Monday, November 17, 2008

Secure Virtual Network Computing

With the ever increasing speed of internet data transfer, virtual network computing (VNC) has become a viable alternative to stand alone work stations with duplicate software installations. VNC enables users to access the desktop of a work station remotely via the internet through a slim client computer for the processing of data with heavy-weight applications. Commonly, a window server application needs to be installed on the work station and a viewer application needs to be installed on the client computer to display the work station's desktop. Once the client is connected to the server, the user can work on the server like on any other desktop. Modern VNC versions even allow drag-and-drop file transfer between client and server.

Commercial VNC software is available for Linux/Unix, Microsoft Windows, and Apple's OS X operating systems (e.g. RealVNC). Apple provides simple remote desktop connectivity for its computers in Leopard (ARD 3.2). Redstone Software offers only the Vine 3.0 server for OS X (formerly OSXvnc) free and charges for a sophisticated server/client combination with which you can drag and drop files. However, Chicken of the VNC can be used for viewing on OS X as a free complement to the Vine server.

A great advantage of VNC is that the connectivity between client and server is platform-independent. Their operating systems need not be identical. I currently use TightVNC. TightVNC is an award-winning open source project offering a highly functional package for UNIX- and Microsoft Windows-based operating systems. I installed the server on a computer running Microsoft Windows XP-64. I view the desktop on a machine running Ubuntu 8.10 or on Apple computers running OS X. TightVNC comes with a platform-independent, Java-based viewer that can be used as stand-alone application, provided the Java Runtime Environment (JRE) is installed. JRE is included with OS X and can be easily installed with the Synaptic Package Manager on Ubuntu. In addition, a viewer applet can be accessed on the server through the browser. The latter option does not require any install on the client.

VNC connections commonly use ports with numbers equal to or greater than 5900. The last digits identify the display number. The user needs to register a user account with username and password on the server. The regular login dialog is unencrypted, rendering the server vulnerable to break-ins. This hazard is perhaps tolerable on a local network protected by a firewall. However, if the server is slated to be accessible over the internet at large, unencrypted login exposes the server to excessive risk. Remote login to the server through a secure shell with RSA encryption is preferable and SSH protocols provide this option.

SSH encryption is fairly safe, particularly when passphrase encryption is employed. As additional precaution, the administrator may wish to ascertain that root login is disabled in the SSH configuration script. I once made the mistake to administer a computer with superuser privileges choosing a common English noun as password. I did not know that root was enabled by default as username on port 22 in the SSH configuration script. It took some miscreant five years to guess the password, turning my machine into a reflector for evil data transfer, until the gate keepers found out about it. To preempt complications of this nature in the future, I use sudo these days, if I need to execute commands with superuser privileges.

Remote login to a VNC server from a VNC viewer with SSH entails two steps: first the connection to the VNC server needs to be successfully established via the SSH protocol, and then the viewer has to be opened using the connection. I developed a Java-based application on the intel architecture from open sources for Apple's OS X 10.4 (Tiger) and 10.5 (Leopard) that achieves this goal in a convenient amalgamated process. This sVNC client combines jcraft's SSH login with the TightVNC viewer.

sVNCIf you like to use the sVNC client, you may wish to download the zipped folder containing the application bundle with a click on the logo on the left (trademark application #77642277, pending). Copy the application to a folder of your preference. Double-click on the application's icon to launch the SSH dialog. You are asked to enter your username @ the VNC server identified by name or IP address. Subsequently, you need to provide a listening port:host:remote port combination, specifying the local host and the ports for the displays. Commonly, you can use the default combination 5900: This combination specifies the host and serves from and to displays with the number 0.  If the VNC server uses a different display number, e.g. display 1, change the first number to 5901. If you wish to use a different display on your home computer, you need to change the last number accordingly. There is no need to change the address for the local host.

After you provided this information, the SSH dialog generates RSA keys. Your consent is needed. You must enter your password for the VNC server. The connection is attempted. In case of success, you need to provide your password once more for the VNC viewer, the display of the remote desktop should pop up, and you are ready to go. The configuration options to the viewer can be found in the README file included with the application in the zipped folder.

The client works well for me. If the remote desktop seems unresponsive to clicks, hit the refresh button on the viewer's top panel. The viewer may crash when the server is accessed in a sleep state. Do not be discouraged. The viewer will work on the second attempt. I hope sVNC will be useful to you.

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Sunday, October 26, 2008

2.5-inch Hard Drive Enclosures: A Journey

Hard drives have become small theses days. I needed a handy external storage device for travels with the laptop. After considering enclosure size and prize range, I opted for a Hitachi TravelStar 200GB 2.5-inch hard drive and sought the enclosure, separately. The latter turned into an adventure.

I looked up enclosures with USB-2.0 connectivity. USB cable and a protective pouch are usually included. The first I ordered from an internet retailer of national renown had a nice steel case and the option to power it with a separate supply that was not included. It cost $30.- and came with a hefty rebate offer. I never received the rebate, because the rebate center did not accept the only proves of purchase I had, that is copies of the order confirmation and the packing slip. You will not see advertisements of this retailer on my sites.

