My laptop battery has been steadily losing capacity since I bought the machine. Right now, I have about 60% of the original capacity remaining, according to coconutBattery, which translates into about 2 - 3 hrs of battery life. Apple had a replacement program for Macbook batteries, but my battery had about 450 charging cycles on it, and the replacement program requires less than 300 cycles. I still have almost 2 years left with AppleCare, so I am planning to go by my local Apple store and ask them if I can still get a replacement, otherwise I will have to shell out $129 for a new battery. I suppose I could keep the old battery as an emergency spare, so it is not a total loss.

Wordpress 2.1 is out. I was able to upgrade using the recommended procedure and had only one issue relating to link categories, which are now in the same database table as post categories. It would be better if I did not have to code the SQL by hand, and there is probably an API function for the query I want. WorksForNow™.

I use the excellent IM client Adium to connect to Google Talk, AIM and MSN. Today Adium ran into issues while connecting to Google Talk and MSN from the JHU network, probably because it was trying to use the default port 5222, which is blocked by the Hopkins firewall. After changing the options to those below, I was able to connect just fine.

Google Talk (from this Adium bug tracker entry):

• Change port to 443
• Enable "Allow plaintext authentication" and "Force old-style SSL"

MSN:

• Enable "Connect via HTTP"

I thought I received e-mail today from a Nobel Prize winner today — Bishop Desmond Tutu himself.

My Dear Beloved,

I'm Mr. Desmond Tutu, it's my delight to email you this business deal. I'm the west african regional freight officer with a belgium shipping company having a new branch office in Accra Ghana.

On the 30th of November 2006,our office here in Accra Ghana despatched 14consignments into USA but only 11 was successfully delivered while others were kept in the U.S storage vault impending the rightful claims through my good office as the sole signatory to this very consignments.

My dear friend, one of the unclaimed consignments belonging to Mr.George Koshy contains cash of $14.7million USD, the cash is unknown to the U.S authority because the silver metallic trunk boxes where neatly package here in Ghana under my supervision before there despatch. This consignments has been lying there for five weeks now, please can you assist to receive the consignment if am able to change the ownership manifest record keeping from George Koshy to your detailed information?

I'm also willing to pathway with 50% of the total sum as my percentage once you're ready to corperate with me in order to inherit the african valuable treasures and liquid cash of $14.7m.if my situation interest you, please reply by email for processing the claims in your favour.

Yours truly,M
Mr. Desmond Tutu.

We have really reached a low point when Nigerian scammers are using a Nobel Peace Prize awardee's name as their alias. What does Bishop Tutu have to do, register a trademark?

Since getting my Macbook, I have switched to using POP3 instead of the GMail web interface for my e-mail. I like the fact that I have all my e-mail on my laptop with me wherever I go. I still use GMail hosting for its excellent spam filters and save a copy of all e-mail there as a backup. Of course, not using a web interface for my e-mail meant that that I needed an e-mail application on my laptop, and thus began the search.

Why not Apple Mail?

When I first got my Macbook, I started using Apple Mail. There were a few things that I did not like:

• Mail does not perform well once there are a few hundred emails in a folder.
• I had some problems getting signatures to associate correctly with accounts.
• It stores email in a proprietary emlx format, which then requires a special converter to export your email.

Why not Thunderbird?

On my previous systems (either Windows or Linux), I always used Mozilla Thunderbird. It is open-source and very well supported, and one cannot really argue about its price. Furthermore, it is really easy to get data in and out of Thunderbird. Unfortunately, Thunderbird on the Mac behaves much like ... Thunderbird on Windows. In order to be truly cross-platform, it does not use basic OS X facilities like Spotlight and Address Book. This failure to use OS-native facilities also applies to Mozilla Firefox, but I still use Firefox for its excellent collection of extensions.

Why Entourage?

For a little over a month, I have been using Microsoft Entourage as my primary e-mail application. For those of you who have never used a Mac, Entourage is the Microsoft Office for Mac equivalent of Outlook. As far as I know, Entourage uses a completely separate codebase, and there are certainly feature disparities between it and Outlook.

The best part of Entourage is that it is a true Macintosh application. It inserts entries into the Spotlight database, making finding emails very easy. You can also use Applescript to automate frequently used tasks, and very easily bind them to a keyboard shortcut (more on that in a second). You can set it up to sync with iCal and/or Address Book, which is useful if you use iSync.

Entourage is not perfect by any means. It is a behemoth of an application and it stores data in a proprietary database format, much like Outlook. What is different is the ease with which you can import and export data. Want to export a folder of e-mails as an mbox file? Just drag and drop the folder to a Finder window. Want to do the reverse? Drag and drop works for that too!

Entourage is still not a Universal Binary, but that should be fixed later this year in the new version of Microsoft Office. For now, it runs fine through Rosetta, and is generally more responsive than its Office brethren Word and Excel. Perhaps that is what not being encumbered by a legacy codebase does for you.

