Oy, this is become quite a little pain. The k2 theme rocks and I use it on my own blog where it works just fine. However, on iocean it is really really slooooooww. I’ve spent quite a bit of time looking into why this is and have tried tweaking for performance at every level: mysql optimizations, turning off plug-ins, wp-cache, etc.

I’m still not entirely sure what’s causing the sluggish performance. In the meantime, I’m reverting back (somewhat) to the previous theme, which loads a bit faster. I’m wondering whether we should install the APC (alternative php cache) extension to enable compiled php caching in apache. This could help somewhat?

I’ll wait until Mason returns in a couple weeks to figure some of this stuff out. For now, this site, although functional, will remain in a state of limbo.

Thanks for the patience.

-Shaun

This site may be a little broken for the next few days as we complete the transition to a new and improved WordPress theme.

Trust me, it will be worth it.

One of the improvements is already seen in the global navigation bar. We’d like to provide a more logical structure for the static pages contained within this site. The addition of the About, Projects, Groups, and Tools pages will give us a good framework for placing related content.

For example, the Matlab Group page is now located under Groups.

More stuff to come in time…

-Shaun

Giving WordPress Its Own Directory - This WordPress Codex contains the instructions for storing the core WordPress files in a sub directory. This removes the clutter of wp-* from out document root.

There may be a few buggy links at this time while we complete the transition to WordPress 2.0.4 and install the k2 theme.

• It’s responsive. For anyone who has used Google Spreadsheets, this is a key point. There is not a lot of, if any, time spent waiting for the program to catch up.
• Writely’s built-in collaboration capabilities make it a suitable alternative to other versioning software for use during the beginning stages of editing, when changes by different individuals are being made often. At first creation or any time further along, you can decide to invite others to collaborate on the document(s), allowing them write, read, or both priveledges.
• Past revisions can be viewed individually or compared to each other, with the capability of reverting to and saving a version of the document that existed before any unwanted changes were made. There is also the option for having an RSS feed of the document changes, though I’ve not used this.
• If at any point it is decided that the document should be saved locally to a more secure location, Writely allows you to save in any of these formats: RTF, Word, OpenOffice, HTML, or PDF.

In conclusion, Writely seems like a capable resource for collaborating on documents, with many features that extend way beyond what was described above. Although Google says that user’s documents are very secure, it might be wise–the beta meter is at 62%–to beware the use of Writely for documents that contain any private data. Still this web-application is definitely something that should be tried out.

Here’s a couple reviews:

Cnet
About.com

I’ve recently made a couple of changes to subversion and the apache2 instance through which we access our repositories.

First, I’ve upgraded subversion to the latest stable release, 1.3.2. This update contains boh new features and bug fixes; you can read about them fully in the relase notes. The repository format has not changed since 1.1.x (we had 1.1.3 before), so our repositories were able to remain in place.

Second, I’ve recompiled apache2 with LDAP and SSL support (this instance can be found in /usr/local/apache2). This changes our repository access in two ways. Because SSL is enabled, connections to the repository need to be made with https, not http. Current working copies can be updated by using this command in the root of the working copy:

svn switch --relocate \
http://oceaninformatics.ucsd.edu:8800/svnrep/[path] \
https://oceaninformatics.ucsd.edu:8800/svnrep/[path] .

Also, LDAP support means that apache2 is now authenticating against our OpenDirectory server, not an htpasswd list. Whenever subversion requests a name and password, use your OpenDirectory name and password (this is the same name and password you use for your coast/IOD email account).

If you find any strange behavior or cool new features with the upgrade, please post about them here.

Last month I disabled all email notifications for new posts and comments. I did this for a few reasons:

1. We had been getting lots of comment spam, and these were generating lots of unnecessary email notifications. (I’ve since set stricter blacklist filters to immediately remove any spam).

2. More than one user had requested to have their notifications disabled.

3. Email notifications are, well, annoying.

That’s right… email notifications are annoying. They clutter up your inbox and make email more distracting than it needs to be.

Fortunately, there’s a much better solution to staying up-to-date with the latest blogs and news sites: RSS!

What is RSS?
RSS = Really Simple Syndication
It’s basically a lightweight XML file format that distributes articles w/ appropiate metadata (author, date, time, headline, news snippet, etc.) to any RSS Reader.
Another term for RSS is ‘feed’.

Here’s how it works (brief):
A server (like this blog) generates an XML file in RSS format.
A client (any RSS Reader) periodically checks the server (our blog) and retrieves the latest XML file. The client then displays the contents of that file in a human-friendly interface.