Installation of the hard drive into this enclosure was simple. You had to remove a tiny lock-down screw on each long side, pull out the front of the enclosure with the USB interface, attach the drive to the connector, slip the assembly into the case, and re-secure the front with the screws. Sadly, the drive would not start up.

The next enclosure I bought cost only $10.-. No rebates were involved. Installation was simple. Again, the front needed to be pulled out of from the case, and the drive had to be connected. This time no screws were needed. The drive was supposed to be powered by the USB connection. To my frustration, the drive attempted to start up with plenty of clicks, but did not succeed. What was the problem?

I did not read the specifications in the extended description of the enclosure. Apparently, the USB interfaces of some SATA drive enclosures are limited in the storage size of the drive they can handle. This limitation is not related to the price. I eventually found a suitable enclosure that red.populus offered on ebay for $11.-, shipping and handling included.

The top and bottom shells of Dragonext's USB-2-0 2.5-inch SATA external hard drive case must be slid backward to open the enclosure. The drive must be connected to the interface and secured with four screws to a bottom plate, and top and bottom shells are slid forward over the drive until they snap into the front. Once connected to the computer with the included cable, the drive started up without complaint.

The cable is special in that it sports two USB connectors on the computer-side; one for power and one for data. Taking up two USB connections may seem a nuisance, but constitutes a small inconvenience for a functional case that does not need a separate power supply.

Of course, if you choose to avoid any hassle and are looking for a drive that is more sturdy and extravagant, but bulkier, you may opt for the product below:

Friday, October 10, 2008

Ginkgo & Stroke

Today, Oct. 10, 2008, Tara Parker-Pope informs us in a post under her New York Times health column Well on recent research suggesting that Ginkgo tree extracts may reduce brain damage after stroke. The study is published in the journal Stroke. The researchers affiliated with Johns-Hopkins University and La Fondation Ipsen temporarily blocked the middle cerebral artery in mice to induce an ischemic stroke. In mice treated with Ginkgo extract, the volume of brain tissue affected by the stroke was only about half that observed in untreated mice. The extract had no effect in mice that lacked heme oxygenase 1, an enzyme known to reduce oxidative stress caused by free radicals. These findings may encourage further basic research, ultimately opening a path for future pre-clinical and clinical trials.

I developed a liking for Ginkgo trees ever since I saw my first one on a high school visit to Heidelberg. The tree stood in the park outside the castle, solemnly holding its own one of a kind. They are not native to Germany. A lord long gone had purchased a seedling from China and planted it as a curiosity.

Ginkgo biloba is a species of ancient plants. Herbivorous dinosaurs already dieted on their broad leaves. The leaves are misleading. The trees are more closely related to conifers than to broad-leafed trees. Ginkgos are abundant in the Southeastern United States where I live. The leaves add a wonderful bright yellow to the panoply of foliage colors in the fall.

The leaves' peculiar shape caught the eye of the eminent German poet scientist J.W. von Goethe two centuries ago. Eternalized in a remarkable poem, Goethe calls to our attention the fact that the observer cannot tell from the leaves' shape whether they constitute one leaf split into two or two leaves fused into one. I quote "...Eins und doppelt bin."

This notion of ambiguity applies immediately to the discussed stroke research. As long as we do not know precisely which substances in the Ginkgo extract affect the ischemic brain tissue and what underlying molecular mechanisms reduce the impact of the stroke, medication with Ginkgo extracts is ill-advised. Particular prudence should be exercised, because the extracts are known to diminish blood clotting, exposing patients on blood thinners to additional risk.

Wednesday, October 8, 2008

Social Data Mining: Work in Progress

Demographic data mining is a recent enterprise in social networking on the internet and appears to be still in its infancy. Social web sites commonly ask the user to create a profile to help them find friends, that is the like-minded they wish to communicate with. The collected personal information is used to define the users' context of life and attempt to match it against that of other users. In my experience, the most widely-applied data mining strategies quarry only the simplest information, e.g. residence, school or employer, and only the most fundamental personal characteristics are examined. That is, age, gender and marital status are used to draw conclusions about the interests and preferences of the profiled.

In addition to providing matches for users, these data are used to steer advertisements to the users' web pages that inform on products and services they may be interested in. This seems only fair, because the service on the web site is provided free of charge. However, the conclusions drawn from the users' profile seem at times unrefined and presumptuous, painting a startling image of the average person.

I am 53, male and married. I provide these demographics in my profiles. On my page on one popular social network site, I recently found advertisements of services entitled "Dating for Seniors" and "Meet Married Women in your Neighborhood". Welcome to the real world? A look at my profile however suggests that I am not a likely consumer of these services. Such misguided targeting may only convince users to develop avartars, i.e. virtual cyberspace personalities, bearing little resemblance with their actual lives. Credibility suffers, while professional advertising agencies must be interested in finding true clients for their customers. Obviously, there is ample space for improvement. Until more suitable targeting has been developed, we must tolerate these inconveniences with a ;). They are minor compared with the great opportunities social sites offers.

