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Safari 5: Proceed with Caution

By Michael on June 13, 2010 10:57 AM | 4 Comments | No TrackBacks
Apple has recently released the first public version of Safari 5 with some cool new features, which make it very tempting to download and install.  But I would like to recommend caution before you click on that download link.

We are aware of several problems with Safari 5 -- some of which can break critical features in Sente.   And it is likely that there are more problems yet to be discovered.

The biggest problem we have seen is that installing Safari 5 on systems running OS X 10.5 will simply break web browsing in Sente.  Attempts to load many web pages in Sente's embedded browser will cause Sente to crash.  It does not matter whether you are actually running Safari 5, just whether you have installed it or not.  There is no approved method for uninstalling Safari 5, so you will be stuck until you either upgrade to OS X 10.6 or Apple fixes the bug.  We are not aware of anything we can do to fix this problem.

The problem is that installing Safari 5 is not like installing a new version of Firefox or any other browser.  Installing a new version of Safari changes OS X's internals for web access, the very code that Sente and many other applications depend on.  

I have some confidence that Apple will address the problems with Safari 5 quickly, but it seems that their public debates with Adobe may have lead them to rush this out the door without as much testing as it deserves, given how critical Safari and WebKit are to real world users.

I am sure that many of you will have found this post only after installing Safari 5 and experiencing problems.  The best that I can offer for the problems that we are aware of is to consider upgrading to the most recent version of OS X.  Even if this does not solve the problem, it makes it far more likely that you will see a quick fix from Apple.

Michael

Sente 6.1 Beta, Round 2b

By Michael on March 4, 2010 4:18 PM | 4 Comments | No TrackBacks
We are ready now to begin general beta testing of Sente 6.1 and we welcome the participation of anyone who cares to help.

The complete list of new features for Sente 6.1 is provided below, but the big changes are:

  • User-specified attachment filing and refiling.  You can now decide how your attachments should be filed and named, even when placed in the library bundle.  Further, it is easy to change your mind on the details (at least until synchronization is turned on).

  • Synchronization of attachments filed outside the bundle.  It is now possible for Sente to automatically synchronize attachments files outside the library bundle.  We still strongly encourage people to store their attachments within the bundle for many reasons (like how easy it is to move a complete library from one place/computer to another).

  • Ability to delete PDF annotations.  You can now remove annotations (e.g., highlighting) in a PDF within Sente.

Unfortunately, supporting synchronization of attachments with user-selecting filing requires some changes to the Sente 6 library.  This means that when you first open a Sente 6.0 library in Sente 6.1, you will be asked for information on just how the update should be performed.  Specifically, Sente needs to know how attachments should be filed, and it will apply the specified rules to all existing attachments.  This means that existing attachments are likely to be moved during the update.  Please take seriously our statements about creating a complete backup before updating your library!

One more important issue to be aware of is that synchronized libraries will have synchronization turned off as part of the update from 6.0 to 6.1.  This is necessary to support the new-style attachment filing options.  Unfortunately, this means that you will need to re-start synchronization from scratch once you are happy with your attachment filing strategy.  We know that for large libraries, it can take hours for the initial sync to complete, but we could not find a way around this requirement.

So, if you are willing to try the beta release of Sente 6.1, here are the instructions for doing so.  Please give us your feedback on the software as soon as possible, so that we can release it to everyone soon.

Michael



Sente 6.1 Beta Instructions -- PLEASE READ BEFORE RUNNING THE SOFTWARE


The current beta can be downloaded here:


http://thirdstreetsoftware.lunarpages.net/Sente-6.1.2.zip


PLEASE NOTE: launching this version of Sente, and doing a Library Update (which you must do to run the beta) may result in all of your attachments being moved!  Do NOT proceed with the beta if you are not prepared to first make a complete backup of your library and attachments!


We have done a lot of testing on this beta, but your library may be set up in a way that we have not been able to test and so you may encounter problems that we are not aware of (that is why this is BETA software!).  We appreciate your help in testing the new release, but please be aware that it could cause problems for you that would not be easy to recover from if you do not have good backups.


Sente 6.1 is not entirely backwards compatible with Sente 6.0, so it is important to proceed carefully during the beta test period.  To use this beta version:


0) Review the release notes for Sente 6.1 below

1) exit Sente

2) make a copy of the library you are going to open in Sente 6.1 -- you will be using the copy for testing

3) make a backup of all of your data, including PDFs, because Sente 6.1 may move your attachments and if something goes wrong, you will need to restore from backup

4) select the copy of your library in Finder and control-click (or right-click) on this file, and select Open With > Other...