A new filing system

Thanks to Spotlight's excellent search capabilities and Entourage's Applescript integration, I have done away with the complex hierarchy of folders I was using to save my e-mail. Inspired by Sharon Sarmiento's 7 Ways to Tame Your Inbox, I now have just three: Inbox, Sent and Archive. All new e-mail arrives in the Inbox and either gets deleted, move immediately to the Archive folder, or gets moved after I have performed some action on it. So, my Inbox generally has all new e-mail plus old messages that I need to act on. All other e-mail that I want to retain is in the Archive folder. I also have an Applescript set up to use Ctrl-A to move messages to the Archive folder (for you Windows folks, Apple-A is what does Select All on a Mac). This minimalist approach saves me time both while filing away e-mails and while searching for them, since I no longer have to decide where something goes and then remember what decisions I made in the past.

I wanted to make my other web pages (see Home and About Me) on this site look like my blog, which uses a slightly version of the WordPress theme Blog.Txt. Managed to tweak a RapidWeaver theme to look like the WordPress theme. It is not perfectly identical, but it is close enough for now.

Finally updated the basic placeholder genebrew.com page to a decent looking site. I used RapidWeaver, which has some nice looking templates. I had always coded my web pages by hand till now and I must say that to reach the aesthetic level of some of these templates would take quite a while, even though I do not shy away from CSS/HTML/Javascript. Moreover, I can always hack the built-in templates to satisfy my geeky urges.

Got my Christmas/birthday present today. It's a Crumpler Salary Sacrifice laptop backpack. I had been coveting it for the past month or so and received it today as a complete surprise gift from Shalini, my significant other. The construction is really solid and it is very light and comfortable to carry. I love it -- only slightly less than my Macbook!

Since I am now in grad school, I needed a new laptop to replace the one I used to have from work. So today I bought a 2 GHz white Macbook, and I must say that I love it. I am still learning my way around OS X, but it has been a positive experience thus far.

I am debating whether to buy Microsoft Office for Mac. I can get it for the educational price of $150; however, it is only available as a PowerPC binary, not a so-called Universal Binary compiled for the Intel Macs. I hope Microsoft gets their act together and releases a recompiled version soon.

Just installed Roundcube as my new webmail program. Very nice AJAX-based interface, though not really as good or fast as Gmail. Still, quite a step up from my old Squirrelmail install.

As I started up my Thinkpad T42 yesterday, it beeped loudly and continuously. I thought that it was an alarm, so I checked the BIOS and all alarms were turned off. Finally, Google found me a page that mentioned that leaving the internal microphone turned on for playback can cause this problem. Muting the microphone did fix my problem, so now there is one more page that documents this fix.

After seeing Tom, Dick (yeah, that one) and Harry (no, the other Harry, the non-geek) publish photos on Flickr, I decided to stop maintaining my own (admittedly empty) photo gallery. So here goes: Google Images, here I come.

I tuned my spam filters today. I was forwarding all mail with a SpamAssassin score greater than 10 to spam.at.genebrew.dot.com, and ended up with about 8000 emails from April to November 2000. Looking through the spam box today, it seemed that there were really no false positives, and I can completely discard emails that score above 20. So I added this to my .filter file:

$h_X-Spam-Level contains "XXXXXXXXXXXXXXXXXXXX"+++++++/dev/null
$h_X-Spam-Level contains "XXXXXXXXXX"+++++++spam@genebrew.com

add_header all Level _STARS(X)_

I finally got my favorite IDE Eclipse working with Cytoscape. Here are the steps I took:

1. Create a new project using "Checkout Project from CVS", using the information at the bottom of the Cytoscape download page.Make sure you create a new Java project after checking out from CVS. Designate src as a source directory and use a name other than bin for the project output directory (there is already a bin directory in CVS).
2. Add all the JARs in the lib directory of your new project. You should then have no compile errors.
3. Create directories called fake_src, fake_src/cytoscape and fake_src/cytoscape/view.
4. Symlink or copy the resources directory to fake_src/cytoscape.
5. Symlink or copy the images directory to fake_src/cytoscape and to fake_src/cytoscape/view.
6. Symlink or copy the help directory to fake_src/cytoscape
7. Modify the build properties of your project and designate fake_src as a source directory.
8. Create a "Java Application" run configuration that uses the cytoscape.CyMain as the main class.
9. Run it!

The above steps essentially duplicate the actions in the run target of the ant build file, except for the compile and copying of resources/images/help files that Eclipse does for us automatically.

After having used Ubuntu for a week (current uptime: 7 days, 9 hours), I understand why it is the most "popular" distribution on Distrowatch in recent months. The focus is on the user and on the home desktop, unlike larger distributions like RedHat which focus on enterprise servers and desktops. Debian's apt/synaptic combo is nicely packaged into an update manager that notifies you, much like up2date in RedHat.