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Tuesday, September 30, 2008


With Aqua, Apple provides its customers with an intuitive graphical user interface (gui) and an appealing desktop display. Apple's OS X, also known as Darwin, is a UNIX-based operating system. This permits frugal users to run free open-source software on their Apple computers. The main obstacle that needed to be overcome was that much open source software is developed for operating systems that use the X11 window system, whereas Apple uses its own Quartz Compositor. Apple solved this problem with developing This application consists of a command line terminal that is run from an X11 window server. Open-source applications that were compiled for Apple computers and use X11 can be run from this terminal. A number of such applications can be found under the Unix & Open Source tab on Apple's Mac OS X Software downloads site.

The X11 windows system does not take fullest advantage of Aqua's capabilities. The X11 project develops very rapidly, progressing faster than the three-year release cycle of Apple's OS X. Incompatibilities may result. Hence, I decided to adapt available open source software that scientists commonly use, e.g. desktop publishing and graphics applications, to run with the Quartz Compositor as back end. The applications take advantage of Aqua and do not need They are compiled for Tiger (OS X 10.4) and, more recently, Leopard (OS X 10.5) on the intel (i386) architecture. The applications can be downloaded from my project site on called "Software for Small Budget Science".

Last week, I completed my first Aqua-build of Inkscape for Tiger. I named it AquaInkscape. A version for Leopard is in preparation. Inkscape is a versatile vector graphics application with a great number of tools and options similar to Adobe's Photoshop®
and Illustrator® CS4
or the open source application GIMP. These applications feature freely-floating tool bar, control and navigation windows that are detached from the main window with the canvas. This is great when you have two monitors attached to your computer and are able to reserve one for the tools, control and navigation, leaving the view of your work unobstructed on the other. However, if work needs to be done on a small display like a PDA, clutter ensues and free-floating windows quickly finish unretrievable in the stack of open windows.

By contrast, in Inkscape the tool bar is integrated into the main window. This may seem old-fashioned. But I found it truly helpful when working in a confined space. Detached popup windows provide further options. But these windows are task-specific and do not need to be left open. This design profoundly enhances the user's experience of an uncluttered workspace.

To software engineers, Inkscape offers the advantage of an application that can be accessed by and integrated into programs written in Python, a programming language widely used in science and for internet applications (e.g. the Google App Engine).

Below,  I briefly summarize my experience with a number of issues pertinent to building AquaInkscape.
  • I compiled 35 packages to build this application. The needed packages were identified using configure --help, beginning with Inkscape and proceeding through the packages required subsequently. I used the latest stable releases for most packages and developmental versions for gtk+-2.0 and cairo
  • For compilation, I followed GNU standard procedures, that is the commands aclocal, autoconfig, autoheader, and automake, if the package was unconfigured. Sometimes, packages provide an autogen script that can be used instead. Then, I execute configure, make, make test and, if all goes well, make install. I install into the default location, that is /usr/local
  • In order to be able to run the packages with Aqua, the compiles have to be configured without X11 and with quartz, if configure --help indicates these options. The packages gtk+-2.0 and cairo are instrumental for rendering Inkscape's gui. They can be built for quartz. 
  • The demos in gtk+-2.0 and tests in cairo instruct about the potential performance of these packages with Aqua. In the demos for gtk-2.0, not all options worked because the default collection of theme icons known as hicolor icon theme was incomplete. I found a full set that fulfilled the necessary requirements in the Mac4Lin Leopard gtk icon theme package. 
  • With my cairo build (version 1.7.4) a third of the tests failed. Most failures involved tests with very large font and some svg options. Only few failures were associated with quartz. I decided that the chances were good for a functional version of Inkscape for Aqua.
  • It is important to configure the font usage accurately, because faulty instructions may result in ugly font output and Inkscape crashes. I use fontconfig and freetype2 for font management. On my system, the path to the default fonts needed in the configuration of fontconfig is /usr/local/etc/fonts.  You may furnish additional font with ghostscript or gutenprint. Both packages will install fonts in /usr/local/share by default.
After all required packages had eventually been installed, I was prepared to compile the inkscape binary with the MacOSX build script provided in Inkscape's packaging folder. I specified the options openoffice files, internal perl, LittleCms, Inkboard, Poppler-Cairo, ImageMagick/Magick++, Libwpg, as well as with and without internal python. For Python, I compiled and installed version 2.5 on my system. Precompiled MacOS X binaries of Python 2.5 cannot be used because they are incompatible with the Numpy package that Inkscape requires. Therefore, the python version of AquaInkscape contains Python 2.5 modules.

Finally, I had to edit the scripts for packaging so that AquaInkscape would launch without asking for X11. The resulting application seems in good working order. I have not tested all possibilities. The only shortcoming I found so far and have been unable to resolve is that the program does not respond to the quit button in the application menu once inkscape-bin is running. The application can be quit, however, with the button in the pulldown menu under File and with the button in the icon menu on the dock. Clicks with the mouse expand the compressed tool icons in the side bar. Have a try and be patient at start up! The application takes some time to launch.
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Friday, September 26, 2008

Subprime Lending: Truthiness & Delusion of Mind

After Citigroup collapsed late last year, I wondered whether the underestimation of risk in securitized investments was the result of a failure in using scientific methods of risk assessment. Read my post dated Dec. 5, 2007. Soon, I learned that such methods were widely employed in investment banking and insurance. Apparently, misconception prevailed about the reliability of the predictions that these methods provide.

