Mac OsX 10.8.2 Freezing Issue

There is a known issue with OSX 10.8.2 that will cause Cite While You Write to either freeze while formatting or give you a -1712 (time out error). While a bit technical, this is what is currently “known” about the problem:

• The problem is specific to the OS X 10.8.2 update specifically, not EndNote or Word.
• The problem is directly related to the use of the AESendMessage/AESend functions used with typeApplicationBundleID or typeApplSignature for the target type.
• Using typeKernelProcessID for the target type still works. However EndNote uses the bundle signature.
• Killing the appleeventsd daemon fixes the problem temporarily (Antonin Hildebrand discovered this fact). This can also be done by logging out then logging back in.

Note: We recommend those experiencing this issue should contact Apple directly. This can help prioritize the effort. Here is the link to contact Apple:http://www.apple.com/feedback/macosx.html

 

To kill the appleeventsd process directly please do the following:

1. If EndNote or Word are stuck, restart both applications.
2. Go to Applications : Utilities.
3. Run the Activity Monitor found there.
4. Set the "Show" option at the top of the window to All Processes (not My Processes which is default). 
5. Click the column header "Process Name" to sort alpabetically.
6. Highlight the appleeventsd process.
7. Click the “Quit Process” button.
8. Try using EndNote or Word now.

[Reproduced from the endnote.com knowledge base:

http://kbportal.thomson.com/display/2/index.aspx?tab=browse&c=&cpc=&cid=&cat=&catURL=&r=0.3222928]

EndNote: Direct Export with Safari or Internet Explorer for the Mac

There are known problems using Direct Export with Internet Explorer and current Safari browsers on a Mac OSX system. In most cases, instead of importing directly into EndNote, it will instead save a file onto the desktop. This is due to the way these browsers handle MIME types; they interfere with the ability to directly export from certain websites into EndNote.

Try accessing the website and exporting using a Mozilla based browser instead (see http://www.firefox.com/). Mozilla based browsers like Firefox allow you to specify how to handle the data when you initiate a direct export, permitting you to select the EndNote application.

[Reproduced from the endnote.com Endnote FAQ pages]

Mac Deployment of Connection Files.

Recently, I have run across some problems for people using Macs with Endnote. Unfortunately, I do not have a Mac with Endnote to play with, but I have managed to find some information. The next few posts will give some solutions (hopefully) to some of these issues.

Firstly, Endnote does not by default deploy all its connection, style and filter files. This means that, for example, the connection to Durham U is not available in default deployment of Endnote.

The method to deploy all the files is below. For PCs there is an earlier post on this blog describing how to deploy all the files.

EndNote X3 and later have the ability to modify the installation to include additional content files. While this article focuses on Connection Files, it is of note that similar steps can be used to add Styles and Filters as well. 

On Mac OS: 

1.      Start EndNote to go to the "EndNote" menu and choose "Customizer."
2.     To install ALL Connection Files, place a check next to "Connections." Alternately, you can expand the Connections drop down and check only the Information Provider of interest to you.
3.      Click Next twice until the changes are complete. Click Done to close the window.

Notes and Research Notes

I am sure many, if not most of you have experienced the following scenario:

You are reading a book or a paper. It is very, very useful, and you start frantically scribbling notes, underlining sentences, marking paragraphs, reading bits out to your friends, colleagues and anyone passing who you think might listen.

You get to the end of the document, and you have several pages of notes. The question then arises: what do you do with them?

Classically, of course, you would attach them to the document with a staple or paper clip, and place the original document and your notes reverently in a filing cabinet draw, so you could find it all again.

These days, of course, we store the document in Endnote as an attachment, and so putting notes in alongside seems to be impossible.

There are, however, a couple of things you can do to keep your notes alongside the original, in a form which is easy to retrieve.

Firstly, you can type your notes up in a word processor, and attach that file to the Endnote record. You can, in fact, attach up to (I believe) 44 different files to a record, which is a lot of notes. So your file attachments to a given record in Endnote can include the work itself and several sets of notes that you might have taken at different times.

