Assay the Essay

Wait a second

2011-12-31T23:43:00.000-08:00

For many, 2011 has been a long and economically challenging year, and the start of 2012 is a welcome new beginning. I think that most can attest that no matter one's level of patience, it can be a stretching and growing experience to wait on God for a year or more of rocky times. But if the year of 2011 has been a long time to wait on God, then how much longer is 2011 years to wait for "the second coming," Jesus' promised return? If Jesus were to come again, I have often wondered why he has taken two millenia--and counting--to do so. I mean, if people still aren't believing in him, what better way would it be to convince them than to make a dramatic appearance?

But then I got to thinking of his time course in the past, and why he might even choose to delay his coming for longer. It took him quite some time to attend to his first coming. If we measure from the time of the first writings of Scripture in the Torah, one could argue that he waited a good millennium or so to make his first appearance. And if we were to count from the beginning of creation, then we're looking at up to a multi-billion year delay before his first arrival. With that in mind, a 2,000 year delay in his reappearance is paltry at best.

More importantly, I realized that he may have an actual purpose in not returning so soon. For one, he has already expressed that his appearance by itself would not necessarily change hearts, as his first arrival had only emboldened many to bring him to his crucifixion. Instead of rushing his second arrival to turn hearts toward him, he may have in fact delayed his coming for this same effect.

Indeed, perhaps one of the most powerful points of his credibility is the fact that he has stood the test of time. Even for those who do not believe in him as God and Savior, the persistent longevity of his wisdom, of his message and example of love, justice, and forgiveness, still ring true thousands of years after he first spoke them. It would be one thing to hear this message spoken at an inspirational seminar, harbor a warm fuzzy feeling in one's heart on the way home, and promptly forget about it upon returning to work. It's another to inspire a generation to sacrifice their lives for a fiery orator's cause, only for the next generation to shun or forget such philosophy. But it's another entirely for the message to live on, no matter how misused, abused, or misinterpreted, to continue to humble and convict and energize those from all walks of life to live a life of service. Had Jesus returned in 70 AD to set up his kingdom, we would never know in our hearts whether his message would stand the test of time. If he had swooped in during the Plague or returned during the World Wars, we would never know if his message would have persisted on its own through some of its greatest tests.

Perhaps he will come tomorrow, or next year, or perhaps it will be another billion years before his next arrival. In any case, his message is alive and well, and so is he.

Android 4.0 (Ice Cream Sandwich) on Virtualbox

2011-12-01T09:39:00.001-08:00

Yesterday to my utter delight I realized that the Ice Cream Sandwich version of Android (4.0) can run in Virtualbox. I've been contemplating programming an Android app for the tablet form factor but don't quite have the resources to purchase a spanking new ICS tablet, and a virtually free virtual machine fits the pocketbook much better.

For Android ports, I normally turned to the venerable Android-x86 project. Indeed, they have just released an ICS port designed for the AMD Brazos platform, but the build apparently does not support internet connectivity or use of a mouse, which of course makes use within a virtual machine on a laptop rather challenging. Fortunately, I found another blog posting that referenced a Japanese site whose developer has provided a .vdi virtual hard disk file for loading directly within Virtualbox. Best of all, this not only includes mouse support and networking, but also hooks up with ADB for Android app development.

To set up the Virtualbox environment, I followed these steps:

Download the pre-made .vdi file with Android 4.0.
Create a new virtual machine with the following settings:

OS Type Linux 2.6
512MB RAM
Acceleration: VT-x/AMD-V (which is apparently required for ICS at least on this build), nested paging, and PAE/NX
Bridged network adapter (but see below)
2GB hard drive (not required)
Hard disk pointing to the .vdi file. Note that the disk will be attached by default to a SATA controller, but the disk should be removed from there and attached to the IDE Controller instead.

The virtual machine booted and worked out of the box! Next, I needed to connect the virtual machine to ADB so that I could load up my app for testing:

Open a command-prompt in the directory of adb.exe (ie Shift-right-click in android-sdk-windows\platform-tools and choose the "Open command window here" item).
Enter adb connect [ip-address]. This turns out to be the most difficult step because unlike using netcfg in the Android-x86 builds, I haven't found an easy way to determine the local IP address. One method is to log into your router and check the DHCP client list. The list usually shows IP addresses for the various MAC addresses of devices connected to the router. You can find the MAC address of your device by right-clicking on the networking icon in the Virtualbox status bar, choosing "Network adapters...", and then opening the "Advanced" section.

One of the challenges I've faced while on the road is the inability to connect while completely disconnected from the internet or any router. In this case, I need a way to make a solely local network connection from ADB to the virtual machine. Fortunately, this posting describes a simple method to make that connection:

In the same network adapters page from within Virtualbox, change the "Attached to" selection to "NAT".
Choose "Port forwarding", and in the "Host Port" and "Guest Port" sections, type "5555". If you have multiple virtual machines and want to connect to each of them, you could increment the host port for each of the forwarding rules while keeping the same guest port for each device (eg host port 5556, guest port 5555 on a second virtual machine).
From the command-prompt in the directory of adb.exe, enter adb connect localhost.

The Android 4.0.1 device should pop up in the DDMS devices listing from within the Eclipse development environment, and packages should transfer to ICS with glee.

Chicago Cloud

2011-11-13T20:21:00.001-08:00

Making use of the panorama function on my phone camera provides a thin slice of of the city of deep-dish pizza with the Cloud Gate in view at Millennium Park in the heart of Chicago.

Compiling with Android ADT 14

2011-10-19T15:09:00.000-07:00

Hong Kong is not so far away when the live video feed is broadcasting the announcement of all the latest Android goodness from the illustrious Ice Cream Sandwich release right to my laptop. Perhaps more importantly, the new Android SDK and developer tools is even closer by once I had downloaded the newly available releases to my Eclipse installation.

Actually using these tools, however, couldn't have felt further away when I launched my app only to be greeted with the dreaded "Conversion to Dalvik format failed" error message. Yikes!

Fortunately, the Android community is an active one, and an issue was posted fairly quickly with a follow-up workaround to the issue. The problem that I had encountered was that the OpenFeint libraries that my project depended on had duplicate classes that ended up conflicting with each other, perhaps because one of these libraries in turn depended upon the other (GameFeed on the main OpenFeint library). The solution was to removed duplicate references of these libraries to ensure that there were no conflicts. Here are the steps I took for my project

Open the .project file for my project, which may not be visible in the Eclipse project explorer but is in the project's root directory as found through a normal file browser.
Remove the entire <linkedResources> section.
Refresh the project (File > Refresh).
Navigate to Project > Properties > Java Build Path > Source and remove the library folders, which will probably be conveniently highlighted in red now that their reference as linked resources has been removed.
Repeat for any library that depends on another library included in the project.

My project now compiled fine for debugging. While exporting my project, I again ran into the Dalvik conversion error, but this time for an old rather than a new problem. Back when Android SDK Tools R12 was released, a bug was reported where projects failed to export because an older, incompatible version of ProGuard was included with Tools. The workaround was to download ProGuard 4.6 directly from its maker and replace the proguard.jar file. After upgrading to ADT 14/SDK 14, my manually-upgraded ProGuard file got replaced with the older version, and I had to swap it back. Here are the steps:

Download ProGuard 4.6 directly and unpack it.
Navigate to android-sdk-[platform]\tools\proguard\lib (eg in the android-sdk-windows folder).
Replace the proguard.jar file with the one from your newly downloaded ProGuard 4.6 folder.
Refresh the project and export it!

I hope these tips will get you up and running on the latest Android ADT and Tools, even if you (as I) don't yet have a device running Ice Cream Sandwich. And now, time for me to grab some midday dessert...

No failure to thrive

2011-10-14T11:50:00.000-07:00

As if in full anticipation of Halloween, our faithful dinner guest has emerged for another appearance, bigger and better than ever. He's meeting all milestones along his growth and developmental trajectory.

And this is how he got there.

App development with Android-x86 on Virtualbox

2011-09-12T21:46:00.000-07:00

I initially used the Android emulator when I first started developing an Android application. I quickly realized, however, that its performance was not quite up to par with efficient development practices. I looked for alternatives, and at last a wonderful device came to my wireless provider, AT&T, in the form of the Motorola Atrix. Development speed took a great leap.

I realized though that there are still times when some sort of virtual device is important for developing Android apps. For one, with virtual devices I can test the application on multiple versions of Android, from the latest Gingerbread or Honeycomb releases to the first incarnations of Android, all without purchasing a single device. I also don't have to worry about crippling my phone with extensive tweaking. And perhaps most importantly, I can run the virtual device directly from the computer, without having to leash my phone to the computer by the USB cable.

Of course, I couldn't go back to the emulator, at least in its current form. I did hear about Android-x86, a port of Android to the x86 platform that offered considerably improved performance. Best of all, it can hook up with the ADB for seamless Android debugging. The challenge was actually getting all the correct settings, and in case you're interested in doing the same, I've gathered here a few tips to help speed your development process.

Installing Android-x86 in a virtual machine

Download the Android-x86 generic iso file. Most recently I tested a nightly build from the Gingerbread (Android 2.3) version. I used it with VirtualBox 4.1.2 on Win7.
Create a VirtualBox machine with the following settings: OS Type Linux, 512MB RAM, Bridged network adapter, 2GB hard drive, and CD pointed to the iso file. As you might imagine, the sizes can all be adjusted to your liking.
Start the machine and choose to install it to the hard drive. In the partition manager, I created a Linux partition for the entire space, flagged it to be bootable, and formatted as ext3. I also made a fake SD card, which is important for installing some applications, and gave it 200MB of space. Note that on previous versions, you had to leave enough space from the ext3 partition to create the SD card, or else it would silently fail, but the new version seems to take care of that. It might also be helpful to choose to make /system writeable for debugging/tweaking.
Shutdown the system and unmount the iso file.
After booting, choose Machine > Disable mouse integration to make the mouse visible.

Adjusting Android-x86 screen resolution

The screen orientation of Android-x86 is in landscape mode, but you may prefer portrait mode. To add this configuration, close VirtualBox completely and open the .vbox file in the machine folder found in the the VirtualBox VMs directory (most likely in your user directory). In the <ExtraData> section, add the following line: <ExtraDataItem name="CustomVideoMode1" value="400x600x16"/> or some other multiple of 320x480. Other ratios work but seem to have poorer performance. Save and close the file.
Restart VirtualBox and reboot the machine. At the boot screen, press "e" to view the command-line configuration, and "e" again to actually edit it. Where the line has DPI=240, change it to DPI=160, and add vga=ask to the end of the line. Press Enter and then "b" to boot with this configuration. Changing the DPI allows the device to adopt a more natural size and resolution similar to what you would actually see on a phone. During boot you'll be prompted to see available resolutions and can choose the number for the resolution you entered.
Optionally, you can avoid having to retype all of this with each reboot by editing the GRUB menu list. After booting, press Alt-F1 to enter the command line, and then mount the grub folder as follows: Enter su, then mkdir /data/fs, then mount -t ext3 /dev/block/sda1 /data/fs. Next edit the grub.lst file (eg vi /data/fs/grub/menu.lst, if you're familiar with vi) with the changes from above.

Connecting Android-x86 to the Android developer kit

To connect the virtual machine to your Android development platform, you'll simply need to connect to the machine from ADB. To find out your IP address, press Alt-F1 in the machine and then type netcfg at the command-line, which should show the IP address on your local network on the eth0 line (eg 192.168.x.y).
Open a command-prompt in the directory with adb.exe (eg \path\to\android-sdk-windows\platform-tools). Enter adb connect [ip address], and you should see "connected to [ip address]". In DDMS, your device should also now appear.

Now when you launch your Android application, you should be able to choose the virtual machine from which to test your application!

Extra dinner guest

2011-09-04T17:08:00.001-07:00

This little critter dropped in unannounced for dinner. Only I think he thought I was the dinner.

Beer bear

2011-08-14T13:25:00.001-07:00

I came in to find this forlorn story strewn across the living room. Looks like this bear had a beer too many?

Feeling down?

2011-07-31T17:57:00.001-07:00

This bear can commiserate.

auf Wiedersehen!

2011-07-30T20:25:00.000-07:00

Bidding a fond farewell to Colin & Rachel as they head off to Germany. Looking forward to beer and sausage sometime in Deutschland! And perhaps customs would allow me to export a piece of San Francisco in the form of a slice from Milano's.

Logcat

2011-06-30T16:37:00.000-07:00

I've always wondered why some will say they keep a diary, while others will say they journal. In many cases, I bet that if we were to lay our eyes on these private collections, we'd find them to be the same despite the difference in name. Perhaps some prefer the term "journal" because it has a more objective ring to it, like the grown-up version of a diary, even if they're really the same thing. Or at least that's why I try to convince people that I "journal."

Now if I wanted to sound really sophistiqué, perhaps I'd say that I'm actually logging, which has the ring of "science log" or "captain's log." And it turns out that with my Android device, I actually am logging all the time, at least in the form of a constant stream of debugging logs from my phone. And in some rare instances, I might actually want to read those logs.

While attempting to track down some very nasty and elusive bugs prior to releasing an update to tXtFL Mobile, I was using CatLog, a nifty log reader that lets me view debugging and--alas!--crash reports from these logs right on the device. But for some reason, try as I might, I couldn't see RuntimeExceptions in the stacktraces from my crashes. Rubbing my eyes, I wondered if I was missing something--I mean, logs shouldn't lie, right? Yet the traces of my crash disappeared without a trace.

This couldn't be right, so I decided to hunt for an alternative log viewer. While scouring the Android Market, I landed on an app called Logcat Live Wallpaper, with an alluring description, "A must-have for geeks =)". And it lived up to the hype.

A lonely picture cannot quite capture the aura of such artistry.

The beauty of the app is at least in part from the animations. It apparently takes inspiration from retro computers with "features" such as interference banding that routinely traverses the screen as in old monochrome monitors. It even has random speckling and and an "old phosphor" effect to mimic poor latency. What I liked most about it, though, is the fact that it's a live wallpaper, meaning that as soon as your program crashes, you find yourself staring at the stack trace, laced with the nostalgia of the 80s just to soften the blow.

As much as I enjoyed the wallpaper, I still needed a more dedicated way to view logs for actual debugging purposes. Fortunately, the CatLog developer was responsive and figured out how to restore the full output from logcat so that I could dissect out the RuntimeException stacktrace from the logs.