A year on, we find out that the statistical software did not fail. Any scientific method will provide a realistic prognosis only, if the entered data are correct. We presume that a loan is approved with the assurance that the applicant is going to be able to service the payments through the loan period, provided that the applicant's financial situation does not change dramatically. This good practice seemed to have been widely ignored in the subprime and prime ARM (adjustable rate mortgage) loan market of the past eight years. Too often, applicant naivety and lender carelessness took sway over prudence.

In hindsight, the considerate risk analyst would have welcomed an additional column in the input spreadsheet with a truthiness factor weighting each loan. That is, the loan agent is asked to assign a score estimating the applicant's ability to service the loan once the interest rate resets. The agent could be rewarded for good judgment and the improvement in the quality of loans issued. Perhaps such estimates from the field would have helped to predict the risks with the ensuing securities more accurately.

In the absence of such information, the analyst is left to look at the foreclosures on the loans to examine risk retrospectively in the hope that forward projections gain accuracy. Paul Jackson reports on in a post dated Sep. 5, 2008, that the Mortgage Bankers Association (MBA) announced in early September that more than 9 percent of U.S. mortgages were delinquent or in foreclosure at the end of the second quarter of this year. “Subprime ARM loans accounted for 36 percent of all foreclosures started and prime ARMs, which include option ARMs, represented 23 percent,” Jackson quotes MBA's chief economist Brinkmann.

  • As The New York Times reports today, I am not far off with my assessment. Listen to this incredible story (11/5/08).

Thursday, August 21, 2008

Cell Phones & Brain Cancer

Remember Jon Krakauer's account of tragedy on Mt Everest? We have an irrational perception of acceptable risk. For sheer enjoyment, we frequently are willing to expose ourselves knowingly to the possibility of severe injury. Just three weeks ago about a dozen climbers succombed to an ice fall on K2. In any good summer, roughly 100 people perish in mountaineering accidents in the Swiss Alps alone. V. Lischke and others report 462 fatalities for 1997 Europe-wide. According to the U.S. Dept. of Transportation, 4,810 Americans perished on motor bikes in 2005, translating into 73 riders per 100,000 bike registrations. The fatalities continue to rise. Last year 5,154 Americans died on their bike.

By contrast, according to every year fewer than 50 in 100,000 Americans battle glioblastoma multiforme, that is the most aggressive and fatal type of brain cancer. Recent research studies link brain cancer with electromagnetic radiation from cell phones. A discussion of some studies can be found here. The debate has become ever more intense since Senator Edward Kennedy was diagnosed with malignant glioma, probably a glioblastoma multiforme. I discussed this type of brain cancer in my post dated Jun. 3, 2008.

Prudence is advised in the debate on a possible association between cell phone-related electromagnetic radiation and brain cancer. The energy of electromagnetic waves is directly proportional to their frequency. The spectrum of the frequencies ranges from meter-long radio waves via the nanometer-long waves of visible light to atom-sized gamma rays. The shorter the wave length, the higher the frequency and the greater the energy that potentially can harm our genes. DNA may be altered directly through the absorption of radiation energy or indirectly through radiation-produced free radicals that may react chemically with the DNA. Even low amounts of energy can damage DNA and may theoretically result in uncontrolled cancerous cell proliferation. However, our cells are provided with DNA repair mechanisms. Commonly many hits are needed to overcome the defenses and cause noticeable damage. Alas, the defenses appear to wear out with advancing age and we may become more susceptible to cancer.

To determine thresholds for harm from electromagnetic radiation, epidemiological studies are conducted that compare the health records of people with known exposure to those of people who match this group in all aspects, except the exposure. Professionals with job-related extraordinarily high exposure are frequently enrolled in the group of the potentially affected to improve the chances of discovery. Hardell and others (2005) observed that Swedish long-term users of analogue mobile (NMT) phones like the now obsolete car phones developed a significantly higher risk for auditory nerve tumors (acoustic neuromas) on the side of phone use. Digital mobile (GSM) phones like our modern cell and cordless phones did not increase this risk consistent with findings in Denmark (Christensen and others, 2004). The prevalence of acoustic neuroma in the U.S. is low. Less than 1 in 1000 Americans is affected. According to, roughly 264 million wireless subscriptions are active at present.

Though the results of such studies provide important leads on the type of the potential harm to our health and may be instrumental for safety considerations at the work place, they cannot be easily extrapolated to regular phone users. The amount of radiation energy deposited in the auditory nerve can only be estimated. Moreover, the effects cannot be ascertained with the data collected at higher doses because of the non-linearity of the relationship between dose and effect and the increasing scatter of the observations at progressively lower doses. The concerned may opt to use plug-in extensions for ear and mouth pieces or voice-activation as precaution.