Alternatively, if your notes are not too long, you can use either the ‘Notes’ or the ‘Research Notes’ field in the record. Both can store up to 64,000 characters, which is reckoned to be about 16 pages of text. While this may not be as flexible as a Word document, it does have the advantage of being immediately visible in the record when you open it.

If you have downloaded the record from a library or database, it is possible that the Notes field will already be populated by some information, such as the size of the book and the number of pages. In general, you can remove this without fear of suddenly requiring that information (who needs to know how big the book is, after all?).

Endnote X6 Has Arrived

Endnote X6 has arrived on my desktop. I confess, I was not expecting very much additional functionality from it (it was flagged by Adept, at least, as more of a tidy up than a redesign).

What it does have, however, is a redesigned user interface, presumably to make it more Windows 7 in style.

As you can see, the preview pane that used to be at the bottom of the window has gone, replaced by a tabbed pane on the right which shows the selected reference, its preview in a bibliography and the PDF attachment (if any).

The search screen is now hidden and can be reached from the show search button on the icons menu.

The rest of the user interface seems to be fairly familiar, but there are two new features which might be useful.

The first is a button to mark items as read or unread. Imports into the library are automatically marked as unread so consistent use of this feature might help you to stop building up mountains of unread texts in your library.

The second is a rating system, based around the inevitable stars. I would guess that this might be useful if you are sharing a library with other people, or just for your own reflection on whether the paper was good or bad. However, I think that it might be less useful than the read/unread marker.

12xxxx Connection Errors

A recent puzzle was a sudden failure of Endnote to connect to Web of Science directly.

The software used to connect quite happily, but had suddenly stopped doing so, giving an error in the 12000 range, along with a connection error message.

The usual cause of this is a change in your machines internet security options; a quick check for this is to turn off your machine’s firewall software and see if Endnote will then connect.

Multiple Authors in the Author Field

One thing I have noticed that catches people out is entering multiple authors into the author field.

If you create a new reference (References | New Reference on the menu), you can enter the authors into the Author field. It is natural to do this in a continuous fashion:

Unfortunately, this does not render properly in the output, as can be seen from the preview pane:

The solution to this is to split the separate authors onto separate lines in the author field.

This now outputs correctly:

  

The same is also true of the Editor field.

Westlaw and Endnote

For a long time it has not been possible, much to the irritation of people engaged in law research, to download from the Westlaw database to Endnote.

Recently, this has changed, and journal articles (although not cases) can now have their references exported to Endnote.

First, you need to run your search on Westlaw:

The results are shown. Click on the check boxes on the left to select the items you want to download.

The download functionality is cunningly hidden in the top right hand corner next to the envelope. Click on the down arrow and select Export to Endnote.

This takes you to the Export page

Click on Submit. A .ris file will be downloaded to your local disk. Open this and it should load into your Endnote library.

Hanging Indents

Occasionally, I get asked how to remove the hanging indents from a bibliography.The hanging indents, as I’m sure you know, are the bits where the first line of a reference hangs out beyond the second on the left of the page – this is much harder to describe than to show:

This can be referenced (Burn, 1969), and so can this (Aristotle, 1984).

Aristotle (1984) 'Politics.' In: J. Barnes, (ed. The Complete Works of Aristotle, the Revised Oxford Translation Princeton University Press, 1982-2129.

Burn, A. R. (1969) 'Hammond on Marathon: A Few Notes.' The Journal of Hellenic Studies, vol. 89, 118-120.

Some referencing styles want this, and some do not. It is not something you can control from the style.

To change this, you will need to middle tab from the familiar (at least from the last few weeks posts) Format Bibliography dialog, accessed by the box with an arrow in it in the Bibliography group of the Endnote tab.

The entry in the bottom left ‘Hanging indent:’ controls the size of the indent. Setting this value to zero will remove the indent entirely.

As you can see from this dialog, there are a number of other things you can control – the font and size of the bibliography, a title for it, the line spacing and so on. It is worth having a bit of a play with these settings to see what you can change, and select some which you like.