Notice the exception appearing in full force.

So after dissecting out the bugs that caused those RuntimeExceptions from my code as well, I was finally able to upload tXtFL Mobile 0.99.8. Of course, there will be more bugs (and features!) to come, so I won't stop "logging" quite yet.

Trying to sack some bugs. The new X's & O's animation from tXtFL now depicts QB sacks.

Gnome 3 on VirtualBox

2011-05-27T21:27:00.000-07:00

With all the fervor for Unity vs. Gnome 3, I've been itching to see a live demonstration of the two interfaces. The irony of course is that Unity has dis-unified the world of desktop Linux by branching from the otherwise Gnome standard, but I'm enjoying the differentiation and new options for customizing my computing environment.

I turned to the trusty VirtualBox to test each of them in a virtualized environment, and Unity turned out to be the relatively straightforward, if not entirely exciting, install. Gnome 3, on the flip side, has a revolutionary interface involving an entirely new workflow, complete with a beautiful cascade of window previews and application overlays and slide-out workspaces to quickly and seamlessly shift back and forth from focused to bird's-eye view for each task and make fuller use of the entire desktop space.

The initial effort to get Gnome 3 working on VirtualBox was a slight challenge, so here are a few tips that might streamline your experience:

Upgrade to VirtualBox 4.0.8, which has some handy fixes for Gnome 3.
Fedora 15 works almost out of the box with Gnome 3. I downloaded and installed the Live 64-bit version to (virtual) hard drive.
My first install hung, for unclear reason. On my second pass, I deferred encryption, but the eventual installation success may also be from preventing power management, which was a problem I faced in Ubuntu on Virtualbox, or some other hidden cause.
After install, Gnome 3 failed and dropped back into old-school mode. I updated the packages via the command line (the graphical package hung), using the "sudo yum update", then "sudo yum upgrade" commands.
Apparently, SELinux can also conflict with Gnome 3 on VirtualBox, so I disabled it by editing the file, /etc/selinux/config.
After rebooting, I also had to install the VirtualBox Guest Additions. Prior to installing the additions, I also had to install gcc and kernel-devel to compile the additions kernel modules. "sudo yum install kernel-devel gcc" does the trick. Then I mounted the additions media and installed the .run package from the command line.
On another reboot, Gnome 3 was good to go!

Freezes and crashes also come with the install, but the experience gets smoother with each Fedora update.

SF FS

2011-05-02T00:08:00.000-07:00

A short urban hike the other day reminded me that living in San Francisco is not such a bad deal.

Coit tower is but a short hike away.

Just a quick pivot at the base of the tower brings you to another spectacular view.

And using FGFS (FlightGear Flight Sim), here's the view of Coit tower I really wish I could have seen.

And just to throw it in there, a virtual view of SF bay that would have made my day, any day.

HP LaserJet 1012 on Windows 7

2011-04-27T17:18:00.000-07:00

As I sit here typing a brief guide to installing outdated software on low-end hardware, I'm also struggling to install outdated hardware using unsupported drivers. This time I'm justifying the waste of time with the assertion that I'm actually saving myself time from researching the purchase of a new printer.

So here's the dilemma. I have an HP LaserJet 1012 black & white printer, a stalwart of the Cold War, which in the transition to Windows 7 has been lost from HP's blessing. The drivers are still available from HP, but alas, only for Vista. Fortunately, those drivers do include a 64-bit version, which just may be compatible with my Windows 7 64-bit laptop.

Through numerous forums, I wandererd through alternative LaserJet drivers with subsequent "Unsupported Personality" errors but eventually landed on a solution that has at least printed the 18 papers required for my upcoming small group session. Here is the solution, in the off chance that you too might find the need to print some papers in a hurry using a venerable LaserJet:

Download the HP LaserJet 1012 drivers. In my case, I chose the Vista 64-bit version, even though I actually have Windows 7 64-bit, as there are no Win7 drivers available. I extracted these files to a folder.
Install Windows USB Printing Support. When I first plugged in the printer, it tried to install itself as a DOT4 device, but apparently I needed it as a USB device. Since the USB driver was not initially available, I had to manually add it by selecting it through this very short trail: Control Panel > System and Security > System > Device Manager > IEEE 1284 (eg "IEEE 1284.4 devices") > DOT4 USB printing support > Driver > Update driver > Browse my computer for driver software > Let me pick... > USB Printing Support.
Add the printer. Back in the Control Panel, I went to View Devices and Printers > Add a printer > Add a local printer, and I chose USB001 (Virtual printer port for USB). At the driver selection page, I chose Have Disk and navigated to the drivers previously downloaded. Thus hp LaserJet 1012 HB drivers appeared in the printer list, ready for installation.

Looking back, the solution is simpler than I had anticipated. But reading through the all the articles that I've finally been able to print...not such a simple task!

XScreenSaver on Ubuntu

2011-04-27T16:43:00.000-07:00

The screensavers on my Ubuntu desktop and laptop installs silently ceased launching power management over the past few months. As an eco-frienly aspirator, I realized that this simply cannot be, and decided to fish out an alternate screensaver source.

Fortunately, a screensaver with working power management that could be installed with only a few steps proved readily available. If you find yourself in this situations, feel free to follow the template outlined below. And if it saves you a few cents on electricity costs, don't forget to re-invest that in a Prius.

Install xscreensaver and uninstall gnome-screensaver. The Synaptic Package Manager will do just fine for the job.
Launch xscreensaver. The easiest way is to open a terminal and simply launch, "xscreensaver".
Changes settings to your delight. For me, I used the Advanced > Display Power Management tool to enable power management controls so that my display went to standby in a timely manner. Note that "standby", "suspend", and "off" here refer to the display, even though those names are so acutely reminiscent of the entire computer.
To ensure that xscreensaver launches automatically, open a terminal and run the command, "sudo ln -sf /usr/bin/xscreensaver-command /usr/bin/gnome-screensaver-command".

And voila, your brand-new 2009 software is ready to take your monitor into the next decade!

To Hell With Hell?

2011-04-18T22:41:00.000-07:00

Yesterday the pastor at my church preached on the reality and eternality of hell in light of the recent popular controversy surrounding its existence. I agree that hell is a very frightening place, yet a place whose existence we must embrace just as we must with any other inconvenient truth. But the paradox that remains in many of our minds is this: how can God allow, let alone send people to, a place of such tortuous proportions as hell?

One might argue that even a loving God must send people to hell because he is also a just God. He is a God who must exact payment for sin just as a judge, no matter how much mercy he might have on a sinner, must sentence him to punishment for what he has done. But I think that with hell, there might also be a simpler answer: if hell is by definition a place apart from Christ, then ending up in hell is simply the natural result of choosing not to follow Christ. In other words, we might say that those who have chosen to reject Christ, to turn away from rather than follow him, are getting in hell exactly what they want--to never ever have to be with Christ. In fact, we might wonder whether for them, to be in heaven would be a hellish experience, for they would have to be with Christ, the very one whom they wish not to be with, for all eternity.

If so, God is not being malicious or cruel by sending people to hell. On the contrary, we might argue that he is being merciful and gracious by giving people what they want. So what then about the fire and brimstone of hell portrayed in the Bible? Does he not appear to actively and excessively punish people in hell, rather than merely allowing them to go where they please? I wonder if the fire and brimstone of hell may not be so much a depiction of God's active punishment. Instead, it may be describing what it sees as the end result of being apart from God--a feeling akin to what we may feel on earth when distant from someone we should be with, a feeling of emptiness and loneliness and dissatisfaction, something we might almost describe as a burning longing. Multiply this feeling by eternity, and the product is a gnawing and agonizing sense of discord, what we might even call a fiery feeling, a hellish experience.

As Christ himself tells us, "God did not send his Son into the world to condemn the world, but in order that the world might be saved through him" (John 3:17). He did not come to punish, to send us to torture, but the very opposite--to provide for us a new relationship with him, a way out of this eternal loneliness. Instead of judging those who choose not to be with him, he simply asserts, "This is the judgment: the light has come into the world, and people loved the darkness rather than the light" (v.19) Rather than coming to condemn or to judge, he allows us ultimately to choose our paths for ourselves, and if we could not stand to be with him--even then he gives us what we love.

Blogger dynamic views

2011-04-03T01:57:00.000-07:00

Today I noticed that Blogger offers new "Dynamic Views" for visualizing blog content in alternative layouts. All I had to do was add "/view" to the end of the blog URL, and voilà, I could view the blog in layouts reminiscent of Picassa collages, Gmail on the iPad, or a slightly confusing but innovate view called Timescale. The layouts seem like a nice way to get an overview of the entire blog from different angles, like sorting files by name vs. filetype vs. date modified timestamp. The Picassa-style collages (Flipcard, Mosaic, Snapshot), for example, have tiled and mosaic modes as well as a way to look at all the pictures in posts.

I personally liked using Gmail-on-tablet-style mode (Sidebar), which makes it easier to see each posting at length while separately scrolling around to see other articles. To get to additional articles, I had to use the mouse scrollwheel over the sidebar, or just clicking on an article lower in the list scrolled the bar.

Timescale also seemed like a useful organizing scheme by organizing articles in three columns, each with decreasing level of granularity, sorta like looking under a microscope at different magnifications. Somehow, Timescale seemed to figure out which of the articles were the more "interesting" ones on Voice of Text Flex, although many of the articles with images on this blog didn't seem to "make the cut" to the first column.

But the most ironic thing was viewing the dynamic layouts on Android. On Android's stock browser, I received the following message:

which would almost seem to imply that the mobile browser isn't quite "modern" enough and up to snuff for the technology, whereas on Firefox for Android, it works just fine:

Good to see Firefox is still alive and kicking. Well, enough about lay-outs for now...now it's time for me to lay-down to bed!

The Disappearance of the Sun

2011-03-24T01:22:00.000-07:00

I saw an article today on the apparent arising of the "Java renaissance" from the dark ages, referring to Oracle's recent acquisition of the Java platform. "With Oracle's acquisition of the slowly fading Sun, things are looking brighter and 'we' can finally make some progress." The Sun they are referring to, of course, is none other than the fabled Sun Microsystems of old, maker of Java, and the question that inevitably comes to our minds is, What will the new day bring? Java's new owner purports to bring a brighter future for the platform. As an avid fan of a Java-based platform, Android, I've been somewhat discouraged though by the recent litigation brought by Oracle against Google and Android. I can only hope that this new day and the blossoming renaissance of Java apparently in our midst will herald not the darkness of lawsuit, but the warm glow of many new smartphones in the hands of common folk and rain down new wireless spectra into the hungry antennae they hold. Only time will tell how long the night will be before the new day arrives.

But more importantly, the article reminded me of a completely unrelated musical piece I came across entitled, "The Disappearance of the Sun," coupled with a montage that casts the daily disappearance of the sun as a sort of daily celebration of an honest day's work. The sun may be fading, and the next day so uncertain, but there is reason to rejoice in the conclusion of another day of life and work that God has granted us.

And one day when "the heavens will be set on fire and dissolved, and the heavenly bodies will melt as they burn," when the sun itself melts and disappears one last time, we can look forward to the rising of a new sun, the "new heavens and a new earth in which righteousness dwells" (2 Pt 2:12-3), and the everlasting Son who awakens us there.

Stats browser

2011-02-12T19:23:00.000-08:00

One of the fun things about tXtFL is learning all sorts of nifty little Android tricks. I finally read how to hook up a database cursor with a list scroller, which allows me to directly bind teams, players, etc. along with individual statistics into a single stats browser. The beauty of the binding is that it still has the flexibility for converting that data in an intermediate step, such as transforming a game ID number into "PIT@GB", or calculating the complicated passer rating from QBs' raw stats rather than trying to output it from a single sql query.

Here are a few shots of the stats browser following a rematch between Roethlisberger and Rodgers in superB bowl XLV.

Super Bowl XLV, Windows VII

2011-02-10T14:51:00.000-08:00

As an avid Linux fan I'm admittedly a Windows 7 fan as well, and this year's Super Bowl only made me fonder. My buddy Mike recently moved to the city, and he dropped by for a low-key bbq with some great weather. With bbq coals purchased only minutes prior to kickoff, we needed a way to view the game from the backyard while tending to the meat at the same time. Fortunately I had finally gotten my Hauppauge digital TV tuner working, which recording the broadcast on my desktop Windows 7 box. With my laptop in place close to the coals, I was able to wirelessly stream the game to my laptop. And because the game was recorded, I could start and stop the stream at will based on the unpredictable nature of flaming cheese and missing ingredients.

The net result was that we were 2 hours' behind by the end of the game, but we got to skip through the halftime show and still enjoy Rodgers' rally.

End of 3rd year in sight...

2011-01-30T18:13:00.000-08:00

It seems like an eternity since I first embarked on the 3rd year journey. When I finished my first clerkship, I thought that the worst was behind me now that I had supposedly re-integrated back into the clinical life. Needless to say, I was sorely disappointed when I entered my surgery block and found myself starting from scratch. I didn't remember a thing about anatomy, let alone how to fix it. Things got better with pediatrics, and I finally got to see neuro and psych from the human standpoint rather than that of the mouse. (The mouse is still very intriguing, mind you!) Delivering a baby was in fact quite incredible, and now in the final weeks of ob/gyn and 3rd year, I'm making a full circle and preparing to be beaten down in the OR again.

Of course, the trail doesn't end there, nor the travails. But if there's one thing that's been drilled into me, even more than the endless need to study and be flexible, is the everlasting need to take refuge in God. No matter how "the nations rage" (Ps 2:1)--as do the attendings and residents and nurses--He keeps extending the reach of his refuge from the chaos. Each day the psalmist reminds me when I wake in the darkness, "Let all who take refuge in you rejoice; let them ever sing for joy" (Ps 5:11). Amen to that!

My first Android Market app

2010-12-25T13:45:00.000-08:00

To enjoy vicariously the thousands of new Android users this Christmas, I've posted my first app to the Android Market! I don't think it will be the big sell (it's free, after all), but I had fun making it and hope it brings some fun to fellow football fans as well.

Merry Christmas!