  • NPR's All Things Considered ran an interesting update on this issue today. You may wish to read the report and listen to Allison Aubrey's podcast entitled "Doctors Urge Research On Cell Phone-Cancer Issue" (09/25/08).
  • On Aug. 24, an ice fall swept away a party of twelve on the Mont Blanc du Tacul, a smaller brother of the White Lady. Eight are missing. I once stood on this mountain at a different time in the year. I was fortunate to have a friend as guide who understood risk well (10/21/2008).
  • Maggie Fox reports in her post with the title "U.S. senator promises look into cellphone-cancer link" published online on Reuters today that the chairman of the Senate Committee for Health, Education, Labor and Pensions Senator Tom Harkin plans to encourage more research to examine whether the use of cellphones may cause cancer. The fear persists (09/14/09).
  • The environmental working group lists the head-absorbed power [W/kg] of the radio waves emitted from a number of cell phones in this table (06/16/2010).
  • Volkow and others (2011) report in this week's issue of the Journal of the American Medical Association that cell phone radiation is statistically significantly associated with an acute increase of glucose metabolism in the temporal and frontal lobes of the cerebral cortex by, on average, 7.2 percent on the side the active, but muted, phone was held for 50 minutes. The researchers used the [18F]fluorodeoxyglucose method and positron emission tomography (PET) to determine regional cerebral glucose utilization rates in 47 healthy volunteers. They conclude in the abstract of their communication that “this finding is of unknown clinical significance.” Indeed, the finding does not provide any insight into the cellular mechanisms underlying the observed increase. Under healthy physiological conditions, brain glucose metabolism does not rise to levels posing a health hazard. I have written on this topic in my post with the title "Good News for Brain Energy Use" published Sep. 12, 2009. If the sole aim of this study had been to investigate the potential influence of modern-day cell phone radiation on brain energy metabolism, the study could have been conducted with mice at lower cost, sparing the participants unnecessary exposure to ionizing radiation from PET (02/24/11).
  • Epidemiologists have recently come to discrepant conclusions on the risk of cancer associated with cell phone use. According to Scott Hensley's report with the title "Cellphone Use May Be A Cancer Risk After All" on National Public Radio's All Things Considered today, a recent World Health Organization review conducted by 31 experts from 14 countries found sufficient evidence that may support a correlation between cellphone use and gliomas and acoustic neuromas. The study will be published in the July issue of the journal The Lancet Oncology. By contrast, a comprehensive case–control study with 2708 glioma and 2409 meningioma cases and matched controls from 13 countries published last year by The INTERPHONE Study Group (2010) could not establish any elevated risks with mobile phone use with certainty (05/31/10).

As the eminent film director Werner Herzog so aptly documents in his public service announcement video below with the title "‪From One Second To The Next‬", cell phone use may pose other, more prevalent effects proven to be absolutely devastating to our health (08/20/2013):

Wednesday, July 16, 2008

The Body Surface Area

Today I deployed my first Google application developed with the Google app engine (GAE). You have to be connected to the internet and establish an account with Google to use it. BSA Calculator is a body surface area (BSA) calculator with a simple layout in font that the visually challenged like me can read without squinting.

The large font may also be helpful to the busy physician using an iPhone.

Physicians regularly use body surface area to calculate drug doses for their patients. Notably, the dosing of chemotherapeutic drugs like Cisplatin is determined according to BSA. I use it to control my diet. When my BSA climbs over 2.1 m2, it is high time for me to act.

Estimating human body surface is not trivial. It is difficult to develop one formula that fits all, simply because we come in a wide range of shapes and sizes and the relationship between body height and body weight changes considerably while we grow up. Medcalc provides a handful of methods and references. The suggested formulas have been empirically derived from measurements of height and weight. J.D. Current, 1998, and Than Vu, 1999, critically review the methods in use. Boyd, 1935, published one method that is still widely employed. In recent years the method of Mosteller, 1987, has gained popularity. Both are available in BSAcalc.

  • Boyd E (1935) The growth of the surface area of the human body. University of Minnesota Press, Minneapolis.
  • Mosteller RD (1987) Simplified Calculation of Body Surface Area. New England Journal of Medicine 317: 1098.
The BSA calculator accepts only metric dimensions (Système International). You may use the converter below to convert body height and weight from inches and pounds to centimeters and kilograms, respectively. Enter the body height in inches in the inches box and click on the centimeter box. In analogy, enter the body weight in lbs into the pound box and click on the kilo box:

[in] :
[kg] :

 Converter © You may donate for further development through PayPalhere.
Proceed to the BSA calculator.

  • A authoritative study by Sacks and others (2009) in the New England Journal of Medicine (360:859-873) demonstrates that we can diminish our weight on reduced-calorie diets (02/26/09).

Thursday, July 10, 2008

Who Owns Your Site?

Recently, a friend of mine was pondering some existential questions about websites. She had started an own business selling customized arts and crafts over the internet. She found an appealing name for her site. She tells us on the site, how her real business grew from an unreal idea. The site offers to customers options to create the product they like to purchase. Sales have been taking off. The business shows all signs of success.

