Monday, December 24, 2007

Who Controls the World?

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!)

Saturday, December 15, 2007

Flyby Mt. Parnassus

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.

Friday, December 07, 2007

Basically Green

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.

Saturday, November 03, 2007

Monday, October 22, 2007

Weekend Wedding Spectacular

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)

Saturday, October 13, 2007

"Whose mind is stayed on you"

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

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.

Saturday, September 22, 2007

Visiting My Brothers


Andrew and I while crossing the Brooklyn Bridge.


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

Monday, September 10, 2007

Install Notes: Fedora 7 on Dell 700m

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.

Sunday, August 05, 2007

Summer in the Sunset

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

Wednesday, July 25, 2007

Australian Awe

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.

Monday, June 25, 2007

Fedora 7 Installation Notes

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!

Australia!

Just got back from vacation to Australia with my parents! You can take a glimpse of our journey here:
http://picasaweb.google.com/davematthew/Australia

Sunday, May 13, 2007

At Clearlake on the Sonrise Spring Retreat

This past weekend Sonrise ventured to Clearlake, about an hour north of Santa Rosa, for a lakeside retreat and speaker series on "Faith, Hope, and Love." I had a wonderful time conversing with many I've never had a chance to talk with extensively at Sonrise. The scenery was gorgeous, expect perhaps...the lake. The name "Clearlake" was accurate in all parts except the "clear" portion. But the retreat was still more than wonderful, and one of the highlights was a hiking trip to Table Rock, glimpsed below:



A few rolling fields greeted our entrance to the hike. We wanted to stop and roll down them, but the rocky road lumbered on.



One of the crags that afforded many photo ops and a lookout of the road ahead.



One of those photo ops, with Rich and his friend Chris.



Another groupie, this time with Ken.



James, Elaine, and Debbie haul themselves up the final sprint to Table Rock on a path resembling rock-hardened mud.



After we viewed the first sights of impressive heights, Johannes showed us another rocky projection, this one with a 500+ ft sheer drop.



Elaine and Irene perch atop the projection, with the entire valley below as backdrop.



Ken rests after scaling the face (j/k).



Ok, let's try to remember to step *for*ward after this shot's taken...

Why was this vista called "Table Rock," if it didn't have any "table"? Maybe the ground itself resembled a tabletop, with the entire view as a feast for the eyes. And for our retreat at least, God's gift of sweet fellowship all around us.

Friday, March 02, 2007

Neuro class trip to Tahoe

This past weekend my neuro first-year class took a trip to Tahoe. A weather-less drive up and clear morning lulled us into the cheerful complacency you see below.

30 mph winds of whipping snow ground us down, but the joyous powder offset any complaints and kept us smiling at the day's conclusion.

If you look closely, I'm buried in that pile on the right side of the picture, next to the guy ready to shovel me out. j/k...this is a shot of our cabin not long after we left.

We noticed a missing chain after returning to our ski rentals. Fortunately our NASCAR pit stop crew rose to the challenge and gave their thumbs of approval.

You might recognize the cup, from In-n-Out while driving into Tahoe. But our Tahoe experience proved to be something more like In-n---------Out, as the snowy, slowy road suggests.

My driving companion tried to frighten away the snow, but alas--to no avail.

It's good to be home!

Saturday, February 03, 2007

tXtFL Super Bowl 1.0


I've been playing the Colts vs. the Bears in auto-mode as a way to test the tXtFL game model and make a few hazy predictions about Sunday. The conclusion so far in the 7-game tXtFL Super Bowl series is that the Bears will win...but also that the tXtFL game model still requires considerable refinement.

So will Chicago come out ahead? Will Grossman gross 600+ yds, according to our game model? Probably not, but it'll be fun to see how Manning mans his terrific offense against the determined defense of Urlacher and friends.

Monday, January 29, 2007

Struggling with who to root for in Super Bowl XLI?

Apparently I'm rooting for the Chicago Bears.

http://playoffs.nfl.com/bandwagon/

A simple "5-question, 1 Answer" psychological test could mean the difference between celebration or sorrow this Sunday evening.

Sunday, January 21, 2007

Update: VMware-Tools in Fedora Core 6

I recently installed Fedora Core 6 on VMware Server 1.0-beta on my laptop. I later updated it to Server 1.0.0 and updated Tools through a lengthy procedure. Today I attempted a similar installation, this time with Server 1.0.1 on my desktop. Installation worked without a hitch, but configuring VMware-Tools was another story. Apparently most of the tweaks employed during the last installation have been fixed, but a few new tweaks were necessary here.

Installing Fedora Core 6 on VMware Server 1.0.1

I installed Server on a Windows XP SP2 Pro system. To install Fedora, I used the Red Hat Linux configuration and created a fixed-size SCSI hard drive with LSI Logic since FC5 at least didn't detect BusLogic hard drives. FC6 installed without incident.

Installing VMware Tools

Server 1.0.1 comes with VMwareTools-1.0.1-29996. I mounted it via the menu entry, VM > Install VMware Tools, and installed the RPM. Next I configured Tools with the command, vmware-config-tools.pl. That's where a couple problems began.

Fix vmxnet for Kernel 2.6.19

Linux kernel 2.6.19 apparently introduces a change where CHECKSUM_HW has been dropped in favor of CHECKSUM_PARTIAL. This change causes the Tools configurator to stop while compiling vmxnet, a VMware ethernet adapter superior to the default Vlance module.

The fix posted on the VMware user forums is to cd /usr/lib/vmware-tools/modules/source, extract vmxnet.tar, and edit vmxnet.c to change all references from CHECKSUM_HW to CHECKSUM_PARTIAL.

vmxnet now compiles...but now vmhgfs compilation fails. Another fix is necessary.

Fix vmhgfs for Kernel >= 2.6.18

vmhgfs is a component for the Shared Folders feature of Tools. The first problem during its compilation was with a function HgfsChangeFileAttributes in driver.c of vmhgfs resulting from a change introduce in kernel 2.6.18. The fix is to extract vmhgfs.tar and edit driver.c with a patch from this post.

Another tweak to driver.c remains. References to u.generic_ip need to be changed to i_private, and inode->i_blksize = HGFS_BLOCKSIZE; must be commented out.

And VMware Tools installs without a hitch (besides a few warnings)!

Notes
  • Incidentally, vmhgfs is actually for VMware Workstation and irrelevant for Server. So why go through the trouble of fixing its compilation? If you ever want to save the virtual machine and install it on VMware Workstation, the Shared Folders feature would become available and utilize vmhgfs. Of course, it might be useful to look into this ahead of time to see if it's worth hunting for the fixes...
  • The desktop running FC6 on VMware has twice the RAM (1 GB-->FC6) of that devoted to FC6 for a similar setup on my laptop. FC6 took several hours to install on my laptop, so I figured that I would start the installation just before heading to bed and let it install in my sleep. Perhaps because of the RAM increase, the installation was finished...before I even finished my evening prayers. The desktop has a newer processor and a speedier hard drive, which may have also contributed to the speediness.