Galaxy Tab Emulator

2010-12-09T23:34:00.000-08:00

The latest and greatest Android tools release brings with it a new emulator—and none other than the Galaxy Tab. I got to handle one of those tabs at the AT&T store recently and now understand what's generated all the buzz behind the tab. Alas, I don't have the funds to take one home with me, but I can cough up the bandwidth for a new emulator. Here's a peek at what tXtFL would look like on the Galaxy Tab.

Iterations on Android

2010-11-27T13:57:00.000-08:00

While discussing tXtFL on the mobile handset, I realized that one feature that would keep a person from ending a game is a good end-game. In other words, some sort of celebration or high scores posting at the end of an arduous football game is much more satisfying than a simple score summary. I decided to try integrating the social platform OpenFeint, which I first discovered while playing a simple iPhone game, for posting high scores and point margins after playing a tXtFL football game. Now in the latest iteration of tXtFL on Android, you can track game stats and drive summaries throughout the game, and then share your score with the world through leaderboards!

In my search for social platforms I also came across Scoreloop, which has fancy features such as virtual currency, not to mention a very friendly and responsive support staff. I may give that a shot as well.

Black Friday Best Deal?

2010-11-26T19:01:00.000-08:00

This time last year I picked up one of my favorite Black Friday treats, the very laptop on which I'm now typing. A year later and none the richer, I was looking for even better deals to sweeten the holiday. How about a nice Android phone? Or a new Android tablet? (ok, you can tell what's on my mind)

But what do I really need? Ever since upgrading my desktop from Windows Vista to 7, graphics performance has taken a nosedive. Yes, for some reason, Vista has been superior. Previously, I could cruise the skies of San Francisco on FlightGear with wings like eagles, but lately I've been stuttering the skies at 1-2 frames per second on the same simulator. I didn't even bother testing Need For Speed. And it certainly couldn't handle the stunning and intensive graphics of tXtFL (j/k).

So this Black Friday, I thought I'd treat myself to a new graphics card. I'd always been wary of my low-end ATI Radeon X1550 graphics card. My Dell Inspiron 9200 isn't the newest, and one could potentially argue for a complete system upgrade instead, but I'm actually quite fond of the machine. My buddies even told me that I could pick up a handy dedicated graphics card for the likes of $10. As much as I like that deal, $10 can buy you at least 6 sodas at the cafeteria, so I tried an alternate route they suggested.

I tried out a graphics card stress test called FurMark (don't ask me why it's named that). I was reassured that the 32-bit version works on my 64-bit machine, but to my surprise, it aborted a test with an error message saying that my card was not OpenGL 2.0 compatible. Aha! That sign very likely meant that my card was underperforming because subpar graphics drivers forbade OpenGL 2 capabilities. The default Win7 drivers were probably the generic type and unable to tap into the latent graphical prowess of the X1550.

A little forum searching later, I learned that Vista graphics card drivers up through version 9.1 are compatible with Win7. Fortunately, these drivers are freely available and installable. Moments later, FurMark was churning away at graphics card benchmarks, and I was flying my F-4 Phantom through the San Francisco fog. And all at the price of one download, I think it's my best Black Friday deal thus far.

tXtFL revisits the Android

2010-10-30T20:27:00.000-07:00

I still don't have an Android-based phone, but fortunately I do have my trusty emulator, and now I finally have an application to test on it. I worked on a prototype of tXtFL on the Android a few months back, but as you can see it's not much more than a Android port of the command-line version. After releasing tXtFL 2, work has shifted to modularizing tXtFL so that it can plug into specially-designed interfaces for smartphones or web-based platforms in addition to the standard desktop interface. Here's a first pass at the new interface for the Android. Too bad all I carry around is an iPhone.

Suffering II

2010-10-20T22:07:00.000-07:00

Awhile back I reflected on the age-old question of why God allows suffering in the world. The topic recently arose again as the pastor from my church shared a summer series on just such questions, which evoked another discussion with my brother.

I've always found it interesting how our experience colors our view of God--and it should, for how else could we know anything in this world--but how the same experience can have such a dramatically different impression upon different people. We who live comfortably while watching the carnage in Haiti, Rwanda, Darfur, and Afghanistan are in an odd position because we have not experienced any of the things that we have seen on the media reports, yet we are tempted to cast judgment from our couches and computers. I don't think that this is a matter of not patronizing the suffering or checking our anger so as not to exceed theirs, but rather to realize our fundamental inability to fully understand their situation, and to acknowledge the need to hear from their own voices how one might respond. But of course we are all human, and they just as well as we will have inappropriate responses. We can only do our best to assess the situation as objectively as possible and to consider the multiple valid interpretations.

The pictures of Haiti are undeniably gut-wrenching. As anyone who has embarked on even a touristy excursion to foreign countries knows all too well, even the pictures are less resonating than what the eye can see in person. The destruction is undeniable, and unfortunately it is not unique. I remember how the media would report of the death tolls in Iraq during the height of the conflict, with counts reaching into the thousands, and protesters marching out in the thousands as well, and feeling a twang that--however horrible those deaths are indeed--we had but a twinge of emotion or evocation of sadness at memory of the battles during WWI, in which up to 100,000 would fall in a single battle. And then that compared to the bubonic plague or the Holocaust, and what we have is a recurring cycle of maddening destruction. Yet all of this has happened, and the world has marched on, some faithless, some faithful, and many in-between, regardless of depth of experience.

I agree that just because people respond in a positive way toward God does not necessarily justify him. But I'm hard pressed to compare God to a physically or verbally abusing husband who elicits positive feelings simply by withholding abuse--as some have--simply because a husband is not a god to his wife. He may act as if he were god--indeed he may think that he is--but he is human just as she is, and he will die one day and disappear just as she will. I think that the assumption made is that God is an abuser, and no matter what the abused say, we should always condemn the abuser and free the abused. We, in a sense, act as god to pronounce to the abused that we know better than they do about their situation and will intervene to restore our view of morality. This works fine and well when we know what that morality is, but I would dare to say that we don't know what the morality is when it comes to judging God whether he has done right to let these things happen. From the outset, one of the cruxes of this question is whether or not he has done these things or simply allowed them to happen, and the corollary, whether allowing them to happen is just as wrong as not allowing them to happen. These are troubling to answer, and subject to much debate.

Let's consider the opposite scenario. Suppose that God were to intervene whenever something bad happened. That would have a ripple effect on potentially everything, threatening our freedom at every moment. And where would it stop? Surely if he staved off 99% of the earthquakes, we would chafe at the 1%. In a sense, assuming that he does answer our prayers, we do know that he intervenes, and for all we know, he may in fact have staved off 99% of the natural disasters or even man-made terrors that would have happened. If we believe in the spirit world, particularly the fallen spirit world, we should only expect to have infinitely deeper terrors than we could ever handle if God had not countlessly intervened.

We're bound to come back to the story of Job, which already sounds like a broken record because it's merely a "story." But I think that God's response to him in that encounter has relevance. I've always been appalled by it, to say the truth, because God's answer to him really doesn't answer anything directly. He just says, I am God, so you don't understand what I have to do. I think that as hand-waving an answer as that sounds, it has merit because it's like how we in the populace tell the President what he should do, as if we have all the answers and know how to run the country and patch everything up, when in reality if the vast majority of us, even the best and the brightest, took seat in the White House, national chaos would ensue. Most of us are simply not as smart as we think we are. Similarly, God manages competing interests far deeper than we realize, including perhaps one of the deepest conflicts of all, that of freedom both to love and to do evil. But I think that God may have another message embedded in his response. One lesson I've learned is that sometimes we are simply never satisfied with something. There are moments and there are people where nothing, absolutely nothing, that one could ever do would bring fulfillment. I think that the same is true in many scenarios of life, in which no matter what answer we are given, we are never convinced, we are never satisfied. I think that God may have responded the way that he did because he realized that Job--and the humanity who would read his account--would be unsatisfied no matter the answer that God gave. He says, Being God is simply too complicated to explain, so what you need to do is to let me be God, while you perform your duties as a human being. Even that answer might not satisfy everyone, but there we go again.

I write all this rather uncomfortably because I'm discussing the plight of the suffering or deceased from a cozy academic station in comfortable California. I agree wholeheartedly that those Christians who declare "goodness and love" as a rote expression chafe at the experiences of the suffering, but I also know that there are many who have experienced such suffering and would still declare this of God. Although we could discount their response as the deluded reaction of the lesser mind, they might be the ones laughing at us if they realized that we had rejected God for the same suffering that had instead strengthened their faith.

tXtFL 2 is out!

2010-10-20T21:30:00.001-07:00

After a year of development, tXtFL 2 is out. I was meaning to add a number of additional new features, but in the end I feel it's better to get the release out before the 2010 season rushes us by.

And of course...now on to tXtFL 3!

tXtFL on the Android

2010-09-09T20:11:00.000-07:00

One of the nice things about Android is that it reads Java code, even if it doesn't exactly run Java programs. I couldn't believe it when tXtFL started up on Android with only a few small hacks to hook it up to the Android graphical toolkit.

Hooking up the database was another ordeal, as the the Apache Derby database that I use in the simulator doesn't run on Android. Fortunately, the Android API does support JDBC, meaning that the main code conversion was switching from one SQL-style syntax to another, with a few additional changes to work around some apparent limitations to the JDBC drivers available for Android. Right now performance isn't pretty, but it works!

Enjoy the first day of season 2010!

To fall or not?

2010-08-27T10:24:00.000-07:00

As a kid the fall always simultaneously spelled impending doom and incredible delight. On the one hand I had to contend with the coming school year, always a consistent cause for mourning. But on the other hand, the coming of school meant the coming of fall, and the coming of fall meant none other than the coming of football.

Ten years out of high school and yet still in school, things don't seem to have changed much except for one simple fact. School is now year round, and I've passed the point of hoping for it ever to end. So that means that all fall really brings is football, and that means celebration for all.

Well, one other new thing this fall is that along with the football season is the inaugural year of tXtFL seasons. I realized that just as most games have some sort of endpoint—a quest accomplished, a task achieved, a nation saved—so also tXtFL needs a tangible goal. The latest alpha builds feature this progression through seasons marching relentlessly toward playoffs and the final challenge, the tXtFL Bowl. Alas, those alpha builds stop precipitously at the end of a season, but I've just checked in some new code featuring the first round of playoffs. More to follow! In the meantime, I hope you enjoy another round of preseason progress tonight.

tXtFL on the iPhone

2010-06-27T23:14:00.000-07:00

tXtFL has (sorta) finally arrived on the iPhone! via telnet in helmet-to-helmet mode...

Arena Football

2010-06-26T14:00:00.000-07:00

I attended my first Arena League Football game back in 2002 when the Arizona Rattlers took on our very own San Jose SaberCats. If you've ever been to an Arena game, it's quite a different experience--indoor court roughly a quarter the area of an NFL field, players crashing into mini-fences bounding the sides, sky-high scores. It was a wild game with a thrilling if not unsettling ending as fan interference stole the game from the Rattlers and kept the SaberCats on their march toward the Arena Bowl. I came home with a single thought--wouldn't it be awesome to incorporate Arena football into tXtFL?

8 years later, tXtFL finally has built-in capacity to apply new leagues and rule-sets. I've just added separate Canadian and collegiate rules, while holding off on Arena rules because I had heard that Arena had gone bankrupt and was no longer. But today while browsing the infallible wikipedia, I realized that Arena football is coming back! And that includes none other than the SaberCats at HP Pavilion.

So look out for 50-yard fields, 4-point drop-kick field goals, and players smashing into sideline walls at HP Pavilion...and in future versions of tXtFL!

Yet Another Useful Feature from OpenOffice.org

2010-06-20T15:42:00.000-07:00

Awhile back a labmate told me that he was considering using Ubuntu on his laptop. I of course was thrilled at the prospect and only with tremendous difficulty suppressed expression of incredible delight so as to answer his questions more objectively. He asked what I did for word processing in place of Microsoft Office, and I told him that I used OpenOffice.org. When he asked how I made do with it, I realized that not only did I know OpenOffice.org, belovedly known as OOo, better than I did MS Office, but that I had "gotten away" with OOo for a full-on ten years. OOo my goodness--a decade.

Today I realized yet another reason why OOo is so special. In addition to its completely open-source (and thus free) code base, multi-platform compatibility, and integration with Zotero and other open-source tools, I learned that I could also use it to connect with Apache Derby database. What, you ask, is that important for? Why, for none other than tXtFL databasing, of course. While I was prepared to write a completely separate graphical tool for managing the finer aspects of the tXtFL football database, it finally dawned on me that any graphical front-end to Derby could do just as well, if not way better. As expected, OOo lived up to its expectation, as I've attempted to document step-by-step here.

LT Rounds

2010-06-18T23:11:00.000-07:00

Today I finished my first clerkship. For the past 6 weeks I had the privilege of drinking daily from the fount of medical knowledge in the office of Larry Tierney, in addition to LT's daily musical selection from classic American rock-n-roll and the ever-distracting views of the Pacific coastline just outside his window. I'm gonna miss those LT rounds.

Ubuntu upgrades from 9.10 -> 10.04

2010-05-21T22:27:00.000-07:00

I recently upgraded my mom's laptop and brother/sister-in-law's desktop from Ubuntu 9.10 to 10.04, with the full intention of making these the final, definitive upgrades now that 10.04 is the longed-for "LTS," or Long-Term Support, release. After sequential upgrades from the last LTS release, 8.04, I've realized that these computers have met their match in hardware capacity and are well suited to live out the rest of their days with none other than the latest enduring LTS release.

Unlike previous upgrades, however, the Ubuntu upgrade to 10.04 did not come without hiccup. In an effort to allay your upgrade grievances in case you encounter similar issues, I'll briefly outline the solutions I found.

Dell 700m Ubuntu upgrade

One forum poster commented that the diminutive Dell 700m laptop was simply too reliable. Simply put, it would not die, and that means that software has to keep on dealing with it. I tried upgrading the trusty 700m using the Software Upgrade tool, only to find the screen go black and lock up during start up.

The problem lies in the fact that the 700m graphics chipset was actually blacklisted for the latest release. The solution is to de-blacklist it, which involves adding some boot options.