My friend is not a web expert and outsourced site development and administration.  Now, questions arise about the ownership of the site. The details of site registration have fundamental implications for ownership, particularly when the site name is synonymous with the brand and the businesses vitally depends on brand recognition. The person who registers the domain name of the site with the registrar may actually own that name. This person may also own the administrative privileges to add and delete data and permit other parties access to site administration. The administrator can potentially read the e-mails on the site.

For those who are not savvy in the use of the terminal command line, I found an easy way to obtain information about your site. Go to Broadband Report's whois browser application, type in your domain name, that is the site name without "www.",  and hit return. Check carefully that the entries match your expectations.

Small Business Tip #1. Click here.

Wednesday, July 2, 2008

How to Build a Silent PC: Episode II

In episode I, I narrated my first experience with building a personal desktop computer, describing important discoveries I made in the process. Earlier this year I build my second PC. Below I shall summarize the essential lessons I learned.

The purpose of this project was to provide my son with a powerful computer to use for his graphics and arts work as well as his games. My son is learning animation with Maya Learning Edition and chess with Chessmaster.This computer would be stationed in his room. The first machine I built boasts 7 fans. The noise these fans collectively produce is considerable. You would not want to have them in your bedroom. Therefore, I was looking for a very quiet design.

On my search for the noiseless machine, I happened on cases for home theater personal computers (HTPC). Computers for the control of high fidelity entertainment centers must be designed noiseless. Compared with standard cases, the fans in these cases commonly run very quietly. As a drawback, I did not find a case with a small form factor. Even the cases, that can house micro-sized (mATX) motherboards, are not much smaller than mid-size towers. At the high end of the price range I are the impressive cases by Zalman. I opted for Antec's Fusion V2, which is comparatively low in price.

Owing to my good experience with Micro-Star International and Advanced Micro Devices, I chose the K9MM-V motherboard and an Athlon 64 3500+ Socket AM2 central processing unit (SKU:CP2-AM2-3500 AV). I purchased both in a bundle for a bargain price from TigerDirect. The "V"s are important. They indicate that board and processor are designed to fully support virtualization. Microsoft's Hyper-V virtualization software is under development and can be tested with a compatibility check utility that AMD provides for download. I opted for Microsoft's Windows XP Professional x64 as operating system to let my son run his applications smoothly and perhaps will use Xen for virtualization.

In my first assembly, I had the CPU pre-installed. This time, I mounted it myself, before placing the board in the case. It was straight forward. A close check of the instructions in the MSI manual sufficed. You must ground yourself, before you start! The designated corner of the CPU and has to match up with that of socket on the board. When the chip is properly aligned, the pins slip smoothly into the holes of the socket. No force is needed. The chip is fastened by pushing down a lever. Then, I applied an even layer of thermal grease and mounted Ultraproduct'son top. The fan has a diameter of 92 mm and provides air flow at 53.5 CFM. The motherboard was ready to be placed in the case.

Next, I filled the the board's memory slots with a pair of PNY 1GB memory modules MD2048KD2-667.
Before you order the memory modules, validate the specifications with the recommendations on the manufacturer's site.

The case came with a 430-W power supply with all necessary connectors attached and provided two internal and one external drive bay. I loaded one internal bay with a Seagate SATA hard drive. I used a Barracuda 7200.10 320GB drive.

The SATA cable came with the motherboard. The board features a second SATA input. I may install another SATA drive in the empty bay. The external drive bay was reserved for the DVD/CD drive. I installed Mad Dog's multimedia IDE drive and connected it to the motherboard with the round cable included in the MSI kit.

Micro-ATX motherboards are about 2" shorter than the regular ATX boards, but still accommodate standard PCI and AGP cards. This was important to me, because I had PCI cards in stock and wanted to be able to use AGP graphics cards. I swapped out the ATI Radeon 9600 PRO card used in my first project for a 9800 series card and installed the old card in this computer. The reason was an important discovery. If you use a mATX motherboard, ensure that the graphics card you intend to use matches the shorter length of this board. The ATI Radeon 9600 card was sufficiently short.

The motherboard accommodated all connections from the case, except the firewire port. Therefore, one of the three PCI slots had to be reserved for a USB/firewire card. I purchased Ultra 8 Port USB 2.0/Firewire PCI Combo Card.
Another slot was taken by a wireless network adapter card. I chose Cisco's Linksys WMP54G PCI Wireless Adapter v41.The Linksys software does not function properly with Windows XP x64. A compatible driver for the card can found at Ralink support. The driver that matched my card can be downloaded at PCI/mPCI/CB(RT256x/RT266x). After insertion of the PCI card, restart the computer and the hardware wizard will announce that new hardware was detected and prompt you for a driver. At this juncture, the wizard has to be manually pointed to the RT61 file in the Ralink folder under program files (x64). If the wizard does not prompt you, the driver can be loaded manually for the network adapter in the device manager. Should Ralink terminate its support for XP, the driver I used is available for download at BMI under downloads.

As useful amenities, I added Gyration's gyrotools.The compact keyboard is light-weight and short. The buttons have a good feel. The optical air mouse doubles as remote control.

You may wish to check out this book, if you seek more advice. I own a few books in this series and found them helpful.
Compusa (Systemax, Inc.)