5) select the beta copy of Sente 6.1 as the application to open this copy of your library

6) answer the questions on the Library Update window that appears and click on Apply


Please send us feedback on the beta to our support address using the form on our web site.


Thank you for your help testing Sente 6.1.


Michael



New in Sente 6.1.1


Attachment Filing and Refiling


Attachments can now be organized using a user-specified filing and naming strategy, either inside or outside the library bundle.  Further, it is now possible to synchronize attachments that are filed either inside or outside the library bundle.  (We still encourage filing attachments within the library bundle because it makes moving the library from one location or machine to another much easier.)  Starting with 6.1, all attachments in a library must be handled in exactly the same way -- that is, you cannot have some attachments filed by Sente and others not.


With a synchronized library, each copy of the library can place the attachments either inside or outside the library bundle, but the filing and naming must be the same on all copies.


It is now possible to change the filing strategy on a library and Sente will automatically refile all attachments automatically.  Once synchronization is turned on, the location, but neither the filing strategy nor the naming strategy can be changed.


The interface for configuring attachment handling is under the Setup category in the source list.


Miscellaneous


- Updated support for AppleScript.  Please check the AppleScript dictionary for details

- Reorganized portions of the main menu

- Added ability to turn sync off permanently for a copy of a library

- Added commands that used to exist only in the top bar of the attachment view to the main menu

- Added ability to select and delete highlighting in PDFs

- Added ability to click on links in PDFs when in region select mode

- Added ability to increase or decrease the text size in the embedded web browser

- Updated targeted browsing support for ACS, Web of Knowledge, ACM beta site, EBSCOhost, InterScience, Science Direct, JSTOR, National Library of Portugal and Springer.


Bug Fixes


- Fixed several bugs with scanning of Pages documents: citations were sometimes incorrectly combined into a group; text attributes (like italics) were not being correctly applied when generating rescannable files

- Fixed a problem in handling clicks on the red button on a Sente window

- The attachment view in the main window now correctly remembers its height

- Corrected a problem that sometimes resulted in the reference editor being stuck in a closed state

- Corrected a problem that resulted in the footer saying Synchronizing even after sync was complete in some cases

- The date added is now updated correctly when a reference is copied into a new library

- Corrected a problem that caused tag values to be ignored when searching or filtering on "all fields" (for this to work on existing references, you will need to do something like add and then remove a bogus tag to all references -- this will update the cache of searchable text for each reference)



Sente 6.1 Beta, Round 1

By Michael on February 12, 2010 4:25 PM | 2 Comments | No TrackBacks
We are ready to begin beta testing on Sente 6.1 with improved attachment handling and other enhancements.  Because of the extent of the changes, we want to ease into the beta testing by releasing it only to experienced Sente users who are currently filing attachments inside their library bundle. 

If you file your attachments inside the library bundle and are willing to test the new release, please use our support system to send us your email address.  We will send release notes and instructions to you.

Michael

Sente on the iPad

By Michael on January 30, 2010 9:06 AM | 21 Comments | No TrackBacks
Well, Apple has now made the iPad official.  We think it looks like a wonderful device and one that will be very useful in the academic world.  Now many people want to know what our plans are for supporting the iPad.

The bottom line is that we are excited about the new platform and we will release a version of Sente for the iPad as soon as we can.

We are not yet prepared to commit to any particular functionality, but we think some of the key characteristics of iPad Sente are rather obvious, so there is little advantage to keeping them secret.  Here are some of the key features that we expect the application to include:

Mobile libraries synchronized with desktop Sente.  Frankly, many of the design decisions that went into synchronized libraries in Sente 6.0 were made with the rumored tablet in mind and we think Sente's synchronization mechanism is well-suited to the task.  One library, multiple devices.  New references and edits show up everywhere almost immediately.  And "download on demand" for attachments means that you can have as many or as few PDFs on your iPad as you want, and quickly obtain any others as needed with a single click.

On-the-go PDF reading, markup, tagging and note-taking.  The iPad is clearly much better suited to reading PDFs than the iPhone.  To make this most useful, it is essential that users be able to do markup, note taking and tagging as they read.  And, of course, all markup, notes and tags will be quickly and automatically synchronized.

We would not normally make such public statements this early in the development cycle -- one never knows exactly what kinds of unexpected hurdles will be found as we work on the software --  but in this case we think our users should know where we are headed.  We have been hoping for and planning for the iPad for some time, and we are very excited to be able to begin serious development.  