Instant Formatting

Mostly, when you insert a reference into a Word document from Endnote, the citation is quickly updated to be the fully formatted citation and the reference added to the reference list at the end of a document.

Sometimes, this is not the best or most convenient method of having your references formatted. For example, I mentioned last time the problem with using brackets for notes of the same type as Endnote uses for its in text citation delimiters.

If you have just one example of this, every time you insert a citation, you will get Endnote asking you which reference your bracketed comment refers to.

If this gets annoying (and it almost certainly will), you can turn off Endnote’s instant formatting feature.

To do this, click on the little arrowed box at the bottom right of the Bibliography group on the Endnote tab.

This brings up the format bibliography dialog box.

If you click on the Instant Formatting tab, you can turn the feature on and off.

Click on Turn Off and then OK.

Your citations will now remain unformatted in your document until you instruct the program to format them yourself. To do that, click on the Update Citations and Bibliography in the Bibliography group on the Endnote tab (top picture of this post).

Bracket Bother

Sometimes, you just need to put things in brackets: perhaps a note to yourself to add an argument, or finesse a point, or, perhaps simply, an aside to the reader. In the latter case, of course, round brackets (like this) are the norm, so for others you might wish to use a different shape of brackets.

When you do this, you can have some odd, and annoying, things happen when you use Endnote.

Say, for example you had the following text:

This is one example of bracket failure {it is not fatal but annoying}. This can be referenced

You then insert a reference from your library. It is quite possible that you will get a dialog box looking like this:

Endnote is asking you to track down the reference which is in the curly brackets ‘{…}’. Of course, it does not exist, because it is not an Endnote reference.

If you have only a few of these, you can just click through and ignore them. But if you are using Endnote intensively, it can get frustration that, every once in a while, Endnote will prompt you for this.

What is happening is that Endnote is looking for the particular combination of delimiters which tell it where citations are to be found. In this case it is the pair of curly brackets.

You can change the settings of Endnote to use different delimiters. You need to click on the small arrowed box on the Bibliography group on the Endnote tab.

This will bring up the Format bibliography dialog.

In the middle of top tab are the temporary citation delimiters. You can change these (preferably before you start writing!) to avoid using the same bracket type which you use for your notes and comments.

For example, if you want to use curly brackets for your note, change the delimiters to square brackets ‘[…]’. As long as you are consistent in your usage, Endnote should stop asking you to identify references for what are your writing notes.

Invalid Class String

Occasionally, you get error messages from Endnote.

Unfortunately they are sometimes less than informative.

A case in point is when you get an error message saying ‘Invalid Class String’.

There are a few possibilities here:

You may be running Word and Endnote at different levels of permissions (e.g. Word as Administrator and Endnote as a user). This seems to confuse matters.

You may be running a different version of Endnote to that installed as the cite while you write tools in Word. The answer here is to reinstall the tools in the correct version.

Fixes, depending on your versions of Word and Endnote, can be found here:

http://www.endnote.com/support/faqs/CWYW/faq13.asp

Endnote Training Videos on You Tube

Just to draw your attention to the Endnote You Tube channel:

http://www.youtube.com/endnotetraining

This contains over 50 videos of Endnote training, including quick start lessons, downloading from databases and some more obscure bits like the importance of the .DATA folder.

The only problem I can see with them is that some are a little out of date, like the JSTOR video. JSTOR changed their interface recently; this is the problem with this sort of documentation: it goes out of date quite rapidly.

Still, worth a look, and they are nice, and useful, videos.

Displaying Multiple Authors

You may have found that later versions of Endnote (X5 in particular) displays by default all the authors of a multi-author reference.

You may find this slightly annoying, as I do, because the column in the display is too narrow and so the additional information is wasted.

Furthermore, the initials of the authors are displayed, and this can be inconsistent in the references. In extreme cases you can get one author with last name then initials displayed, and then the next reference has last name and full first names. This looks a bit confusing, in my view.

There is a fairly easy fix for this one, found on Edit | Preferences and choose the Display Fields link.

Click on the checkbox at the bottom to switch off the all author display. Click Apply and OK, and the display should look neater.