On the other hand, I do not see much difference from Fedora. Most of the desktop related improvements are flowing upstream into Gnome, and some improvements such as Fedora's NetworkManager are missing. Fedora is better supported for Java development by jpackage; I can find no such Java package repository for Ubuntu. Multimedia and "non-free" packages are not included in either distribution (Gentoo beats both in sheer package coverage).Finally, I am heartened by the fact that much the same people who work on the enterprise-class RHEL also work on Fedora, and bring at least some of the associated QA mentality to their Fedora work.

For instance, since the release of Hoary, there has not been a single kernel update on Ubuntu. My experience on Fedora was quite different; my low uptimes were invariably due to new kernels with security fixes. Perhaps the current hiatus is due to Linus' SCM issues; otherwise, despite shipping a very recent (relatively unstable and untested from a security standpoint) kernel, Ubuntu is not keeping it up to date.

Well, that did not last very long at all. After a few days of playing games and burning DVDs quite easily, I realized that not only was I spending too much time on those activities, but that I was feeling out of place when doing any development (especially Perl and R). So I am putting my Windows XP CD away (along with FIFA 2004, Halo, Far Cry and Nero). Next stop: Ubuntu!

I have been playing around with Cytoscape for a couple of hours now and it is quite an impressive tool. On my Athlon XP 2100+ with 1 GB RAM, it can render a network of ~3000 nodes and ~7000 interactions (edges) in 10-15 seconds. It also has a very extensible architecture through plugins, though there seem to be only a few available. One plugin that would be cool is to automatically annotate the current network with Gene Ontology (GO) terms.

Now that I am having no wireless issues, I decided to turn encryption on. Since WEP is easily broken (the FBI does it in three minutes), I decided to try out WPA-PSK. Now WPA is more secure than WEP, but the PSK mode is still hackable. Till we have a router-agnostic version of TinyPEAP, home users may be out in the cold when it comes to wireless security. So keep those firewalls up, and use SSH, VPN and SSL.

Dave Massey from Microsoft says that IE is not a part of the OS. I would agree, in the sense that it does not run as part of the OS kernel. However, the issue is that the HTML rendering component that IE provides is used by so many applications on Windows, including several provided by Microsoft. The tight coupling of the IE HTML control with so many applications is what makes IE a de facto part of the OS. If Microsoft were really serious about decoupling Windows from IE, they would provide a rendering component API that could be implemented by using Gecko or KHTML. Of course, Microsoft's dirty little secret is that IE helps to tie people to Windows, so they have no motivation to fix the situation.

After almost 3 years of using only Linux on my primary computer at home, I am now running Windows XP Professional. I had several reasons for venturing back into the belly of the beast:

• A lot of the applications I like from Linux are also available on Windows (Firefox, Thunderbird and OpenOffice.org to name three).
• As the "tech support" guy for my family and friends, I felt lost in Windows XP, where things were just that slightly different from Windows 2000 (the last Microsoft OS I ran).
• I like to play games to burn off steam and I was tired of fighting with Cedega to get them to work.
• DVD burning is much easier in Windows, especially with applications like Nero.

There will definitely be tradeoffs though: Windows XP is nowhere as friendly to developers who do not use .NET or Java. I am not looking forward too much to wrestling with Perl and R on XP. Windows XP is not a hacker's OS, in the original sense of the word "hacker" anyway.

Let us see how long this episode lasts.

In the interests of being fair to both desktop environments, I have decided to switch to KDE 3.3 on my home desktop. Still using Gnome 2.8 on my laptop though.

Well, KDE 3.3 is more of the same - very customizable, but somehow not as clean looking as Gnome. It may just take some time to get it looking and working the way I like. Also, though KDE/Qt applications were far ahead of Gnome/GTK, that is no longer true. Firefox, Thunderbird and Gaim are killer apps for Gnome. Yes, I know that you can run apps based on any toolkit in both environments, but I like seeing all my apps look and feel alike.

Well, that last message actually showed up. I am amazed when things work as they should.

Yes I can!

Have been checking out other blogs on Blogger and it's not looking good. I am using the most popular theme out there. Aw heck, maybe someday I will change it to something else. At least I removed the Blogger button and replaced it with a Firefox button.

The Altix machines are very nice. We have an Altix 1350 at work and it rocks to see the 320MB of memory I need for my program translate to about 0.1% of the total memory in the machine (64GB). It makes using large in-memory data structures a viable option, rather than having to store the data in a database or a file. Oh, and it runs Linux. Put that on my Christmas wishlist!

Have been trying to get gnome-blog working and it does nothing when I try to get it to find my blog. Might be proxy issues at work, so I will try from home later.