Anticipating the next question... we do not yet know when this application will be released.  When we know more, we will tell everyone, but right now we simply do not have a schedule.

Now we want to hear from you.  Would you like to see Sente on the iPad?  How would you use it?  What do you think the must-have features are?

Michael

Sente 6.1: Attachment Filing Enhancements

By Michael on January 17, 2010 12:01 PM | 8 Comments
Since the release of Sente 6.0 we have had a lot of useful feedback from users.  Early on we recognized that one of the most important messages we were getting from users was that the way that Sente 6.0 filed and named attachments in the library bundle was a problem.  We made a commitment to address this issue, and we have begun testing a new approach that I would like to describe here.

First, some background. In 6.0, if you asked Sente to store attachments within the library bundle (which is required if you want attachments synced) they were given a name based on an internal identifier.  This was great for us because it let us sync attachments with confidence that we were not going to accidentally overwrite files on any of the machines on which a synchronized library was installed.  However, it caused a number of problems for users, including:

  • Sending one of these files to a colleague gave them a file with a long, incomprehensible filename
  • Requiring the attachments to be held within the bundle made them less accessible to other programs, like DEVONthink

This is changing in Sente 6.1, due out in a few weeks.  In this new release, you will be able to specify how attachments will be filed and named, much like in Sente 5.  For example, you can have your files organized by journal, year, author and then named with the title of the paper.  Or organized by year and named with the author's name + year + title.

Also, you will be able to have attachments filed outside the library bundle and still synchronized.  So you can place your PDFs in ~/Documents/Sente instead of the bundle and still have them synchronized across multiple computers.  Further, the location can be different on each synced computer.  It can even be in the bundle on some computers and outside the bundle on others.  The folder hierarchy has to be the same on all computers, but the starting location can be different on each.

There is a catch to this, however.  We have to know that the file 2007/Smith/My Paper.pdf is intended to be the same on all computers because when it is updated on one computer, it will be copied to all others, and we have to be confident that we can simply replace the similarly filed/named file on each machine.  For this reason, the folders in which Sente attachments are filed must not be used for any other files.  That is, you cannot intermingle other PDF files with your Sente PDF files, for example.  For this reason, when filing outside the bundle, Sente will always insert a folder with the library name in the path.  For example, if you specify ~/Document/Sente as the root folder for filing attachments for "My Library" Sente will start the filing in ~/Documents/Sente/My Library.

There are some other limitations on the new approach.  For example, the file naming patterns are hard-coded into Sente (as opposed to being bibliography formats, as in Sente 5).  This is done because we have to know that the naming scheme is supported on all synchronized copies.  We will add new options based on user requests, but you will not be able to create your own formats using bibliography formats.

Sente 6.1 also includes the ability to refile all existing attachments based on a new scheme.  For example, you can convert from having PDFs organized by journal and year, to being organized by author and year.  Sente will automatically move and rename all attachments for you.  However, this cannot be done once synchronization has been turned on for a library.  If you need to do this, you will need to make a new copy of the library, set up attachment filing the way you want it, and then turn sync on for the new library.  You can move the entire attachment hierarchy on any copy of a synced library (e.g., you can move it from within the bundle to somewhere outside the bundle, or from Documents/Sente to Documents/PDFs); you just cannot change the organization or naming below that level once sync is turned on.

Here is a shot of the attachment configuration screen:

Screen shot 2010-01-14 at 4.07.27 PM.png

One other change we have introduced since 6.0 was released is that we no longer support "mixed state" for attachments.  That is, if you have told Sente to file all attachments inside the bundle with a particular filing/naming scheme, all attachments in that library must be filed in that way.  You cannot have any attachments in that library stored anywhere else.

We are still encouraging users to store attachments within the library bundle because it is much easier to make many common changes (e.g., just move the entire library from one location to another and everything will still work).  But we are also making it easier to handle changes like the migration from one computer to another even when the attachments are filed outside the bundle.

We are currently testing these changes internally and expect to make them available to a few outside testers in the next week or two.  Not long after that, we will make the official release of Sente 6.1 with these changes.  