Hold both shift keys during boot. The tricky part for me was figuring out how to add the options in the first place, since the boot screen has no instructions. Simply press and hold both Shift keys during boot to get the GRUB menu.
Type "e". The editable boot options will display.
Scroll to the end of the line ending with "quiet splash" and type " i915.modeset=1". Note that's modeset, not modset.
Press "Ctrl-X" to boot. The system will boot up, and then you can follow the next steps to make the change permanent.
Open a terminal and type the command "sudo gedit /etc/default/grub" to open the GRUB config file.
Scroll to the line that reads "GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"" and add " i915.modeset=1" to the end.
Save and close the file.
Type "sudo upgrade-grub" to apply the changes.

The 700m lives on in Long-Term Support land! Additional forum and wiki information here.

Rescuing upgrade from "too many errors"

While attempting an upgrade from a desktop that's run the gamut from 7.04 through 9.10, I ran into numerous upgrade conflicts that eventually coalesced into a complete upgrade halt with the final, auspicious message: "too many errors."

Normally I wouldn't mind if the upgrade software protected me from the upgrade because it encountered too many errors, but the trouble here was that in halting the upgrade without unrolling any changes, I was left with a half-upgraded system where the new packages could not properly interact with the old. I couldn't open any program, even a terminal, and when I rebooted, the system simply told me that it couldn't find the boot image.

The solution was to boot from a rescue disk and run an install fix. In hindsight, I could have skipped the rescue disk step by typing "Alt-F2" to drop into command-line mode for running the upgrade fix from there, although I'm not sure if I would have run into networking errors for downloading any remaining files.

Download and boot from the "alternative CD." The alternative CD is different from the desktop LiveCD and similar to the DVD but without the language packs.
Type "sudo dpkg --configure -a". Not sure if this is necessary, but didn't appear to hurt. When running from the rescue disk, I didn't use sudo because it's running as root by default.
Type "sudo apt-get -f install". The installer will attempt to fix the broken system. Again, sudo isn't necessary when running from a rescue CD.
Follow the prompts til the completion of the install fix, exit the rescue CD, reboot, and voila!

Hopefully your upgrade experience will be smoother, but if you've run into a rut, hopefully the only barrier between you and the land of no-more-upgrades (ie Long-Term Support) is only a boot option or "-f" install!

Off to a new stage

2010-04-25T22:30:00.000-07:00

Lily and I at my thesis defense.

Tomorrow I start the next stage of my schooling. Today when someone asked how my grad career went and I replied, "It was fun," she looked shocked. It struck me then how blessed I am to have worked with such a great and supportive mentor on a project that allowed me to pursue my interests in translational and computational neuroscience all at once, an experience that can be summed up in none other than truly "fun."

It was sad to bid farewell to my Linux workstation, but I look forward to continued collaborations with Lily and the lab. For now, I'll be scrambling to shift my circadian rhythm forward while dredging up clinical skills from four years' past. At least I found my trusty old clipboard.

apy 2.0 in the works!

2010-04-22T18:30:00.000-07:00

I've (finally) had a chance to get started on updating Arthur's website to inaugurate the publication of his first book. Come follow the development on the beta site! Feedback welcome as usual.

UPDATE: One of the most fun parts about this round of development has been my discovery (finally) of jQuery, a clean API for incorporating a consistent set of JavaScript interactivity across platforms. And I just found out that the jQuery conference is none other than this weekend, in my backyard! (well, the Bay Area backyard.) Unfortunately it's already sold out, so here's looking to next year...

alpha3 out the door!

2010-04-21T11:13:00.000-07:00

We're halfway into the NFL off-season, which means it's high time to make another tXtFL 2.0 pre-release (alpha3). This time I've focused on making the off-season the in-season with the ability to follow your fav team through a season in the football simulator. I don't know how much time I'll have in the near future to make full (pre-) releases, so it was nice to get this one out the door. In the meantime, I'll focus on incremental feature "pushes" via the new tXtFL Java Web Start mechanism, just to keep things interesting.

Happy tXtFL'ing!

Dial up!

2010-04-19T23:38:00.000-07:00

This weekend I visited my brother in SoCal and was fortunate enough to tote along an old-school iPhone 2G. I must admit that traveling with an iPhone made the usual frustrations of travel such as airport waits or transfer downtimes unusually enjoyable. But most of the enjoyment came from the books I had downloaded onto my Barnes & Noble eReader and Amazon Kindle software for the iPhone. The dial-up-modem-like speeds of the original iPhone are nothing to brag about, and their main benefit was to help me appreciate the cable connection once back at home or to reminisce on the good ol' days of early college, when simply having a dial-up Internet connection was worth writing home about.

And speaking of college Internet, I came across a news article from today entitled: "Your fastest Internet in the world is found in Berkeley, CA":

Those three spots are Berkeley (average speed: 18.7Mbps), Chapel Hill, North Carolina (average speed: 17.5Mbps), and Stanford, California (average speed: 17.0Mbps).

There's something beautiful about a campus whose student-run computing facility rivals entire IT organizations from other other universities. Now if only San Francisco could connect the Bay Area campus triangle of Internet splendor...

Enabling Java Web Start

2010-04-07T23:36:00.000-07:00

Some folks like to start their mornings with Java, but I like to start mine with Java Web Start. What brew of coffee is that, you ask? It's the kind that's now powering tXtFL, the football simulator written in the Java programming language. With Java Web Start (JWS), launching a program is as simple as opening a browser page and clicking on a link. JWS will identify the platform, download the correct files, and bring you to the football stadium in no time. But as the road from tXtFL to JWS was considerably more arduous than I had hoped or intended, I'd like to take the liberty to describe how to JWS-enable a program, in hopes that it might help if you are planning to do the same.

Getting your John Hancock: signing JARs

The first step to enabling a program for JWS is to set up both the executable files and the files to execute them. As much as I'd like to click on a link to open up a program, I also want to know whether that program has any security issues. JWS gets around this problem by requiring files it launches to be signed, signifying who is the owner of those files. Signing a file usually involves generating a key and then using that key to sign each of the files that will be downloaded by JWS.

The executable can be generated using a standard JAR command. The command usually specifies a manifest file that identifies the main path, the name of the resulting JAR file, and the .class files and other supporting files necessary to run the program. One of the tricks I've just learned is that JARs for JWS require neither the classpath nor the manifest file at all! All of that information will be provided in a separate launch file.

Here's a jar example from tXtFL. If you want the file to also be executable outside of JWS, you'll need to pass it a manifest file.

jar -cf tXtFL.jar com about.txt logo.png logo-draft.png draft

To sign the JAR, I needed to generate a key for signing. The following command creates a key named keystore that will identify who I am using the information I provide it, including company name, etc:

keytool -genkey -keystore keystore -alias myself

Using this key, I can now sign the executable and all the other JAR files that the program requires. tXtFL needs one of a number of SWT files plus the derby.jar database file, which can be individually signed using the appropriate version of the following command:

jarsigner -keystore keystore tXtFL.jar myself

For a more complete example, see the end of the tXtFL build script.

3-2-1...Liftoff: Setting up for launch

Now that the signed JARs are in place, I can generate the file to execute them. JNLP files are the launch scripts that specify where the executable and support files are and how to access them. The tricky thing is that the JNLP specifies where itself is--or should be. JWS will always check this location and use the version there, regardless of whether it's an older version. Be sure to check that "codebase" specification in the JNLP file if debugging is turning out to be a nightmare (more on that below).

The whole appeal of JWS for tXtFL lies in the platform-dependence of SWT, the underlying graphical toolkit for tXtFL. This Eclipse-based toolkit affords many powerful features at the expense of requiring a separate toolkit to be distributed for each platform on which the program is expected to run. Fortunately for us, JWS can automatically detect the platform and specify the appropriate version of SWT to download. Detecting the platform is merely a matter of using the "resources" tag to specify both the "os" and the "arch". That's right--JWS can detect not only whether the user is using a Mac or a PC, but also whether the computer is running a 32- or 64-bit of Java. One huge source of confusion is that for Java, "32-bit" vs. "64-bit" refers to the version of Java, not necessarily that of the operating system. JWS bypasses that confusion by doing the detection process for you. Here's an example of the syntax:


<resources os="Mac OS X" arch="x86_64">
    <j2se version="1.6*" java-vm-args="-XstartOnFirstThread" />
    <jar href="lib/swt-mac64.jar" />
</resources>

Ain't that beautiful? When JWS loads the JNLP file on a Mac running 64-bit Java, JWS learns that it should download the swt-mac64.jar file and also pass the -XstartOnFirstThread argument, a requirement for running SWT-based programs on the Mac. Adding similar code for each of the other supported platforms allows custom arguments and resource files for each targeted platform.

Here's a complete example, from tXtFL.

Embedding a database (perfectly optional)

tXtFL had a unique problem on its hands, and that was the fact that deep in the bowels of tXtFL lies legacy code and legacy ways of doing things that longed for a dramatic overhaul. As a lover of all things Text, I originally wanted to make sure that the player and team configuration files in tXtFL were composed of simple text files, one per player or team. The end result was thousands of files that would be a nightmare to transmit over the web merely to play a simple game of football. Of course, these files could be embedded into the JAR executable, but that would defeat the purpose of the text files in the first place since they would be buried rather than accessible in the executable.

As a long-term solution, tXtFL underwent a dramatic overhaul with the introduction of a shiny new Derby database. Derby takes care of these configuration files by completely doing away with them (or almost, as you shall see). Each player and team file becomes merely a line or several lines within the database. The database is generated on the fly when the user first launches the program, and the database resides on the user's computer rather than requiring any additional transaction over the web.

Of course, one issue remaining is how to get the player and team data into the database in the first place. The program still requires a player and a team spreadsheet containing all of the data. Collecting the data in 2 files is certainly an improvement over the thousands of files previously used, but they still require the program to have a way to access files in the first place. It turns out that the solution is rather simple: accessing files using the getResourceAsStream method allows the files to be embedded within the application jar. Now the player and team spreadsheets are packaged right inside tXtFL.jar.

By default, a new Derby database will be instantiated in the working directory. That's fine if the directory is where I'm testing the files, but becomes problematic when a user launches JWS from the browser, in which case Derby tries to write its files to the browser directory but fails because of permission errors. The solution is to set the derby.system.home property to point the browser to a defined, accessible directory.

Testing tXtFL: Finding multiple platforms from which to test JWS

The first place I like to test my files is, of course, on the local system. I always thought of JWS as an Internet-based solution, but it can also be configured to launch from the local computer. I simply changed the codebase to point to the directory on my computer where I had stored the JWS files (eg file:///home/user/src/txtfl/), and JWS loaded the application files from there. When I was ready to "go live," I copied the JWS files to my server and updated the codebase to the server URL.

When I first put the files onto the server and attempted to launch them, I got a page that displayed nothing more than the title and description of the application. The server wasn't configured to tell the browser that the JNLP launch file is meant to be run by Java Web Start, so the browser tried to display the file as a web page. Fortunately I'm hosting my pages through a Linux-based service that gave me access to configuring the server file type specifications.

Many folk on the web castigate the WORA principle of Java--"Write Once, Run Anywhere." I think that everyone agrees that Java (or life) isn't quite that simple even at it's best, but it's a software principle that I for whatever reason have come to believe in. I guess I like to be able to use my software regardless of whether I'm sitting at a Windows or a Linux or a Mac box, and I want whoever's using my software to have the same options. Most importantly, I want everybody everywhere to be able to play virtual football whenever they can, football season or otherwise.

tXtFL seasons

2010-03-26T00:27:00.000-07:00

Seasons! At last!

As the dust from the NFL season settles, tXtFL finally gets its act together with its first basic implementation of the Season.

In war games, it's called a mission, and in sports simulations, it's a season. In either case, it's a battle to develop your team to face the rising competition and mount a stalwart case for victory. Choosing to start a new season in tXtFL automatically generates a season schedule by shuffling all the league's teams for each week. Seasons can be resumed at any time to bring up the next week's game against the scheduled opponent.

As usual, much work remains, including the option to run automated simulations of all the other scheduled games for the current week. Each game will differentially impact players' health depending on their involvement, and those health levels will carry over into the next game and affect player performance. And at the end of the season, of course, lies the postseason and nothing less than the tXtFL Bowl!

Stay tuned for tXtFL 2.0.0alpha3...

Blogger fest!

2010-03-24T01:09:00.000-07:00

I stumbled upon a swath of new features offered by Blogger while searching for a better way to integrate the Text Flex blog into its main website. Evidently Blogger has such a wealth of new features released or on the horizon that apparently it has a special place in its heart for all of it--http://draft.blogger.com. So what wealth of the new does Blogger in Draft bring us?

Perhaps the most visible feature is, well, what we all around us on this page, the very work of the new Template Designer. Setting up these new web 2.0 design (or is it 3.0 by now?) features was as easy as picking a template, then searching for alternate background pictures and adjusting a few sliders. At first I had trouble integrating the text into the mix of lights and darks in the sky and forestial scene. I tried updating text colors one by one, but I found that the template palette has a single slider that can adjust all colors at once. The sidebar text still gets slightly lost in the lower levels, but I like to think that one "feature" is the effect from the text "emerging" out of the foliage and into the sky above. Pretty deep, huh?

Over at Voice of Text Flex, I tried out a new two-column sidebar format that allows me to group up thin items in the same space. Now the labels, links, and a new "share it" gadget all fit in one neat little square patch of space. An older formatting customization that I found is to remove the navigation bar at the top, which allowed me to replace it with the Text Flex header as a sort of "branding." It's the first step toward making the Text Flex blog more of an extension of the main site rather than a separate entity.

I'm sure that Blogger will keep us on its toes with newer and newer features, and I've probably only just brushed the surface. One thing I'm looking forward to is the ability to add my own background images. In the meantime, I'm just gonna sit back and enjoy and brooding English (or San Franciscan?) sky...

Puff, the Magic iPhone

2010-03-22T23:50:00.000-07:00

Some of my favorite games as a kid were pushing pencils to pound targets across a page, or flipping tightly folded wads of binder paper through open fingers. The games were all fun and good and, besides a little distraction to classmates, provided a simultaneously innocent and inexpensive form of entertainment to pass away the boredom of lazy Sunday afternoons or the doldrums of Chinese school.

But all that time, I never quite new how deprived I was--until today I saw this clip. While my generation toiled with paper and pencils, the new generation of children will be blowing Styrofoam balls across hand drawn courts with potent puffs from their iPhones. All it takes is a piece of scrap paper from the printer, a few brushes of ink, and foam dust from the trash. Oh, and an iPhone.