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Thursday, May 22, 2008

Build Your Own PC: Episode I

I grew up in an era in which kids learned basic car maintenance so that they knew how to fix problems on the road. I have worked with computers daily for decades, and I found it more and more vexing that I did not have the slightest idea of what was going on inside them. I could not even point out the vital parts of the creature, once the abdomen was uncovered. One day four years ago, I decided that the best way to find out was to construct one from parts. Below, I summarize this experience.

The process was actually fun. The computer cost about $1,500.- including the extras. These days, a turn-key PC sells for as low as $200.-. Of course, that version does not come close to the performance of the computer I built and a bare-bones PC with a comparable performance would cost at least $500.-. I can only speculate whether that system would be equipped with the same quality parts. The consideration is similar to buying a home in a new development. The base price for the home may be economic, but the quality of the piping, the fixtures, the flooring, you name it, will be poor. You may look at early and costly repairs. Of course, you are offered pricey upgrades. I opted for quality parts. To keep the running costs low, I originally chose a 350 W power supply, but upgraded to 430 W after I switched to a more powerful graphics card and increased the memory. Assuming that the computer is consuming half that wattage on average, the monthly expense for electricity is about $11.- in our utility district. We have got three computers in our household that essentially run 24/7. The expenses add up accordingly.

It may seem dated to describe my first experience with computer assembly four years after the fact. Earlier this year, I build my second computer incorporating the lessons I learned from the first. Hence, I sum up the earlier experience in a first installment and will post important aspects of the most recent experience in a second installment.

I wanted a machine that could process great amounts of imaging data fast. I chose an MSI K8T MASTER2-FAR motherboard that accommodated two 64-bit AMD Opteron 242 central processing units (CPUs). I opted for this architecture at the time because it is compatible with Sun Microsystem's Solaris 10 operating system and I needed to run an application that was specifically compiled for Solaris. The latter is doubtlessly an advanced operating system geared toward servers supporting large networks and by far exceeds my small purpose. I found it more appropriate eventually to run the machine with Ubuntu's Linux-based operating system (currently version 8.04). The latter provides up-to-date Gnome and KDE desktops and the recent upgrades have proved flawless in execution and very stable.

Unfortunately, my CPUs are not yet the type that is enabled for virtualization. Thus, running virtual machines is not as efficient as with more recent AMD CPUs (look for "-V" in the name). Despite this shortcoming, I am running Microsoft's Windows XP on QEMU with satisfactory results.