Sente 6 Released

By Michael on October 21, 2009 7:06 AM | No Comments | No TrackBacks
We are very pleased to announce the official release of Sente 6.0.  This new version includes a number of important enhancements, like:

  • Synchronized Libraries.   Sente 6 makes it easy to maintain multiple copies of a reference library, including attachments such as PDF files, on multiple computers.  This works well for users who regularly work on more than one computer.  Because permissions can be set differently on each copy, this feature is also useful for sharing a library with colleagues.
  • Hierarchical Reference Tagging.  Sente 6 makes it easy to assign and use tags on references.  And tags can be arranged hierarchically, in which case Sente will treat references with child tags as though they had also been assigned the parent tags.    This makes organizing a large research library much easier than it has ever been before.
  • PDF Markup.  This new version also includes PDF markup commands that can be used to highlight passages or other regions in a PDF file.  This information is synchronized along with the PDFs themselves, so the marked-up copy is available in any synchronized copy of the library almost immediately.
  • Hundreds of New Bibliography Formats.  This significantly increases the likelihood that the format someone needs is already built-in.

Along with the release of Sente 6 comes a new web site design and a new support system.

Sente 6 requires Mac OS X 10.5.8 or higher.

Sente 6 is a free upgrade for anyone who purchased a Sente 5 license on or after January 1, 2009.  Others can purchase an upgrade for $39.95 for a single user license.


If you purchased Sente 5 after January 1, 2009, Please send your Sente 5 license code to our upgrade address with the subject "Sente 6 Upgrade".  Processing upgrade requests may take us as long a 7 days -- we appreciate your patience.

If you purchased Sente 5 prior to January, 1, 2009, you can purchase the update for $39.95 -- see our Purchase page.

If you have a Sente 1, 2, 3 or 4 license, there is not a discount on the upgrade -- you will need to purchase a new license to run Sente 6.

Everyone who purchases a Sente 6 license (either as a new license, or an upgrade) will receive all updates in the 6.x line at no charge.

We would like to thank all of those who participated in the testing and evaluation of our early releases of Sente 6.  You contributions made a big difference in the final product. 

Michael

Sente 6: PDF Markup

By Michael on October 19, 2009 2:13 PM | 6 Comments | No TrackBacks
We have just posted one of the final beta versions of Sente 6, including the last new feature for this release: PDF markup.

When you open a PDF in a single reference tab, you can highlight text or a region (just like previous versions) and you have the choice of:

1) creating a note from the selection (like earlier releases), or
2) highlighting the text selection (or boxing a region selection), or
3) doing both at once

This is obviously a limited subset of what Preview or Skim offer for PDF markup, but we suspect that these are among the most commonly used markup commands.

One of the nice aspects of doing the PDF markup in Sente is that, at least for PDF stored in the library bundle, the markup is synchronized across all copies of the library.  So if you have a synchronized library, any markup performed on any copy will automatically appear in all copies shortly thereafter.  (Because of the size of a PDF file, changes are synchronized only when the single-reference tab is closed; this helps limit the amount of data being sent back and forth between computers.)

The markup that Sente adds to a PDF is compatible with Preview, but not Skim.  (Skim uses a non-standard method for storing annotations on a PDF file.)

We think having attachments synchronized across computers is pretty cool, and replicating markup is, well, even cooler. Try out the beta and see what you think.


Michael

Sente 6: Public Beta Now Available

By Michael on October 10, 2009 12:38 PM | 24 Comments | No TrackBacks
We are pleased to announce that the public beta of Sente 6.0 is now available for download.

Here are some of the highlights of Sente 6.0:

  • Sente 6 is "document-based" meaning that there is one main window per library.  We think this makes for a cleaner interface and it supports coming enhancements better than our old approach.
  • Libraries in Sente 6 are now single files (bundles, actually) that can be placed anywhere on your computer, like in your Documents folder.  Double-click the library in Finder and Sente will pop it open.
  • Attachments (PDFs and other files) can now be stored right in the library.  This eliminates the problems with links breaking when you, for example, move a library from one machine to another.  Copy a library to a thumb drive and you have all your references and PDFs.
  • Libraries can now be automatically synchronized across any number of computers, and this includes all attachments stored in the library.  And different copies of a library can have different permissions, so you can share a library with colleagues without giving them the ability to make changes.
  • Sente 6 supports reference tagging.  And tags are fully supported by Find, Browse and Smart Collection definition.
  • There is a new QuickTag palette that lets you quickly see which tags have been applied to one or more references, and assign and remove tags from any number of references with a single click.
  • Tags can be organized hierarchically.  References with more specific tags (i.e., more deeply nested tags) will be returned when searching for less specific (i.e., less deeply nested) tags.
  • Sente 6 automatically provides a number of built-in smart collections to support many common needs.  For example, there are folders for all recently added references, and all references with specific QuickTags, and all references with particular statuses.
  • There are hundreds of new bibliography styles based on CSL format definitions. And more will be added prior to the official release of 6.0.
  • There is a new, on-line user manual.  This is still being completed, but because it is on-line, you will always see the most up-to-date version when you click on Help > User's Guide.
We still have one or two important features that will be added prior to the official release of Sente 6.0, but we wanted to get this release out to everyone who has been wanting to try out the new design.