From ink well to Inkscape

2010-03-20T23:11:00.000-07:00

I never had the privilege of dipping my pen into ink wells before composing my essay or marking a test. I did however enjoy the modern equivalent of dip pens in the form of Apple ][ and Macintosh Classic paint programs. The revolutionary software greatly simplified the mass creation of posters and handouts, but it didn't quite turn my elementary classmates and I into artists overnight. We had to wait for Adobe Photoshop and Illustrator to do that, and I, ahem, would still never consider myself an artist.

Recently however I had to generate a number of scientific figures at higher than my normal it's-ok-for-PowerPoint quality, and I found myself hunting down new techniques to make use of modern graphics editing software to make up for my artistic inadequacies. As usual, I gravitated toward my old haunt, open-source software, and to one program in particular: Inkscape.

Inkscape is the open-source counterpart to Adobe Illustrator as a vector-graphics editing software. Unlike typical raster-graphics software, if I draw a line, I can shift around its endpoints and even add new bends and twists. Put this together for all lines and many other handy tools as well, and you have the perfect enabler for someone who can't even quite draw a straight line, let alone in the right place.

While browsing the Inkscape news, I saw the results of a class project that used Inkscape to teach 4th graders about graphics software and programming. The artwork isn't exactly Van Gogh (ok, maybe the blobs look a little Gogh-esque), but I was thrilled by the resourcefulness and ingenuity of teaching young students through Inkscape. Using Inkscape's toolset--surprisingly simple to the novice and yet packed with tons of hidden powers--students could draw and tweak without the frustration of the paint programs I grew up with. If they make a mistake, they just drag drag the line's nodes. No need for even a pencil eraser. By learning to draw with Inkscape early on, they can hone their designer techniques through junior high and beyond and, hey, maybe some of their student election posters will one day look better than ours.

Oh, and in today's budget crisis, Inkscape's free. Better yet, you don't even need an expensive Mac to run it.*

* But no need to fear, as you can run it on a Mac, or Windows, or Linux.

Andrew & Miyon Young, DDS

2010-03-15T00:26:00.000-07:00

Andrew & Miyon have officially opened their dental practice in San Mateo! Here's a snapshot of Andrew finishing up on his last patient of his first day's work. That last patient was none other than myself, and of course I give him a two-tooths up for his excellent care!

Soon to come is his new website, currently parked at their domain of choice, youngfamilydentist.com. If your teeth are itching to get their fill of the latest details, you can check out their temporary site hosted on Weebly, a nifty web creation site.

Suffering

2010-03-06T23:48:00.000-08:00

A couple months ago my brother brought up the question on many minds of why God allows such suffering as we see in Haiti and other such natural disasters that seemingly blast every man, woman, and child--not to mention every tree, animal, or home--in its path. It got me thinking about what's going on there and how we can make sense of all the carnage, and I jotted a few notes that helped me to process this age-old but ever-present problem.

Something that came to mind is that none of us have ever experienced such physical devastation as they have, so we are in essence acting as "advocates" for them, onlookers from the outside seeking justice in their plight. But having never experienced what they have for ourselves, we can make one of two errors, either to be be overly complacent as if to say to them, "That's not so bad; God has good purpose in it," to which they might respond, "How dare you say that! What do you know?" or on the flip side, to passionately cry out against their plight, to which some of them might say, "Who are you to say how I feel? I still have my faith." Of course we strive for the balance, but either extreme is always a possibility, simply because no matter how much we try to empathize, we have not undergone what they have.

I was thinking about this topic over the past couple months, and the church I've been attending is actually going over a book on suffering. The chapter I most recently read is on the Holocaust, and it made me think how of all the worst nightmares I could imagine, that is probably one of the worst. I was also thinking that if we are really to make sense of the plight of those in such dreadful and unjust circumstances, we are best to ask them how they themselves have responded. The book cited a survey conducted in the 70s (I haven't viewed the survey itself, so I'm just taking the book at its word) on Holocaust victims, and the surprising result was that for a vast majority of the victims, the Holocaust had no lasting impact on their faith, yay or nay. A small fraction turned to atheism, and a smaller fraction actually grew stronger in their faith. It made me think that from those who have actually undergone such atrocity, and not merely the spectators who do their best to place themselves in their shoes, a large fraction at the very least found the events essentially unrelated to the major thrust of their faith. In other words, they somehow found their God compatible with the atrocities they had suffered.

Of course, these people may be biased in another way, since they may "have no one else to turn to" in such dire conditions, for example. But even then, I find it remarkable that they still turn to and embrace the one whom we might otherwise castigate for having brought such genocide. Maybe it's the Stokholm Syndrome, or maybe they have a different view of who God is and what his obligations are. I was also watching a Frontline episode on "The Children of the Taliban," where they interviewed a girl of about 7 years in Pakistan at an amputee camp. They asked her what brought her there, and she said that a bomb had taken out her sister and father, and before that a mortar had consumed her aunt, and rocket fire had taken her cousins, and her second cousins were wiped out by gunfire, and on and on... I was appalled, but when they asked her what she thought of all this, she replied without expression of anger, "What can I say? It is the will of God. It just happens." I was humbled, and although I of course believe that God does not condone such action, I thought of how spoiled I am to think that God has an obligation to keep us all healthy and well.

CS Lewis wrote about how God allows evil because he wants to give us the freedom to love him. That of course begs the question of why God would then allow those who love him to experience such evil. What I think it may boil down to is the fact that when God allows us individual freedom to choose between good and evil, to love or to forsake him, it's implicit that he also allows for societal good and evil. Because individuals can choose evil, we as society must bear the consequences of their evil action, even if we have chosen good for ourselves. Societal freedom is sometimes an unfortunate but unavoidable consequence of individual freedom. When it comes to cancer or earthquakes or other "acts of God," it becomes more difficult to see the explanation, and perhaps we never will, or at least until we experience them for ourselves. But even in the trivial things that we do experience, we can ask God to give us the strength to respond.

tXtFL Bowl 4.0

2010-02-08T11:09:00.001-08:00

Mike, Andrew, and I had a blast watching yesterday's Saints vs. Colts super shootout, which turned out to be less scoring but more exciting than we had anticipated. We thought that tXtFL [predicted: Saints (33), Colts (14)] was sure to come out the loser after the Colts racked up an early 10-0 lead, but the late surge by the Saints offense and stopping power of their defense kept the Saints and the tXtFL Bowl 4.0 in the game. It's been great having Andrew's and Mike's encouragement to keep plugging along with tXtFL development.

The River and the Road on Amazon

2010-02-02T18:06:00.000-08:00

Arthur's book, The River and the Road: A Journey of Redemption, has debuted on Amazon. One publisher evidently thought that it's worth bumping the price 80x, to $1,165. As much as I like the book, I suggest opting for Amazon's $14.50 price tag—clearly, it's a steal!

tXtFL progress report

2010-01-28T23:13:00.000-08:00

It's funny how some things sometimes happen all at once. For lab I found myself learning statistics, and suddenly I found myself needing those same tools for analyzing tXtFL simulator predictions. And just as I came to the point where tXtFL development needed nothing less than a game management system overhaul in the form of a new database, I found my lab data crying out for a shiny new SQLite database system resurrected from the mothballs of a bioinformatics class I took last year. Perhaps it's mere coincidence, perhaps the lessons from one domain open one's eyes to other areas, or perhaps tXtFL really is absolutely crucial to understanding lab and all of neuroscience.

Last year marked the release of tXtFL 1.0, sporting an entirely updated interface finally designed for a mouse-driven experience. After a few point releases, I'm now focusing on 2.0 development, starting at the core with work on a new database implementation. Here are some highlights included in the latest alpha2 pre-release.

The bulk of the work is summed up in this one line of output at startup. Behind this line is a new system to simplify and extend team and player management. The decrepit system through tXtFL 1.x has been to organize all team and player records in individual files, each acting as a config file with capability for hand-editing. As the number of fields and files grew, it became more and more of a mess to manage these files and, more importantly, more challenging to create modifications that might add new functionality. For example, one of most requested features is to add seasons, but this would likely require another set of files and new fields and sections in current files.

The database simplifies matters because adding new features is as simple as creating new database tables, and I/O transactions are pared down to a single location. While player and team downloads clocked in around 43 seconds on tests with tXtFL 1.1.1, they're down to 25 seconds in 2alpha2, an over 40% performance boost. Right now there are stub fields for new statistics such as stadium attendance, player salaries and years, seasons, and new leagues and rule sets, but unfortunately I haven't had time yet to implement them. Seasons are top priority for alpha3!

So far there are just a few visible changes to the simulator. I've been looking for ways to make tXtFL more web-interactive, and so far I've settled on a new Game Box for displaying news flashes, tXtFL blog postings, and links for getting connected with other football fans. It's sort of like a tXtFL "portal" for keeping up with tXtFL news and activities. As you can see from the URL bar, the current URL finally shows up, and by passing in version information the portal can also deliver version-specific news and update information. It's all truly a work in progress, so please let me know your feedback.

The Game Box is largely made possible because the underlying toolkit for tXtFL, SWT, has a built-in, fully-functional browser widget. Of course, what good is a browser if its size is fixed at 300 pixels? I stumbled upon the sash form SWT widget that allows one to expand a window area by dragging the divider. Now when you click on the wiki page, you can open the sash to view the full page width's contents in one glance. Heck, you can even use this as your primary browser! (not that even I do that, hehe)

There's only a game left in the season, but as usual, the tXtFL season is only just beginning!

Roger that, Rodgers

2010-01-10T23:59:00.000-08:00

Why didn't the Niners pick Aaron Rodgers?!

Even though he lost today (and phew, says tXtFL), he almost led his team back shortly after I had declared, "The game's over," barely losing in OT.

(Source: Christian Petersen/Getty Images)

This is what the Niners said to the former Cal QB on draft day not so long ago. And this, apparently, is what he's saying back.

San Mateo dentistry!

2010-01-07T20:24:00.000-08:00

If you're looking for a new dentist in the San Mateo area, you're in luck!

My brother and his wife are opening up their new practice in San Mateo. I'm unabashedly recommending paying them a visit. Andrew (er, Dr. Andrew Young) and Miyon (ahem, Dr. Miyon Young) work in orofacial pain and pedodontics, as well as general dentistry.

And they have their own website, too! Check it out here: http://andrewmiyonyoungdds.weebly.com/

"200$ of free software"

2010-01-07T20:15:00.001-08:00

I've been noticing more ads promoting free software from third-party sites. That might be fine if the software is open-source, but what's alarming is that these sites often try to charge for membership to download these "products." Here's one from a site advertising OpenOffice.org that was downright shocking, if not downright funny as well:

I suppose that they could mean "free" as in open-source ("free as in speech"), but if so, why would someone need to register for it anyway? For those looking for OpenOffice.org, it's free—as in speech and as in beer.

On The Mark 1.1 for the holidays

2009-12-17T22:10:00.000-08:00

Knowing good and well that all our holiday video and images will fast out-pace out ability to track them, I've posted a small update to On The Mark. Version 1.1 sports a few new goodies aimed at making score tracking and uploading faster. Video and images can be fast-forwarded/rewound in 10 second or 10 image increments, respectively, for quicker navigation. This is key if you're, say, scoring every 10th image, or have carpel tunnel from mouse clicking. Video viewing performance has also been improved on machines with lower-powered graphics by cutting down on user-interface updates.

For the impatient, I have good news: the new double-headed arrows are for faster-forward/rewind than the single-headed arrows.

If you're wondering where the timer went, fear not. It turns out that timer updates—both the slider and even the number label—were causing playback to stutter on slower machines (e.g. my laptop) playing heavy-duty videos (e.g. the Windows 7 sample nature scene). Now the timer updates are postponed until you hover your mouse over them, at which point they'll magically appear and become mobile.

One interface behavior that's been plaguing me is how the program becomes completely unresponsive during login and data import/export. What's happening is that On The Mark is waiting for web transactions to complete, sometimes taking on the order of minutes while uploading many score marks, and all status updates are deferred until the transaction is done. Fortunately, there's a way around this in the form of asynchronous operations via JavaTaskBase for JavaFX. It involves no fewer than three separate classes for each operation, but at least it gets the job done. Now once you've marked your media, you can upload them through a much more responsive data import/export interface—no more lock-down during long operations over the web.

It took awhile to figure out how to get it to show you that it would take awhile, but now at least we're not left hanging.

So fill your free download stockings and mark your holiday videos with On The Mark. Merry Christmas!

Game prediction

2009-11-29T21:07:00.000-08:00

The tXtFL prediction for this week's Niners game was way off target:

I don't mind that at all.

Light

2009-10-30T20:54:00.000-07:00

He was not that Light, but he came to testify about the Light. (John 1:8)

I've been reading an allegorical recreation of Dietrich Bonhoeffer in The River and the Road, where Dietrich encourages and exhorts an Ernest before he embarks on a dark journey. What was that journey, and why did he have to go through it? Why did God send Ernest through that journey of darkness and dampness?

I know, Ernest is a fictional character, but Dietrich was not. Sometimes I wonder what motivated such a man to go back to Nazi Germany to keep preaching when he could have stayed in England, or to write on every scrap of paper his thoughts only to be scrapped himself in a concentration camp moments before the war's end.

I do not claim to know God's purpose or reasoning, but Dietrich knew in himself something that I only hope to know, saw something so clearly that I must strain to see. He saw the Light peering through the tunnel, he saw past the dark journey and into the hidden hope beyond. And he saw this Light precisely because he knew that he is not the Light, but that there is another Light that came to fetch him, and now through him to fetch all those around him to that Light. In his writings and his testimony we see the embers of that Light still glowing strong, still burning bright.

But when...

2009-10-23T01:03:00.000-07:00

...sad, so sad, oh so very sad...

A joyful heart makes a cheerful face,
But when the heart is sad, the spirit is broken. (Proverbs 15:13)

Why is life so hard?

2009-10-05T23:36:00.001-07:00

...and love even harder?

...and harder and harder and harder?

Snow Leopard!

2009-09-15T21:41:00.000-07:00

Installation is a challenging 2 steps. At $25, that's $12.50 per step, or not much more than a bowl of champon at Sakura.

1) Insert disc.

2) Customize.

I hope that's not 2 much!