Where can I find an RSS Reader?
I use NetNewsWire for the Mac. However, it’s a commercial app, and it will cost you the license fee.

There are some cheaper (free!) alternatives, which may be better… particularly for newbies. Safari and Firefox both have built-in RSS reading capabilities. I would recommend using one of those (whichever is your preferred browser), especially if you wish to keep on track with this blog.

Setting up RSS on Safari
1. With Safari open, open the Bookmarks page: Bookmarks > Show All Bookmarks OR bookmark icon on the bookmarks bar (left side)
2. Make sure Bookmarks Bar is selected under Collections.
3. Add a new bookmark Folder: Bookmarks > Add Bookmark Folder OR click the + sign underneath the Bookmarks frame.
4. A new folder appears called ‘untitled folder’. Rename this to ‘OI Blog’.
5. Close the Bookmarks page.
6. For each of the two RSS links below:
- open up the page.. this opens Safari’s built-in RSS Reader
- bookmark this page under the OI Blog folder: you can quickly do this by dragging the link on top of the folder. To drag the link, select the favicon (the icon just left of the link in the url bar) and drag.

Anytime there’s a new post or comment, a number in paranthesis should appear next to OI Blog. This is the number of unread entries in your feed and also your notification that the blog has been updated in some way. It’s much less obtrusive than an email notification, and much more convenient for checking up on the blog.

RSS Links
Here are the ever-important links to this blog’s RSS feeds. We have two feeds, one for posts and one for comments. These links are also found in the sidebar under Extra Stuff.

- Posts (RSS)
- Comments (RSS)

Setting up RSS on Firefox should be fairly similar to Safari, so I’ll forgo the procedure here.

If you made it this far and need some help with RSS, please contact me. Enjoy!
–Shaun

I’ve installed a nice little Perl module called Spreadsheet::ParseExcel on iOcean. This module allows you to open an Excel file in Perl and extract values using row-column coordinates. The module can handle multiple workbooks, and it also provides some basic metadata on the Excel file, including file name, author, number of rows and columns, number of workbooks, and workbook names. All in all, I’ve found it much easier to work with than converting Excel files to comma- or tab-delimited text. For more detailed information, see the Spreadsheet::ParseExcel documentation. As a prerequisite for this module, I also installed OLE::Storage_Lite, a more generic module for reading Microsoft’s OLE format documents.

Video has arrived – If you’re brave! - This is what we’ve been waiting for. We should now be able to do Mac-PC video chats via Skype.

Yesterday, I encountered first-hand an nerve-wrecking issue that has plagued a fellow worker’s PC. Everytime he loaded a page from the CCE LTER website, the browser would slowly redraw the entire background before displaying the rest of the page.

This occured on a rather fast machine, and only with Internet Explorer 6. Firefox on this machine worked fine. Other PCs worked fine (with both browsers). Macs worked fine (with Safari and Firefox). This issue seemed to be isolated to this one particular machine.

To work-around this issue, I resized the repeating background image from 1×4 px dimension to a 50×200 px dimension. This greatly reduces the amount of processing the browser does in drawing the repeating background image (by a factor of 2500 times) while very slightly increasing the image file size. This seemed to “fix” the slow redrawing issue.

Inspiration for this idea came from here: Tiny gifs: not a good idea.

Some important notes:
- I never technically fixed anything. I still have no idea why IE 6 on this machine rendered the page poorly, while other machines (some slower and older) showed no problems at all.
- I additionally noticed that IE6 on this particular machine rendered images very poorly. Jpegs appeared pixelated, etc. Firefox rendered images fine, as well as IE6 on other PCs (in our lab).
- It was important to see and experience the problem first-hand. Otherwise it would have been virtually impossible to diagnose the issue and find a solution or work-around. In other words, for this particular issue, it was extremely helpful to see the problem on this user’s PC.
- I made the same changes for the Palmer LTER website and also this site, both which employ the same design pattern of a repeating tiled-background.
- The Yahoo! User Interface Blog uses a 1px repeating background. Check it out and see how fast (or slow) your browser draws the background…. especially if you’re running IE6/Win.

Firefox cannot natively open PDFs, and the Adobe plugin doesn’t work in Forefox under OS X. Schubert IT has created a PDF Browser Plugin that I’ve found to be very useful. Just download the disk image, mount it, and move the PDF Browser Plugin file to /Library/Internet Plug-Ins (or ~/Library/Internet Plug-Ins to install this only for your account). You should note that installing this plugin will cause it to be used by some other browsers, including Safari and Opera. Acrobat and Quicktime can override this behavior - details are in the Read Me file on the PDF Browser Plugin disk image.