Importing PDFs

It is possibly a little known fact, but you can import PDFs into you Endnote library and, in some cases, Endnote can get the bibliographical detail from the headers in the PDF.

It has to be said that this will only work with reasonably recent PDFs.

To import, choose File | Import | File from Endnote.

The Import File dialog is shown.

Click on Choose… to select the PDF of interest, and make sure you have PDF selected in the Import Option drop down menu.

Click on Import.

A number of windows might appear as Endnote imports and analyses the file. The item should then appear in your Imported References group, with the PDF attached.

Zotero 3.0

I occasionally get accused of being an Endnote evangelist, and being so zealous for the Endnote cause that I ignore its shortcomings and any competitors.

I hope that is not true, but Endnote is the product we have within the university, and it is, in my view, the most powerful and flexible of the products available. That does not mean that it suits everyone, of course, and power and flexibility come at a price, both in financial terms and in complexity.

Therefore, I want to flag up one of the main Endnote competitors today, which has recently undergone a makeover: Zotero 3.0.

Earlier versions of Zotero have, in my view, been hamstrung by the fact that it has to be run from within the Firefox browser. Now, it may just be me, but I’ve found Firefox to be a bit slow and clunky, which has made Zotero harder to use.

Zotero 3.0 comes in a stand alone version, which is good, in my view, and it also integrates with Google Chrome and Safari, which as the former is currently my browser of choice, is a good thing.

You can download Zotero 3.0 standalone from here: http://www.zotero.org/support/3.0#zotero_standalone

It will read your older Zotero files, and you can export and import from Endnote as well, via RIS format libraries.

Once installed and launched, Zotero looks like this:

The toolbar in Word 2010 looks like this:

I’ll try to write a few posts over the next few weeks explaining how to use the software. In the meantime, there is a comparison of the products here:

http://chronicle.com/blogs/profhacker/zotero-vs-endnote/33157

Zotero also works in Mendeley, which I know some folk use; in fact, I believe that it is part of the underlying code for Mendeley, but I could be wrong on that.

Activating Templates

Sometimes, last week’s solution to non-appearing Endnote tools does not work.

This seems to be because Word, somehow, has decided to de-activate the Endnote templates.

Unfortunately, this works in different ways on different Word installations. The instructions below are for Word 2010.

In Word 2007, it is similar but the Word Options are to be found on the big Office button.

In Word 2003, the Templates and Add-Ins dialog is to be found on the Tools menu item.

In Word 2010, go to File | Options

Choose the Add-Ins area.

If the Endnote templates are active (as above) they will be listed in the top part of this dialog.

If not, then go to the Manage menu at the bottom of the dialog and choose Word Add-Ins.

Click on Go, and the list of templates will be displayed.

Activate Endnote Cwyw.dotm by checking the box to the left of the name. Click on OK and the Endnote tools should appear.

Test Video

This is a test of a video of some Endnote functionality, just to see if it can be done.

Endnote Add-Ins

Recently, a few people have contacted me with problems relating to Endnote Add-Ins.

Sometimes, Endnote can simply disappear from your Word installation, or simply not appear at all on installation.

The usual advice is to reinstall Endnote. From Control Panel | Add or Remove Programs choose your Endnote program and click on Change:

The Endnote installer will launch. Choose Modify.

Click on Next. From the options choose ‘Endnote Program and then Cite While You Write.

Click on the drop down menu and choose ‘Entire feature will be installed on local disk.

Click on Next, and in the next screen click next again. The Word part of Endnote (called Cite While You Write) should then be installed.

Downloading Extra Files

As I mentioned before, by default Endnote does not load all the style, connection and import files. On a PC, you can simply modify the installation to achieve the full loading (see http://durhamendnote.blogspot.com/2011/10/full-install-of-endnote-files.html for details), but I’m not sure how to do this on a Mac.

The easiest option seems to be to click on Edit and choose, for example, Connection files from the main Endnote window, then select ‘Open connection Manager’.

The Connection Manager dialog has a ‘Get More on the Web’ button. Click on this.

This takes you directly to the download page on the Endnote web site.