World's Worst Elevators

2009-09-09T21:49:00.000-07:00

The world's worst elevators received accolades in the form of Occupation Safety and Health Standards Board meetings. This was to honor the elevators for refusing input upon button press, breaking down as a regularity, and making elevator rides the adventure they weren't supposed to be. Notices were posted informing all affected employees that they have the right to party hearing regarding the permanent variances inflicted by the elevators.

Evidently affected employees had another idea in mind. And when these elevators get their just desert, who wouldn't want their just dessert?

Another reason to get the iPhone

2009-09-03T22:32:00.000-07:00

KatamariPhone! But I'm just getting Snow Leopard for now...

JavaFX buys me Snow Leopard?

2009-09-03T19:59:00.000-07:00

I was very happy to learn that the JavaFX Coding Challenge awarded On The Mark an honorable mention. At $25, it's not quite the $25,000 first prize, but it does have its perks. Namely, that $25 is none other than the price of the latest incarnation of Mac OS X: Snow Leopard.

"But wait," you say, "isn't it $29?" Ahh, yes, but at Amazon, it can be had for the same price as the JavaFX honorable mention! Sun and Amazon must have teamed up on that one, right??

(Oh, and that other book is for Tiffany...teaming up with me for On The Mark!)

Updating Dell BIOS when running Linux

2009-08-24T13:29:00.000-07:00

Updating the system BIOS is always a nervous task, but updating when running Linux can be even more daunting. Not to fear. Linux has come a long way, Dell has come a long way, and when the BIOS has come a long way in revision updates, it's time to flash that BIOS.

Updating the BIOS from Windows has been as easy as downloading the latest BIOS revision, double-clicking the executable, and letting the installer do its work. In Linux, the task requires booting from a USB key and then running the BIOS executable from a DOS environment. It sounds simple enough, but there are a few tricks involved, documented here before I forget what I've just learned.

Download the latest BIOS

Dell has all the drivers and downloads posted in the Support section of its website, accessible by computer service tag or model number.

Create a bootable USB stick

I've never booted from a USB stick, so here was my chance. A quick search brought me to this Bay Wolf article, which gives a concise overview with links on which files to use to create such a bootable USB drive. Note that while it might be tempting to add the additional Win98 drivers to get CD-ROM access, etc, this temptation must be mitigated. Otherwise, the BIOS installer will conk out with the error, "Can not run in protected environment." Deleting these files while leaving the hidden system files on the USB stick intact creates the proper environment for flash updating. Remember to also copy the BIOS executable onto this drive.

Boot from a USB stick

When I reached to plug in my bootable USB stick, I realized that I had 8+ options for where to plug in the drive. Which one should I choose? I tried a port but got an error saying that no valid drive could be found. At first I thought that there might be some special "USB boot port," but from forum browsing I realized that what I needed to do was to remove any other USB drives, included USB hard disks. Once I had them out of their sockets, the little USB drive took the helm.

Launch the BIOS update utility

Launching the update utility is as simple as typing the name at the DOS prompt. Reminds me of using the one type of DOS command I knew as a kid--"falcon.exe" to launch the DOS-based flight simulator. If you get a "protected environment" error, see above about creating the simplest of simple DOS environments.

Flashing the BIOS can always be a bit nerve-racking, especially when the utility sits there with still text and a blinking cursor for minutes without movement. But at least the cursor was blinking, and soon I had revision A14 sitting on my machine.

The Science of Life

2009-08-14T01:15:00.000-07:00

As true in science as it is in life:

The first to plead his case seems right,
Until another comes and examines him. (Proverbs 18:17)

Wikiarmy

2009-08-14T00:52:00.000-07:00

I just saw this article on newly wikified Army manuals.

“Our motto is, ‘If you ever thought what would I do if the Army let me write doctrine, now is your chance,’ ” he said.

This isn't something I've actively thought about, certainly not on a daily basis at least, but maybe something that's crept into the mind of many a soldier. Tiffany and I watched The Hurt Locker this past weekend, and I'm sure some of the soldier there (or whom they represent) would relish the idea of adding a nugget from their stores of knowledge into the new online repository of Army field manuals. I've always wondered though how much a soldier learns from a manual rather than from personal experience out in the field. But then again, maybe that's the whole purpose of the wikiarmy--a way for all those who through hard-won experience became experts at living and fighting in the field to impart that knowledge to their comrades.

Yet the Army seems willing to accept some loss of control. Under the three-month pilot program, the current version of each guide can be edited by anyone around the world who has been issued the ID card that allows access to the Army Internet system. About 200 other highly practical field manuals that will be renamed Army Tactics, Techniques and Procedures, or A.T.T.P., will be candidates for wikification.

Anyway I could get that ID? Without joining the Army? It must be invigorating, energizing to write entries into the couple-hundred year-old system of field manuals. So much so that it's not just ATP, but ATTP!

David/Matthew

2009-07-20T22:31:00.000-07:00

When the David Young(s) of the world united, we believed we would be a force unstoppable. But as enthusiasm petered out (to the Peter(s) of the world, naturally), hope withered, and hearts fainted.

Well, actually, there's nothing special about being a David Young. Not at all, really. But there is something special about being a David Matthew, if only because there's someone out there named David Matthew who actually is special (or perhaps celebrated is the word), the Dave Matthew of the Dave Matthew's Band.

But you already knew that. What you didn't know is that there's another David Matthew lurking about, so stealthily and so sly that he doesn't even go by the name David Matthew. He goes by the name Matthew David, and just for tricks, he cloaks himself in his last name as Matthew Lewis. But he's there, and he's been there for 3 generations. He's there on your very screens. Yes, he is none other than Neville Longbottom, hero of the Harry, our beloved David/Matthew in disguise. Let us celebrate not once, not twice, but III for Matthew David Lewis III!

On The Mark running on JavaFX 1.2--on Linux!

2009-06-03T14:08:00.001-07:00

Hello from JavaOne! I'm sitting here at the AMD "Hang Space" debugging On The Mark while folk play video games in the space in front of me and The Office themesong resonates behind me.

The best part of JavaOne for me has been...JavaFX 1.2, now on Linux! Yes, the picture you see above is an official screenshot of OTM running on Fedora 11pre, complete with video. Best of all, the video rate controls--critical for marking up videos playing rapid events--work on Linux, however haltingly, even when they don't work yet on Windows.

Now, how do we get OTM to run on Linux? JavaFX 1.2 on Linux needs Sun Java 6u13+ to run. NetBeans ran OTM on the default Java installed--OpenJDK 1.6.0--but that didn't cut it for OTM. Video playback worked for me once I switched to Sun Java 6u14.

Interestingly, I've also displayed media successfully only on Fedora 10/11pre. Video doesn't display on Ubuntu 8.04 or 9.04 even though JavaFX 1.2 on Linux only explicitly supports Ubuntu 8.04. But thanks to Sun, I can run Fedora 11 simultaneously with Ubuntu 8.04 and 9.04 via VirtualBox, all on the same computer!

Pixelated bull?

2009-04-26T23:48:00.001-07:00

This bull looks like it stepped out of a Commodore 64, or a .5 megapixel camera at best. But alas, it's not...welcome to Legoland!

Come out to Veritas at UCSF!

2009-04-03T21:44:00.000-07:00

We're hosting a Veritas Forum at UCSF (our first ever!), and we're honored to have Bill Newsome as our speaker. Newsome is chair of neurobiology at Stanford and renowned for both his work on the intersection of monkeys and ethics and the intersection of science and faith. At our forum, he'll be talking on the latter:

Science and faith: the vantage point of one neuroscientist

I am a practicing scientist and a practicing Christian—commitments that are inconsistent in the minds of many. While I encounter tension at times between my science and my faith, my overwhelming belief is that both science and faith contribute critically to a meaningful, fully-experienced human life. Giving up either would result in a regrettable loss of understanding, depth of experience, and simple joy in my life. I believe that much of the perceived incompatibility between science and religion is specious, although real tensions do exist. In this talk I will lay out the central issues from my point of view, hoping to dispel some of the false conflicts between science and faith while bringing into focus real choices that need to be made.

The event's on May 5th (that's right, ¡Cinco de mayo!) at 6pm, in Cole Hall at UCSF (513 Parnassus Ave, San Francisco). Drop by if you're in the area! And feel free to peruse our planning and Veritas pages for more information.

On The Mark video scoring system

2009-03-15T13:28:00.001-07:00

One of the challenges of behavioral research is getting "high n," or enough subjects for a statistically relevant result. "Low n" is a chief thief because it can raise false hopes with statistically significant results between two or more groups, only to undergo a "zipper effect," where all the groups zip up into essentially one population, and statistical significance is stolen.

Once high n is achieved, another challenge is how to score them. Typically behaviors are recording through surveys, audio devices, or video acquisition. Videos are valuable because they allow one to record, view, and re-view data again and again. They're also a bit of a curse because it can be difficult to juggle all the video controls while writing or typing behavioral events--each time they occur, when they start, when they end, as well as other events in-between. Viewing quickly becomes re-viewing, and re-viewing, and re-vewing again and again for the most accurate records.

It's enough of a deterrent that I've left a ton of my own videos sitting on my computer, waiting to be analyzed. That's when I decided that I needed a simple video annotation system to score behaviors. That's when On The Mark got started!

From scoring videos by hand, I found that just a few key features are almost universally necessary for accurate video scoring. One is a mark function, both for the start and end of an event. Another is a back function, where the video can be shifted back in small increments in case a behavioral moment was missed. A third is simple video resizing to get the best image for the monitor size. Quick export to Excel or other spreadsheets also helps. And ideally, all of this needs to be done with as few keystrokes or mouse clicks as possible.

These are the goals and features that have inspired On The Mark. To mark events, a control unit has a simple mark on/mark off button. Each event type gets its own dedicated control unit (which can be added or deleted depending on number of event types), and all control units are visible simultaneously to allow marking of multiple events back-to-back or even concurrently. Events get fed to a table for ease of display and copy and pasting to spreadsheets. The video itself can be displayed either "inline," so that the entire window takes up just one column of one's monitor, or "side-by-side," where the video can be widened to maximize viewing of subtle behaviors and events, all by dragging the window wider. Playback has the oft-used slider and a one-second rewind button to catch that just-missed event.

What makes writing this so simple is the advent of JavaFX. I've written a fair number of Java programs with GUIs, and while the Java Swing GUI is very powerful, it can be complex and cumbersome to get started and add elements. Hard enough, that is, that I even switched to the Eclipse SWT toolkit for one project, which brought new features but additional complexity as well. Apprently one of the goals of JavaFX has been to resolve the complexity of Java Swing. So how does JavaFX actually do that? From this first forray into JavaFX, it simplifies a lot of the programming into script-like events and makes Web 2.0 features such as animations and shadow effects straightforward to implement.

If you want to give On The Mark a run for the money (it's free though), you can launch it through Java Web Start on the homepage. It's hosted by SourceForge.net, so all the details and source are available there as well. As usual, comments/feedback are more than welcome.

tXtFL 1.0

2009-02-15T11:40:00.000-08:00

I can't believe it! tXtFL 1.0 is here! I can't believe it!

Weather on Vacation

2009-02-15T11:10:00.000-08:00

It's almost the President's Day holiday on the 16th !

And evidently the weather gets a day off too.

Tiffany and I wish our allergies went on vacation too.

Windows 7: First Experiences

2009-01-19T23:00:00.000-08:00

One of the best parts of running a Mac is that now I can install Windows 7 on it via VirtualBox for MacOS.

Of course, it would be better if MacOS allowed itself to be run on other computers...

Egypt!

2008-11-30T22:16:00.000-08:00

More pix on the horizon!

ssh -NfL

2008-10-03T21:53:00.000-07:00

Probably at least once in life you've heard the old adage, "It's more powerful on the command line."

But never before have I encountered a command-line argument this powerful. I thought that ssh was powerful, what with its X11 forwarding and secure encryption and all. But just when I thought that the command line had reached its limit, the command line morphed and merged with the full weight of the NFL. Now introducing: ssh -NfL.

ssh, or Secure SHell, is an encrypted way to log into computers remotely, usually through the command line. VNC, or Virtual Network Computing, is another way to log into a computer remotely, but through sharing a screen. VNC with ssh tunneling is a way to combine screen sharing with the security of ssh.

Several websites give helpful hints on how to create ssh tunneling, and for awhile I used a sophisticated solution I found that involves a single line that creates the tunnel, establishes the local connection, and loops a sleep command to auto-close the client. The only problem was that for some reason the connection always seemed slow. I always thought that it was a limitation of my home internet, but one day I noticed that my girlfriend logged into her VNC server from my home with tremendous response rates.

And that day I stumbled upon a new command. A command alone worthy of the heavyweights of Joe Montana and Steve Young. An NFL command.

ssh -NfL creates a fast ssh tunnel with minimal coding. I don't even know if it's technically superior to the more sophistated command I was previously using, but there's no doubt that it's symbolically more powerful with -NfL by its side. What does the NFL do for ssh? "N" is an option not to present a command prompt to the user after logging in, allowing the user to continue operating from the local command line. "f" puts the ssh tunnel into the background, also to free up the local command line. "L" does the dirty work, creating the tunnel by forwarding a local port to the remote server.

And that's it! I did find the commands a little unwieldy to type in by hand on a regular basis, so I wrote up a little script; feel free to use it and comment on how to improve it as well. Now VNC through ssh tunneling is a speedy matter, bringing me from home to work insuperably faster than even the Grey shuttle can.

Atom-based medical tablets: the way of the future?

2008-09-27T17:54:00.000-07:00

I saw a recent Crave posting on this new Atom-based netbook tablet that will be marketed for use in hospitals and other medical settings. I've been craving a netbook but as a poor grad student still lack the funds to procure even one of these. Maybe when the Atoms become as cheap and ubiquitous as K atoms (or ions), I'll pick one up. Or maybe by then I'll finally be on the wards and can use one of the hospital's tablets.

(CNET photo of a the upcoming Panasonic Atom based tablet)

Dunder Mifflin would be disappointed by the paperless system, but DunderMifflinInfinity.com might be better prepared.

The tXtFL Season Has Arrived!

2008-08-31T21:30:00.001-07:00

The football season has finally arrived, and it feels like forever since I've worked on the tXtFL football simulator. This past Labor Day weekend I've finally had a chance to labor on tXtFL and work on an oft-requested feature: multi-game automation.

