In fewer than 10 steps, you can re-calibrate your touch screen for your Windows Mobile device (I’m using the HTC Touch Pro 2).

1. Click on Start.
2. Click on the Settings icon.
3. A screen containing various settings is displayed.
4. Click on the word Menu at the bottom right corner.
5. Click on All Settings.
6. Click on the System icon.
7. Click on the Screen icon.
8. Click on the Align Screen button.
9. Follow the directions for re-calibrating the touch screen.

…and there you go.  Your touch screen is ready to go!

Why VimOutliner?

1. Vi lovers, this is probably the only reason that you need.  All your Vi keystrokes work in VimOutliner as they would in Vim.  Need I say more?
2. Vim is free, and VimOutliner is also free.  You can have access to a powerful outliner on any of your computers without paying a penny.
3. Vim/VimOutliner is cross-platform.  Whether you are using MacOS, Windows, Linux or some other variant of Unix (even Cygwin!), you can have the same outliner on every platform.
4. VimOutliner files are simple text files that rely on indentation to indicate the level of nesting.  Therefore, the outline files can be viewed using any text editor (not just Vim).  Using Vim with the VimOutliner plugin provides added features like folding, checkboxes, hoisting, and percentage done (just to name a few).
5. VimOutliner can run over an SSH session.  Since Vim can run at the console, VimOutliner inherits this ability.  There’s no need to initiate a Remote Desktop connection or leverage VNC, VimOutliner is text-based so an SSH session is all you need.
6. With complete access to the plugin’s source code, you can modify VimOutliner to meet your needs and do whatever you think an outliner should do.

Installation howto

My customized version of VimOutliner 3.4 provides a straight-forward installation that works on Windows XP, Windows Vista and Windows 7.  I’ve only tested it on Vim 7.2.  If you run into issues using with other versions of Vim, please let me know or post a comment.

1. Download vimoutliner-rayli.zip.
2. Extract it in C:\Program Files\Vim\.
3. This will create a C:\Program Files\Vim\vimfiles\ directory (if it doesn’t already exist).  In addition, this puts the required plugin files in the correct directories.
4. Add to the C:\Program Files\Vim\_vimrc file the following lines:

filetype plugin indent on
syntax on
runtime! ftdetect\*.vim

My customizations

These customizations are already integrated into my zip file.  If you don’t like them, you can change them or remove them.

1. In C:\Program Files\Vim\vimfiles\ftdetect\vo_base.vim, comment out the if-endif block.  For whatever reason, this block causes my installation issues.
2. In C:\Program Files\Vim\vimfiles\syntax\vo_base.vim, search for OL2 twice.
3. On that line, change guifg=red to guifg=#FFAE66.
4. In that same file, search for OL6.
5. Change guifg=red to guifg=#FFAE66.
6. The red syntax highlighting is too bright and doesn’t work well for me, so this change works much better.
7. Search for FoldColumn.
8. Comment out the FoldColumn line.
9. In C:\Program Files\Vim\vimfiles\ftplugin\vo_base.vim, search for foldcolumn.
10. Replace foldcolumn=1 with foldcolumn=4.
11. My outlines usually nest more than 1 level, so it’s nice to see the fold characters rather than the fold level numbers in the fold column.

And there you have it…  this installation has served me well for quite some time now, and I hope the trend continues with your installation.

First, why the confusion?

In grade school, I was taught a simple (but wrong) rule for using a or an:

Use “a” for words that begin with a consonant and “an” for words that begin with vowels.

Although this rule is correct for a lot of words, the actual rule has very little to do with how a word is spelled.  The rule has everything to do with how the word is pronounced:

Use “a” for words that begin with a consonant sound and “an” for words that begin with a vowel sound.

Common questions

Question: A historic or an historic?
Answer: A historic.  The word historic is pronounced with an H sound.  In this case, the H sound is a consonant sound.

Question: A university or an university?
Answer: A university.  Although U is a vowel, the pronunciation of university begins with a Y sound (you-nee-…) which is a consonant sound.

Question: A MBA or an MBA?
Answer: Both.  If you pronounce the acronym as em-bee-ey, you should use an, since it’s pronounced with a vowel sound.  However, if you expand the acronym to Master of Business Administration, you should use a, since master is pronounced with a consonant M sound.  Although the former is more commonly used, both are acceptable.

Question: A user or an user?
Answer: A user.  Although U is a vowel, the pronunciation of user begins with a Y sound (you-zer) which is a consonant sound.

Question: A hotel or an hotel?
Answer: A hotel.  The word hotel is pronounced with an H sound.  In this case, the H sound is a consonant sound.

Tough questions

Question: A one or an one?
Answer: A one.  The word one is pronounced with a W sound.  In this case, the W sound is a consonant sound.

Question: A useful or an useful?
Answer: A useful.  Although U is a vowel, the pronunciation of useful begins with a Y sound (yoos-ful) which is a consonant sound.

Question: A email or an email?
Answer: An email.  The pronunciation of the word email begins with an eee sound.  This is a vowel sound.

Question: A or an before s-words?
Answer: It depends.  For a simple word like secure, you should use a secure, since its pronunciation begins with an S consonant sound.  For a more complex example like SSH, you should go through the same thought process as in the MBA question.  You could go either way for SSH.  However, the more common usage is an SSH.