If you download the public beta, you will automatically obtain a demonstration license when you first launch the software.   We will be releasing the official version of Sente 6.0 prior to the expiration of these 30-day demos, and we will reset all demonstration licenses at that time.

NOTE: When running with a demonstration license, Sente limits the size of synchronized libraries to 50 references.  You will be able to create libraries of any size, but you will not be able to turn synchronization on for any library with more than 50 references.

We will be releasing updates to the beta regularly and using Sparkle to automatically update copies in the wild, so if you download the beta now, you will receive the updates as they become available.

We look forward to hearing your thoughts on the new design.  

Michael

P.S. There are few items on our list that are not included in the first public beta.  These will be added in the coming days and made available through the automatic update mechanism.  These include:

  • Searches are not automatically updated.
  • Spotlight support for attachments is not active.
  • The manual is incomplete and the videos referenced within it are largely missing.

Sente 6: Tagging

By Michael on September 1, 2009 9:46 PM | 18 Comments
One of the most significant features coming in Sente 6 is the introduction of tagging to help people organize their libraries.  I would like to give you a brief introduction to the new tagging feature and let you see it in action.

So, what is tagging and how does it differ from keywords?  Well, there is no universal answer to this question, but here is our answer to the question.

1) In Sente 6, keywords are words or phrases attached to references by external data sources (PubMed, Web of Knowledge, JSTOR, etc.).  Tags are words or phrases assigned to references by the Sente user.

2) In Sente 6, tags can either be created and assigned "on-the fly" by simply typing new values into the appropriate field in the reference editor, or assigned from the new QuickTag palette.

3) Tags in the QuickTag palette can be organized hierarchically.  That is, one can organize QuickTags into categories that nest arbitrarily deep.  Note that this is different from many tagging systems that do not permit nesting of tags. 

For many people, it will be most efficient to work with tags using the QuickTag palette window.  This window displays the entire hierarchy of QuickTags and shows which tags have been assigned to the currently selected reference(s).  Toggling tags in this window will assign or remove a tag from the selected reference(s), which makes it easy to assign tags to many references at once.

In Sente 6, tags can be used in Smart Collection definitions and Sente automatically creates a hierarchy of built-in smart collections matching the QuickTag hierarchy, so you can easily see all the references that include any particular tag.

One thing to note about the QuickTag hierarchy is that if a reference is tagged with a tag several levels down in the hierarchy, it behaves as thought it is tagged with all of the parents of that tag.  For example, if the QuickTag list included a category called "Bicycles" with sub-categories of "Mountain Bikes" and "Road Bikes", any reference tagged with "Mountain Bikes" would be included whenever references tagged with "Bicycles" are displayed.  And these "implied" tags are evaluated on-the-fly, so if you were to change the hierarchy, the new structure would be used when determining which references should be included.

So, enough text about tagging.  Here is a brief video introduction to the new feature:


A public preview of Sente 6 will be released in the coming weeks and officially released a few weeks later.  Everyone who purchases Sente 5 now will receive Sente 6 for free when it is released.

Sente 6: Synchronized Libraries, Part Two

By Michael on July 15, 2009 7:14 PM | 5 Comments | No TrackBacks
In my previous post on synchronized libraries I talked about the needs that we were trying to address in our design of this new feature.  In this post, I thought I would let you see synchronized libraries in action.  I will be demonstrating synchronized libraries using a pre-release version of Sente 6.

The following video demonstrates the use of synchronized libraries on one computer.  The mechanism is exactly the same when the copies are on different computers, but this was the best way to show the updates as they happen.


In the real world, performance will be a bit slower than in the video because you will be further from the servers than we are, but updates will still propagate in just a few seconds.  The biggest difference will be seen when first synchronizing a large library and when propagating PDFs -- which are much larger than typical reference updates -- these will take quite a bit longer than in the video.  But other than when you first create a synchronized library, the volume of data going back-and-forth will be relatively modest, so you should still be pleased with the performance.

Synchronized libraries is working in Sente 6, Preview 3, which was recently distributed to our small group of testers.  We will be making one or more public previews available in the coming weeks, so everyone will be able to kick the tires shortly.

Please let us know what you think -- we want to make sure that our design for synchronized libraries works well for as many people as possible.

Michael
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