One of the tasks for any simulator is simply to figure out whether it's actually a simulator. In other words, it would be terrible news to find out that a football simulator never simulated anything close to reality, or even worse (or better, depending on how you look at it), if a football simulator is a better simulator of baseball or cricket.

tXtFL has simulated scores fairly accurately in recent versions and even came close to predicting the historic final Patriots game of the regular season last year. But it's hard to get a clear grasp of statistics with only a few simulations to compare against each real game, and the same model fell short of predicting the following Super Bowl upset. Of course, one could spend hours sitting on the Enter key to generate hundreds of games and then manually compile them for comparison against raw NFL data. But shouldn't there be an easier and more robust method?

It turns out that the first step to multi-game simulations was easier than expected and only involved centralization of code handling user input and a few automation functions. Now tXtFL can run games in full AI mode of the same two teams theoretically up to thousands of times. Games are played back-to-back and cycle with only initial user selection of teams.

The next steps will be to save that output, ideally in a format that could be fed into Matlab or R or other statistical software for a more thorough computational analysis. We could check individual player stats against historical data and also analyze its predictive power of games and seasons. Hopefully we can figure out how to run it on a cluster. And hopefully our simulated stats will eventually cluster around reality?

Fedora 9 Server Upgrade Experiences

2008-07-18T22:48:00.000-07:00

I recently upgraded my aging server from Fedora 7 --> Fedora 9, now that the 7th distribution is no longer supported. Fedora 7 was an old favorite, a trouble-free experience to both my laptop and server, a 7th-inning stretch if you will. But alas it's baseball season, and the 9th inning has arrived, and it's come time to get on board before the game is over. As usual I'm providing a summary of my experiences in case you might find it useful for your own upgrade.

Netinst Installation CD

My server dates back from the last millenium and is pushing a decade since its birth in 1999. A Pentium III 450 MHz, it's done its share of work but presses on. Even if it doesn't have a DVD drive. I needed a way to install by CD, and rather than downloading the entire 6-volume set, I learned that new to Fedora 9 is a "netinst" disc image that replaces boot.iso, rescue.iso, and diskboot.img and provides "everything the user needs to install a system over the network."

It serves as a small disc that contains just enough to run the installer, download the files for an installation, and even rescue a system. One just needs to remember to point the URL to the official Fedora 9 release rpms, such as http://mirrors.kernel.org/fedora/releases/9/Fedora/i386/os, or of course to a local repository of mirrored Fedora files.

During the upgrade, my internet connection went down, and the netinst install failed at the final file. Not to fear. A retry completed the upgrade, and Fedora 9 came to life on my server.

Web Server Down!

A quirk from the initial release of Fedora 9 is that the httpd Apache web server failed to start on several of my machines. Apparently some libphp module couldn't be found, and the server never started. Again, not to fear. A sudo yum update resuscitated httpd, and it started serving pages immediately.

Subversion Subverted

While updating some CCF web files, I found that I couldn't commit my changes to the server. I got

can't open db activity permission denied

error messages when running svn commit commands. At first I thought that the permission bits had been misapplied, or perhaps files had been overwritten by a different user, but even setting permissions to 777 failed to permit commits.

Eventually I came across a solution on a Fedora forum that pointed to an SELinux context error. Apparently during the upgrade, the security labels got changed, flagging SELinux to prevent those files' usage. One workaround was to switch SELinux from "enforcing" to "permissive" mode via

sudo /usr/sbin/setenforce 0

Of course this change dramatically alters security just for Subversion. An alternative solution is to restore the context of the Subversion files. I saw "httpd_sys_content" several times in forums but didn't find the label to solve permission erros on my machine, so I left the server in permissive mode while making a file commit. One of the files that gets changed during a commit is /path/to/repos/db/current. Using ls -ldZ /path/to/repos/db/current, I found that the file had been labeled to "unconfined_u:object_r:httpd_sys_content_rw_t".

That last bit was what flagged me that a similar "httpd_sys_content" label might work. Using

sudo chcon -R system_u:object_r:httpd_sys_content_rw_t /path/to/repos
sudo /usr/sbin/setenforce 1

I found that I could again commit files with SELinux in enforcing mode. Note that I used "system_u" rather than "unconfined_u" and that SELinux is still much of a mystery to me.

Fun with Fedora? or Fedora frustrations? As with most things Linux, how can there be one without the other?

Foggy

2008-06-24T11:39:00.001-07:00

I just noticed the fog icon for the weather feed on Google Calendar. But I thought every day is foggy in San Francisco? Or maybe that's just because I live in the Sunset.

Google Calendar, SF Sunset Edition

Dual Display

2008-06-08T01:14:00.000-07:00

At a product vendor fair today during the ADA conference, pioglitazone maker Actos made it clear to me that multi-tasking with a penlight can be both fun and productive. The dual snake penlight/laser pointing device can be employed for a majority of tasks, most typically to doubly highlight extremely important points during talks or, while using the LED light to read papers in dark corners of the night, to "virtually underline" text with red laser.

A brief demonstration of the "hands-free" lighted reading paradigm. Guaranteed to impress your colleagues at any time of the day.

Actually, it is a pretty cool contraption, maybe useful for some quiet reading on a late-night shuttle ride home.

A Dream Come True?

2008-05-13T23:48:00.000-07:00

This is almost too good to be true. Ubuntu 8.04 LTS in VirtualBox seamless mode, plus Fedora 9 via VNC, all within Vista SP1. All virtually configuration-free (literally!).

How is this possible? Several recent developments in the open source world collided to make this near-paradise a present-reality.

VirtualBox released a new version (1.6) with "Seamless Mode" for Linux guests. This mode has been available for Windows guests, but only now has it become available in the other direction, a great boon for the ubiquitous Windows desktop in need of Linux support on the side. Perhaps Sun's recent acquisition of Innotek, makers of VirtualBox, propelled the feature? It may have already been on the cooker.
Ubuntu released version 8.04 LTS (Long Term Support) just last month. Although I could not get a Fedora 8 guest to run successfully in seamless mode, Ubuntu 8.04 worked without a hitch.
Give up on Fedora? Not quite so fast. Fedora 9 made its debut today and installed on my trusty Dell laptop without complication. That's it, there's almost nothing buggy/techy to report.

Amateur Architecture

2008-05-12T09:23:00.000-07:00

While searching for a way to launch Text Trix through Java Web Start, I stumbled upon another Web Start application: Sweet Home 3D. This application launched with a simple URL link and took me to an architectural planning grid, with drag-n-droppable walls and furniture items.

I'm no architect, but I can drag-n-drop, so I designed an amateur mock-up of a "living bedroom," a living room with a built-in bedroom. Sweet Home 3D comes with some catchy bird's eye and human's eye views, including a "virtual tour" option with adjustable body and head angles to take in the room's entire view.

If you take a closer look at the living bedroom, you'll notice one of its unique and advanced features: a bench and stool (on your right), suitable for a mini late-night laboratory in case you need to finish up a Western at home. I was hoping also to add an incubator, but could only find an oven.

Of course this all started with a search on Java Web Start for Text Trix deployment. Here's a snapshot of a first launch. It's nothing exceptional, but at least this time there's no exceptions (null pointers included!).

Catching Up on the Past Few Months

2008-04-12T01:38:00.000-07:00

In-between time spent with my mice at lab, I've been blessed to spend time with good friends, good places, and goodness knows what else.

City Church Retreat 2008. Colin, Christine, and I wind our way through the rainy redwood forest surrounding the Mt. Hermon area near Santa Cruz on our first ever City Church retreat.

Veritas Forum at UC Berkeley. Me and my grad buddies Chris and Angela take a photo op with the Veritas speaker, Tim Keller, author of Chris' now-autographed copy of The Reason for God.

Community Group Snow Trip. My car (Colin, Brenda, me) at the start of our two-day ski/board adventure through Northstar at Tahoe. Our smiles grew only bigger as we entered day 2 and found a secluded "secret" lift, complete with access via rope tow. Yes, rope tow!

Tiffany &co. return from Irvine. Cognitive neuroscientist Tiffany pays us a visit after her winter quarter at UCI. The "cool half of the table" (Bernice, Tiffany, Angela, me).

Phone System Prep for The Game at UCSF. Ken and I stress test the automated, menu-driven phone system we're implementing with Colin for the Bay Area scavenger hunt.

U-Haul

2008-03-31T00:48:00.000-07:00

Come to me, all who labor and are heavy laden, and I will give you rest. (Matthew 11:28)

Shining Out of Darkness

2008-02-26T01:00:00.000-08:00

For God, who said, 'Let light shine out of darkness,' has shone in our hearts to give the light of the knowledge of the glory of God in the face of Jesus Christ. (2 Corinthians 4:6)

That was the theme verse my sister imprinted on the T-shirt design for my junior high fellowship, Sonlight. We aligned the words of the verse on separate lines so that the letters SONLIGHT shone out vertically in bright fluorescent yellow. We got it printed and were quite proud of the design, even later when people rediscovered them during a church cleanup and started wearing them for janitorial duties.

To this day that verse—and the fellowship where I discovered it—have left an indelible mark on me. I'm still amazed how God used that little fellowship of little middle schoolers to shine light and life into me. I remember one speaker, a radio talk show host from a nearby Christian station, who asked us how far a candle could be seen in pitch dark. 10 feet? 5 feet? A couple inches, before the darkness quenched it? "30 miles," she told us. "A single candlelight in pitch darkness can be seen 30 miles away."* Imagine what that meant to little junior highers, who felt no bigger than tiny candlelights in the sometimes oppressive darkness of school and society and puberty? My eyes opened like candles as I thought of that, as I thought of God's light shining that far through the darkness, of God's light shining onto me—junior-high-me—and reflecting off me as light to those all around me.

My grad fellowship today is named, coincidentally, Sonrise (no relation to Sonlight!). We're no junior high fellowship, but I am awed at how God continues to shines his light into fellowship as strongly and steadily as I remember him back in junior high. As we travel further along in our careers, new corners of darkness crop up in our lives as we face new dilemmas, disillusionments, doubts, yet into each dark corner he peers in and shines on us with his light, the light of the Son, in such a way that as the old translations put it, "the darkness comprehended it not" (John 1:5).

*I've never had a chance to verify the candlelight distance scientifically, but I'll leave it as a junior high memory and take her at her word.

tXtFL Interface Updates

2008-02-05T02:21:00.000-08:00

While visiting Andrew & Miyon in New York at the turn of the new year, I had a chance to take advantage of East Coast time with a few late-night coding sessions. Back then, the Patriots swept victory from the Giants in the final game of the regular season. But this week New York took it back in the Bowl. Evidently good things happen in New York, and it was good to me those evenings in the form of a long-overdue graphical interface update to tXtFL.

The old view, stable from tXtFL 0.7.0-0.9.2 (2004-2008):

The new view, currently in progress for tXtFL 1.0.0alpha2:

Lots more work left before 1.0.0. Feedback always welcome!

Farewell Luchin!

2008-01-31T02:07:00.000-08:00

Luchin's last night as our roommate. We'll miss you!

Post-Orals Celebrations

2008-01-26T15:29:00.000-08:00

Two friends from Sonrise and I took orals back-to-back-to-back last November. Months of anticipation came to a head in my dual orals (minor+major), which though stressful, proved surprisingly invigorating. So many of those papers I had been intending to read finally came out of their folders, and I finally got a chance to formally justify to myself why I was doing what I was doing. I asked for prayer that I wouldn't try just to get through it, but that God would grow me as a scientist through the entire process. He truly answered.

I'm blessed to have a wise and supportive mentor.

Ken organized a post-orals celebration, introducing me to a nearby southeast Asian restaurant that he (and now all of us) vouches for. Colin later introduced the guys to an even near-erby brewery that we hope to visit again.

The following week, I took my MSTP classmate Marcus to celebrate his orals. Chris, pictured between us, took his orals the week just before mine, which you can tell by the width of his smile in both pix.

Who Controls the World?

2007-12-24T18:34:00.001-08:00

I work in a potassium channel lab. In lab today I came across a posted copy of a National Geographic article from 2005, on spider venom toxins, which apparently paralyze their prey by dysregulating potassium channel function. The highlighted portion in the lab copy read: "So scientists seek the chemical mastery of the spider. Says Kristensen, 'Whoever controls potassium channels controls the world.'"

haha, I don't know about that! But one thing I do know--that He who made potassium channels controls and loves the whole world, no matter how chaotic it and life may seem. Merry Christmas...and in light of the potassium-richness of bananas, remember to eat your banana starch cookies* this season!

* Bello-Perez LA, et al. "In vitro digestibility of banana starch cookies." Plant Foods Hum Nutri, 2004:59(2), 79-83. (But in moderation, of course!)

Flyby Mt. Parnassus

2007-12-15T10:46:00.000-08:00

Back in college I remember discovering one of the only flight simulators available for Linux, an open source project named Flight Gear. I never got it working on my computer, but the screenshots online looked fascinating. And for some reason the project centered its scenery details on KSFO, the airport I passed by every time I drove to college.

Today I decided to give Flight Gear another run, this time on my Windows desktop. It worked. And it was beautiful. I share with you two screenshots I captured of flybys around the San Francisco area. My first orienting landmark was none other than Sutro Tower on Mount Parnassus (aka Mount Sutro), in whose shadow I now live.

The Flight Gear T-38 trainer flying by Sutro Tower, perched atop Mount Parnassus and its UCSF surroundings. The T-38 was one of my favorite jets growing up, perhaps because of its role as an advanced and beloved trainer. In the distance the Golden Gate Bridge pokes through the haze.

Another shot of San Francisco, this time of downtown Market area. Notice the Bay Bridge peeking out from the background.

And of course, next due is a flyby of UCSF Mission Bay.

Basically Green

2007-12-07T09:59:00.000-08:00

California seems to make it into Nature News almost as if it were a country in itself. In this week's issue, Nature reports on green technology as "California's latest gold rush," where venture capitalists pour millions of greenbacks into green technology. Roughly $725 million found its way into CA coffers of the $2.6 billion total venture capital over the first three-quarters this year, up from $1.8 billion in 2006. Of course, to put it into perspective, Genentech apparently spent $1.8 billion on R&D alone in 2006.