I bought most parts from internet vendors. At the time, I did not feel confident enough to mount the CPUs myself and had that done for a small fee by Spartan Technologies from whom I purchased the motherboard, the processors and coolers. Everything else I put together. The assembly did not require a great level of experience and was straight forward. Following the instructions provided in MSI's motherboard manual was a safe route to success. An important rule to obey is ensuring that you are not statically charged by electrically grounding yourself before you touch any parts. That is, tape the exposed end of a copper cable to the skin of your arm with medical tape and wrap the other exposed end tightly around a water faucet in your kitchen or bathroom. Waterlines provide the best connection with the ground. At first, I was confused by the great variety of power supply connectors and the many different adapters. Closely studying the drawings and photographs in the MSI manual straightened out the misunderstandings. My choice of hard drives, the memory, the CD/DVD writer and the graphics card was guided by the list on the motherboard retailer's website of items that other customers bought with the motherboard. In the meantime, I have developed a few own preferences:
  • I prefer Kingston Technology memory for RAM. I purchased HyperX DDR400 PC3200R memory (KRX3200AK2/1G) for this machine when I built it, but expanded with Kingston HyperX 2048MB PC3200when the price fell. Before you order the memory modules, validate the specifications with the recommendations on the manufacturer's site. The safest way for selecting RAM modules that work with your CPU/motherboard combination is to visit the support sites of your CPU and motherboard manufacturers and choose from their lists of verified products. In addition, I learned the basics about DDR memory here and found the MSI user's forum informative. 
  • After three years, I decided to increase RAM since prices have fallen considerably. MSI provides conflicting information about the maximum RAM size. After studying the MSI forum ad nauseam, I came to the conclusion that between my Opteron 242 CPUs and the motherboard, the largest memory I could install was 4 x 1-Gb. I eventually settled on Corsair 1GB 184 DIMM PC3200 ECC DDR RAM (CM72SD1024RLP-3200). The motherboard requires that the modules are registered and unbuffered. Corsair support was very helpful in choosing the correct kind.  The installation, seemingly straight forward, turned into an ardourous journey. My first idea was to add two Corsair modules to the two 512 MB Kingston modules I already had. Mixing different brands, types and sizes did not go down well at all. The machine would not boot and stuck with emanating regular beeps of distress. Removing the Kingston modules solved this problem. However, when I filled the now vacant slots with two more 1-Gb Corsair modules, the bios post hung at the memory check. My bios version is 1.3b5. I first thought I needed an upgrade. After reading a number of harrowing stories about the possible consequences of flashing your bios (one guy ended up taking a kitchen knife to the motherboard), I decided to keep this option as the very last resort. I spent a whole week on shopping for solutions, trying to change all sorts of bios settings. In the end, I actually did not need an upgrade.  The solution was (i) to re-install the old Kingston modules, (ii) set the AGP aperture in the bios as low as possible for the system to work (64M),  (iii) shut the computer down, (iv) swap the Kingston modules with the four new 1-Gb modules, and (v) restart the computer. Voila, the memory check finally worked. With further experimentation, I found that the AGP aperture setting dictates the size of RAM the bios is willing to check. 256M AGP aperture permits 2Gb; 128M 4Gb. So my final AGP aperture setting is 128M. The RAM size count stops about 500 Mb short of 4 Gb. Again searching the MSI forum, I learned that the mismatch between physically available memory and bios count is buried in the design of the bios. I decided to content with what I gained.  
  • I prefer hard drives manufactured by Seagate Technology. They really served me well over the years. One is 15 years old and still works without fail. I decided to use two Barracuda 160GB SATA drivesmirrored in a RAID for user data. Both drives could be connected directly to the motherboard. A 400GB ATA drivestores the operating system.
  • Unfortunately, the motherboard does not provide on-board firewire connectors. If firewire connectivity is desired, a PCI card needs to be installed, taking up one slot. Because I needed an internal recepticle on the card, I used StarTech's PCI1394_4 4-Port FireWire PCI Card.
  • I prefer the more expensive flexible rounded cables to connect the ATA hard drive and the DVD/CD writer to the motherboard over the conventional flat cables. An example is shown below:
    The cables are sold in lengths that match the distances in the case and are more flexible and thus easier to bend. A rounded ATA cable came with the motherboard. However, it was too long and stiff. I bought an extra set from
  • The motherboard provides two SATA connectors for storage devices. I used them to configure two harddrives in a raid. I found the SATA connectors to be flimsy. While moving the computer to another room, the cables shook lose on the motherboard side, resulting in BIOS errors at boot time. I felt tempted to glue them in place with Silicon glue, but refrained.
  • The MSI motherboard has four slots for PCI cards and one for an AGP graphics card. I chose a ATI Radeon 9600 PRO card.This card provides excellent support for a 19" LCD at 1024 x 768. I recommend to use a more upscale card for larger screens and higher resolutions. Moreover, I strongly recommend to ensure that the card of choice fits in the case before it is ordered. The Radeon 9600 card is comparably short. Upscale graphic cards can be quite long and the available space in the case must be shared with the thick cables connecting the hard drives and other peripherals to the motherboard. Room may run out even in a standard case for ATX-size motherboards. I eventually upgraded to a ATI Radeon 9800 SE.
  • The heat sink on the Radeon 9600 graphics card processor and the fan are small. I decided to replace them with a copper heat sink and a larger fan I found at CompUSA (VGA Cooling Kit SKU 336044). The heat sink slightly egged on a capacitor on the card. I ground an indentation into the sink large enough for the components not to touch. Though rough, the solution improved cooling remarkably. Before mounting the heat sink on the processor, it is important to apply a thin layer of the thermal grease provided with the kit evenly on the chips surface. The kit came with a number of additional small heat sinks that can be glued on various integrated circuits on the board. I mounted them all, thinking that every little bit helps. The kit cost less than $20.- and visibly stabilized the cards performance. The screen does not flicker anymore when its hot. Finally, leaving the PCI slot next to the graphics card open considerably boosts heat dissipation.
  • Running a wireless internet adapter PCI card on Linux is problematic. Before you order, ascertain that the manufacturer supports your operating system or, at least, that the drivers are available for the card of your choice. I have had satisfactory experience with D-Link's DWL-G520.Instructions for the installation and the configuration of the driver can be found here. By contrast, NETGEAR does not provide any support for Linux. An open source project develops Linux drivers for ACX-111 chipset-based cards (e.g. NETGEAR's WG311 PCI Wireless Network Adapter.However, compiling and inserting kernel modules is needed, potentially interfering with your next kernel upgrade. You may be facing a new install instead of an upgrade.
  • Finally, I can give some advice on fans. My computer houses seven fans, two in the case's front, one in the rear, one in the power supply, one on each CPU and one on the graphics card. As a result the machine vacuums up air-borne dust with remarkable efficiency. Once we had construction in the house several rooms away. An old wall was broken down. I forgot to turn off the computer on that day. The fine, invisible dust from the construction ruined the bearings of the spinners on the CPUs and the graphics card as well as the large fan in the case's rear. The fans did not stop spinning, but could not maintain the required speeds to cool the CPUs effectively. Temperatures reach more than 100° F (38° C) outside for several weeks over the summer where we live. It does not cool down much during the night and attempting to save on the electric bill exposed the CPUs to the risk of overheating. In this situation, the Cooler Master's Aerogate II fan and temperature control unit I had installed in one of the external bays in the case's front warned me of the impending disaster and saved the CPUs.
  • I installed magnetic levitation fans and one of Y.S. Tech's tip magnetic driving (TMD) fans as replacements. I used teflon screws to mount the TMD fan. It is fabulous. A good demonstration of these fans can be found here.
    You may wish to check out this book, if you seek more advice. I own a few books in this series and found them helpful.