a "note" icon or a "note-with-comment" icon is displayed in the margin of the document.

Tapping on a note-with-comment icon will bring up a small sticky with the contents of the users comments in it, which can be dismissed by tapping anywhere else on the screen.  This also brings up a new edit menu that can be used to make changes to the saved note.

I will discuss Sente notes in a later post, but just to anticipate that discussion, here is a shot of the single reference view after taking some notes in a PDF.  In particular, notice the section of the summary entitled NOTES.