So where is all this money going, and will it turn into not only sustainable resources, but also sustainable technology? Here's a quotation from the article, with a comment on the basic science aspects of the investment:

There is always a chance that the current wave of investment could peter out, perhaps owing to a substantial fall in oil and energy prices, or a fading of environmental concerns — but these are unlikely. The biggest risk is that the pace of basic technological improvements may fail to provide a pipeline of emerging technologies that venture capitalists can feed off. Venture capitalists are not in the business of funding the basic research that will be needed to make the sort of breakthroughs needed to make solar energy cheaper than coal. Without a significant expansion of public spending on basic energy research, the innovation pipeline risks drying up.

"The biggest risk is that the pace of basic technological improvements may fail to provide a pipeline of emerging technologies..." Of course, this is coming from a journal publishing some of the most prominent articles of basic science research. But it's helpful to be reminded that the building blocks, however tiny, being created day by day in basic science labs may actually form a foundation helpful and perhaps necessary for future technology. I have become particularly interested in translational research in my own projects, but even in translational work, the translation to the clinics starts with the basics.

Reflections from The Blind Side

2007-11-25T23:45:00.000-08:00

Inspiration for development of the next version of tXtFL.

Retreat to Pt. Reyes

2007-11-03T10:09:00.000-07:00

Me and my grad buddies on the way to Sonrise Fall Retreat.

Weekend Wedding Spectacular

2007-10-22T01:10:00.000-07:00

I spent this weekend at Andrew Chau & Kelly Suen's wedding extravaganza. Their theme was "Better Together...," and as the celebration unfolded I saw how they not only celebrated togetherness in their new oneness. They also paid such attention to bringing friends from all different parts of their lives together into the same circle as a reflection of their own welcoming hearts.

(a shot of the bridal party from the best man's camera phone)

"Whose mind is stayed on you"

2007-10-13T13:54:00.000-07:00

I came across this verse that had been such an encouragement to me in high school and college but which I had laid by the wayside in grad school. There's no better time than now to re-remember.

You keep him in perfect peace
whose mind is stayed on you,
because he trusts in you. (Isaiah 26:3)

During nightly prayers I notice that my mind can wander as I try to interpret the day's events or prepare for the next day. Sometimes I anguish over what's past or worry over what's to come when ironically I am praying and should be casting my cares on God. I've found it easy to pray, but not always so easy to pray to God, to truly stay my mind on him and trust in him. But when that happens, when my mind focuses less on myself and my perceived troubles, prayer becomes less of a repetitive, fruitless counsel with my own soul and more of a conversation with a warm and wise Father.

And here's another quotation, this one from my brother:

A pastor once said that God likes to do things by process instead of instantaneously. For example, He could have made the heavens and earth in a split second, but He chose to take days or eons (depending on interpretation) to do it.

I hadn't thought of why God took so long to make this world. I guess he has, as the saying goes, all the time in the world. When he tells me to "stay" my mind on him, I suppose that doesn't mean to think about him for one prayer, or one day of fasting, or even one trial. He wants my mind to "stay" on him, for now and for days and for eons, knowing that he will be faithful and trustworthy for just as long and longer.

Sharing an external hard drive: bypassing automount

2007-10-13T12:21:00.000-07:00

With my impending oral exams, my collaborator at lab and I need to pass back and forth multiple image files and data sets. In the past this made for numerous burnt DVDs and shuffling of USB stick drives, but we wanted a way to go green and tap into the hardwired network here.

I had Windows XP Home on my computer, which made for generally seamless computing but frustrating networking issues. After wiping out my drive and installing Fedora 7 Linux, I actually look forward to returning to my desk each morning. Linux certainly provides a more trustworthy set of networking capabilities for my needs at lab. But one thing I've learned: while Linux is more customizable and reliable, it certainly isn't easier, at least for the uninitiate.

A recent issue I ran into was how to share an external hard drive with my collaborator. The system automatically detected and mounted the drive without a hitch so that I could use it without restriction. My collaborator could log into his account remotely and read files at will, allowing me to pass 15MB papers and gigs of past imaging data. The only problem was that he couldn't write to the drive (which was his, to be exact).

The solution ended up being fairly straightforward with the aid of google, and I document it here (in case you don't have google...hahah j/k):

gnome-mount is a tool that automatically mounts drives and discs. It reads from the gconf configuration to apply a limited and restricted set of options that in my guess usually suffice for everyday usage--whoever plugs in the device can use it, but no one else can.

I needed either to add extra options to gnome-mount or to bypass it so that my collaborator could also write to the drive. I learned about an easy way to configure these options by using another tool called gconf-editor, similar to the Windows registry editor. I tried adding the uid and gid (user and group, respectively), but, alas, to no avail--the gid bit just didn't take. Multiple uid's are apparently fruitless as well.

The gnome-mount tool is fairly well-documented in its man page, which said that gnome-mount will check /etc/fstab before mounting to give it priority. In the old days drives were mounted by hand according to specifications found in /etc/fstab. My next option was to bypass gnome-mount by adding the drive to the fstab. I found a site explaining the various options for mounting such a drive and added it to fstab. I placed the relevant user accounts into the same group, added the group to the drive's gid, mounted the drive...and it worked! My collaborator and I could both read and write files from different accounts, while still preserving security.

One caveat is that gnome doesn't appear to treat the drive exactly as an equal. For example, while editing a text file, gedit tells me that it can't make a backup file. I can still save it though, and I'm glad to focus less on computing and more on collaborating here in lab.

Visiting My Brothers

2007-09-22T22:17:00.000-07:00

Andrew and I while crossing the Brooklyn Bridge.

Art with Ashley and Kristin trying to cross the kitchen at home in Boston.

Install Notes: Fedora 7 on Dell 700m

2007-09-10T04:59:00.000-07:00

Networking on my work laptop of 2 years has been having issues, so I decided to wipe the drive and replace WinXP with Fedora 7. I have a standard Dell 700m laptop. Some notes from my installation/configuration experience:

Installation: Fedora 7 installed without a hitch. I downloaded the live CD, which boots into a fully operational version of Fedora for using and testing. I clicked a desktop icon for installation to the hard drive, which apparently copied an entire disk image, without having to choose which individual packages to install, as in past Fedora installations.
First boot: Almost every basic function worked out of the box. Even wireless was up and running without special configuration. One noticeable shortcoming however was the screen resolution. It was set to a standard resolution of 1024x768, even though my laptop has a widescreen 1200x800 display. Going to the Screen Resolution configuration utility, I had no widescreen option.

I read on another blog that the problem could be fixed by installing something called 915resolution, where 915 refers to the Intel 915 chip. The Dell 700m laptop actually has an Intel 855 chip, whose driver was installed by default, but the new 915 driver seems to work better. To install, I opened a terminal and (as root) ran yum install 915resolution. I next edited the file /etc/sysconfig/915resolution with the line RESOLUTION="7e 1280 800". After restarting the X server (logging out and back in), widescreen was up and running.
Suspend/hibernate: I first tried hibernate options, to no avail. Some blogs have posted success using swsuspend2 on Dell 700m laptops, after some configuring. My experience has been that the screen resolution keeps returning to 1024x768 (non-widescreen), although everything else seems to work from cursory examination.

A new database of quirks has been created in preparation for Fedora 8 to show tips on getting suspend/hibernate and other functions working on specific laptops. From running a quirks script I found there, I learned to replace the i810 driver with the intel driver. I changed drivers through System > Administration > Display > Hardware > Video Card, where I picked intel, as advised by the Fedora 7 release notes.

After switching to the new driver and making the configuration updates for swsuspend2, I tried the built-in Hibernate mode, which I think uses swsup included in the default kernel. It worked! Even widescreen and wireless resumed, although I haven't checked much more.
Virtualization: Fedora has been providing virtualization support through Xen for quite some time, continually adding new features. I had a good experience with another vendor, however, a company by the name of Innotek that has released a virtualization software called Virtual Box for Windows, Linux, and MacOS. All versions are open source and free for download, with additional licensing requirements only for large enterprise users. Guest additions for a Fedora guest have worked out of the box for both my Windows Vista and XP hosts. I wanted to see if installation in the reverse direction--WinXP guest on a Fedora Linux host--might work as seamlessly.

Virtual Box recently released v.1.5.0. I downloaded the latest copy (for free) and installed it on Fedora. WinXP Pro installed without issue, and I installed Guest Additions. v.1.5.0 introduced a new features called Seamless mode, where the Windows windows are each treated as another window in Linux, with the toolbar built into the bottom of the screen. This is an improvement from normal modes, where the whole Windows desktop would be contained in a separate window, with smaller Windows windows inside. Enough "windows" to deal with, eh?

One hitch was that the Shared Folders feature wasn't working from the start, so I couldn't read files from Linux on Windows. I had to manually transfer each file I wanted to read or write. Following advice from a Virtual Box forum, I removed the shared folder --> uninstalled the Additions --> rebooted --> reinstalled Additions --> rebooted --> re-added the shared folder, and now I can read/write files in Windows from Linux. I'll keep watching to see if it keeps working.
SD card reader: Linux detected a 512 MB SD card I inserted into the built-in SD reader and asked if I wanted to import the photos. I chose to read the card directly, as I read it in Windows, but the card sporadically disconnected and reconnected. I transfered one file, but the whole computer locked up when trying to open it directly from the card. Perhaps a kernel issue?
Compiz: Desktop Effects looks quite nifty, what with the wobbling windows, spinning workspaces on a cube, and bendable windows. I unfortunately experience window blackout issues with Desktop Effects plus Virtual Box Seamless mode, so I've switched off the Effects for now.

Overall I have thoroughly enjoyed running Fedora on my Dell 700m laptop. A few extra configuration tips helped bring my laptop up to speed with the latest in multimedia effects. Virtual Box has allowed me the best of both worlds, so that I can script and network easily in Linux while still viewing and manipulating my confocal images Windows...all the while listening to iTunes, of course.

Summer in the Sunset

2007-08-05T09:51:00.000-07:00

Every summer day I waken
To the sun's reminder
That its rays are not for me.

-resident of the Sunset District of San Francisco

Australian Awe

2007-07-25T00:26:00.000-07:00

A few photos to recap my recent trip to Australia.

Our (my parents and I) started our journey in sunny Sydney. Oh wait, it's winter there, right? Check out those clouds. Winter in Sydney was no colder than summer in San Francisco, though, so we felt right at home. In fact, Sydney seemed like a bit like a union of San Francisco with its color and casual culture, and New York with its metropolitan flair. But the miles and miles or pristine beach made Sydney something quite unique. Read on.

Traveling into the Circular Quay by train, we emerged onto an impressive, sweeping view of the entire Sydney Harbor at once. To our left was the Sydney Harbor Bridge, shown here. To our right we gazed on the Sydney Opera House (see below). This shot of the the bridge in moody weather was taken from a perch in the Opera House designed to resemble a captain's bridge.

This shot sits atop my desktop as we speak. I still can't get over this ship. Is it a boat, or a brick?

Here's one of my favorite shots. On the Eastern shores of the city, one can stroll across miles of the Bondi beach. It's winter, but no one seems to care. Multiple rocky crags jut out into the ocean and make for picturesque perches of the wild beyond.

Our ferry ride to Manly (yes, that's the name of the Northern section of the city) brought us some unexpected torchlike dusk shots of the harbor. It's hard to tell which one is the boat, isn't it? It's as if the Opera House could sail away at any moment.

The ironic thing is that the kid on the left bumped his head on that green sign as he was standing up. Poor thing. He was headed out to Manly, though, and as we all know, the road to Manhood is a difficult and arduous one.

I don't know if they designed their city to look like a painting, but I wouldn't be surprised if everything's made out of canvas. But the bird's for real, that's for sure. I saw him move and fly away. Or did I...?

Back to Bondi, for a sec. Some people swim in swimming pools. Others swim in the ocean. Still others swim in swimming pools that are the ocean. In this pool you get just that--the calm waters of a pool, but also the occasional ocean wave careening up over the wall and down into the pool. It's just a gym, but I wasn't about to ask what their membership fees were.

"Wait, did you spend your entire trip in Sydney?!" Well, no, not quite. We took a spectacular flight to Uluru, where we stayed in Yulara and saw the mighty Ayers Rock. At the time I had no Internet connection but did have Ubuntu Linux newly installed, and what better way to celebrate Uluru than with Ubuntu? (Ubuntu is actually a South African term that means something akin to "humanity toward others"...South African, so at least we're in the right hemisphere.) One of these Ayers Rock shots sat atop my Ubuntu desktop.

And, yes, I did see a kangaroo. His name was "joey," with a lower case "j". That's because, as I would later learn, all baby kangaroos are called "joey"s. We saw him at a fruit stand in Cairns, and knowing it might be my only kangaroo view, I started snapping away as many shots of him as my little camera could carry.

And the rest of Uluru and Cairns? Alas, they're probably better experienced than pictured. Or you can peruse a wider selection of shots here.

Fedora 7 Installation Notes

2007-06-25T22:09:00.001-07:00

Fedora just released version 7 of the classic Linux distribution, and I've been looking forward to upgrading my server. I chose an in-place upgrade via yum, a handy tool for installing and upgrading files directly off the web. Since it's so easy to forget the details, and others might be interested in learning them, I've cataloged a few notes on my experience with the upgrade process.

http://fedoraproject.org/wiki/YumUpgradeFaq

The upgrade FAQ contained most of what I needed to know. They even have a special "FC6 --> FC7" section, which answered (almost) all of my questions. A few extra notes:

It at least doesn't hurt to run rpm -e rhnlib up2date prior to following the "Instructions to upgrade using yum."
Under the "Tip: Find and review 'lost' packages": yum install yum-utils; package-cleanup --orphans merely lists the packages that are orphans, rather than uninstalling them. That turned out to be a good thing, as I realized that several files are "fc7" versions, meaning that they were just installed with the upgrade.
As the FAQ predicted, my system hung with a GRUB message after install. To "boot into rescue mode," I had to download the rescue disc, which can be found here, for example: http://mirrors.kernel.org/fedora/releases/7/Fedora/i386/iso/F-7-i386-rescuecd.iso (a similar file path can be followed from other mirror sites). After booting the rescue disc, mounting the system (chroot /mnt/sysimage), I had to follow the advice of another website by using the command, grub-install --recheck /dev/sda. Note that I have a standard IDE drive, mapping to /dev/sda, but SCSI and other drives might map differently.

Welcome to Moonshine, Fedora 7!