Click on the download a complete set link and put the file where the instructions (in slightly smaller type) suggest. You should then have the full set of connection files available in Endnote.

Library Modes

One thing that occasionally foxes people are the library modes. You may not ever have discovered them, but they can be disconcerting if you ever accidentally switch to one or other of them.

There are three library modes, and which you are in is controlled by the buttons to the top left of the user interface.

The one to the left puts Endnote into Integrated Library and Online Search Mode. This is the normal mode of operation.

The middle button puts Endnote into Local Library mode. There are no online search options in this mode, although you can import, find full text and direct download references into your library; you just cannot do a search from Endnote to a library.

The rightmost button puts endnote into Online Search Mode. Here, all you can do is search online, via Endnote. Any items you download are held in a temporary library and are discarded when you close, or switch modes. If you want to keep them, you will have to open another Endnote library and copy your items across.

I suppose the next question is ‘why have these modes?’

I think the answer is that in some circumstances, for example using Endnote as a medical librarian, you may get many, many references, particularly if your search is not terribly sophisticated. The online search mode operates as a filtering place for these references, allowing you to select only the references you are actually interested in.

But for most of us, Integrated Library and Online Search Mode is all we need.

Endnote and Travelling Libraries

I occasionally get asked about send Word documents with Endnote references to other people without Endnote.

This does work.

The reason it works is because the Word document carries with it what is called a ‘travelling library’, Essentially, Word packs all the information that Endnote gives it up into the document. Someone without Endnote reading the document does not see all the Endnote bits, but does see the references correctly formatted.

Now, as you may well already know, nothing is quite that simple, and occasionally things do go wrong. Also, if you are asked to submit plain text, you need to remove all the Endnote related bits of processing that go on to render the formatting of references.

You might know that Endnote inserts its information through things called ‘field codes’.

To remove the field codes, make sure you work on the final final copy of your manuscript. It is also advisable to make a back up copy of that.

To remove the field codes, use Control-A to select the whole document.

Then, hold down the control and shift keys and press F9. The field codes will be removed.

Your references and bibliography are now plain text.

Any modifications will need to be done in the original, and the same procedure followed.

Sharing Groups in Endnote Web

Endnote web allows you to share particular groups of references with other people.

For example, you could share a group with a seminar group of students, or with colleagues, or with the members of a paper reading club.

To set up a shared group, go to the Organise Tab of Endnote Web and choose the Manage My Groups link.

Your groups are listed. Click on the ‘Manage Sharing’ button for the relevant group. This gives a summary sheet of who the group is shared with.

Click on Start Sharing this Group.

The following dialog box is displayed. Enter the email addresses of the people you want to share the group with in the text box and click on Apply. You can permit others to add references to the group by clicking on the ‘Read & Write’ radio button.

Your group will be shared, and the others can access it from their ‘Other’s Groups’ link on the Organise tab.

Changing Case

There is a little problem with changing the case automatically in a style.

As you probably know, you can set a style up to automatically change the case of a title. This is done from the Title Capitalisation bit of the Bibliography area of the edit style dialog.

The problem is that using this sort of style means that some parts of a title might well be rendered incorrectly.

Here, the title should be (of course) Henry VIII.

The fix for this is to be found in the Edit | Preferences dialog.

The top entry is ‘Change Case’ which is for exactly this problem. Enter your item not to be changed in the text box, and click on ‘Add’.

Click on ‘Apply’ and then ‘OK’. Your title should now look more sensible.

Complex Authors

Sometimes, an author is more complex than a single person with a surname and forenames. For example, the author could be listed as ‘The Bank of England’ or ‘Temper Longman III’.

If you type these directly into an Endnote reference, you can get some interesting effects. For example:

Gives a reference that looks like this:

This can be solved using a comma at the end of the author name:

With a comma at the end of the corporate name, the author will be rendered correctly.

In a similar way, commas are important for single authors with complex names. For example:

is not rendered correctly....

Putting the name in the author field as last name, first name, appellation enables Endnote to render it correctly.

Again, the location of the commas is important.