Question: A or an before x-words?
Answer: It depends again.  For a simple word like xylophone, you should use a xylophone, since its pronunciation begins with an Z consonant sound.  For a more complex example like x-ray, you should pronounce the word: ex-ray.  Its pronunciation begins with a vowel sound, so its usage is an x-ray.

Trick question

Question: A honest or an honest?
Answer: An honest.  Did I catch you?  The word honest begins with an H which is a consonant.  However, it is pronounced onest.  That’s right…  its pronunciation begins with a vowel sound.

Let your ear decide

The old grade school rule works most of the time for two reasons:

1. The spelling of most words that begin with a consonant are pronounced with a consonant sound.
2. The same is true for words that begin with a vowel — they are pronounced with a vowel sound.

However, the examples given above show the spelling of some words that begin with a consonant are pronounced with a vowel sound.  Some that begin with a vowel are pronounced with a consonant sound.  So when all else fails, say the word aloud, and let your ear decide whether it begins with a consonant or a vowel.

DISCLAIMER: Some of the tips mentioned below potentially leave your system vulnerable.  Although these particular settings work for me, they may not be the best fit for how you use your netbook and your environment.  Please use these tips at your own risk.

• Add more RAM
• Disable performance and appearance options
• Disable services
• Disable start-up applications
• Disable McAfee anti-virus
• Disable sound schemes
• Disable system restore

Add more RAM

Adding more RAM is one of the most expensive and invasive options for remedying a slow netbook.  However, it arguably offers the greatest gains.  My netbook comes with 1GB of RAM and can handle an upgrade to 2GB.  Increasing the amount of RAM available to your system (in this case, doubling the RAM) produces increased responsiveness you’ll notice immediately.

First, find out how much RAM you currently have.

1. Press the Windows key.
2. Type system in the search box.
3. Run the System application from the search results.
4. Under the System section, look for Installed memory (RAM).

Then, look in your Aspire One manual to determine how much RAM your netbook can handle.  You can also rely on the memory experts at Crucial for this information.

1. Navigate to the Crucial website: http://crucial.com.
2. Using the Crucial Memory Advisor Tool, select the Manufacturer (Acer).
3. Select the Product Line (Aspire netbooks).
4. Select the Model (Aspire One 532h, your model may be slightly different).
5. Click Find It.

Crucial displays the default configuration for your netbook and the memory upgrades that are possible.  A list of compatible parts is also listed.  For my configuration, I can get a 2GB DDR2 for about $50.

Numerous guides are available for installing the memory upgrade (just do a search for aspire one memory upgrade).  This is the one I found most useful: How to Add RAM to the 10-inch Acer Aspire One.

Disable performance and appearance options

Adjusting the Windows 7 performance and appearance options is bound to increase the responsiveness of your netbook.

1. Press the Windows key.
2. Type system in the search box.
3. Run the System application from the search results.
4. Click on the Advanced system settings link.
5. Click on the Advanced tab.
6. In the Performance section, click on the Settings button.
7. It’s up to you which options you’d like to keep around.  On my netbook, I uncheck all except:
   Show window contents while dragging
   Smooth edges of screen fonts
   Use visual styles on windows and buttons
8. Click OK.

Disable services

Setting unneeded services to start Manually will definitely free up resources previously used by those services.

1. Press the Windows key.
2. Type services in the search box.
3. Run the Services application from the search results.
4. To set services to start manually, double-click on the service.
5. Set each of these services to start Manually, and click OK.
   Desktop Window Manager Session Manager
   Diagnostic Policy Service
   Distributed Link Tracking Client
   IP Helper
   Print Spooler (I don’t print from my netbook)
   TCP/IP NetBIOS Helper

Disable startup applications

Disabling unneeded startup applications speeds up Windows 7 start-up time and frees up resources previously used by those applications.

1. Press the Windows key.
2. Type system configuration in the search box.
3. Run the System Configuration application from the search results.
4. Click on the Startup tab.
5. Uncheck processes you don’t want running at startup.
6. Click OK.

Disable McAfee anti-virus

Anti-virus programs are necessary in many environments for providing a safe computing experience.  If anti-virus programs saved your computer more times than you can remember, do not take my advice.  However, if you can’t remember the last time anti-virus did anything for you except slow down your system, you are not alone.

Because of the stranglehold that McAfee has on my system, I chose to completely uninstall it.

1. Press the Windows key.
2. Type program and features in the search box.
3. Run the Program and Features application from the search results.
4. Locate the McAfee application in the program listing.
5. Right-click on it.
6. Click Uninstall.

Disable sound schemes

Playing sounds during certain actions in Windows takes up some resources.  If you like the sound schemes, by all means keep them.  If it doesn’t matter to you, disable them so that there’s one less thing taking up system resources.

1. Press the Windows key.
2. Type sound in the search box.
3. Run the Sound application from the search results.
4. Click on the Sounds tab.
5. Set Sound Scheme to No Sounds.
6. Uncheck Play Windows Startup sound.
7. Click OK.

Disable system restore

System restore definitely has its advantages.  When you absolutely must back out of some system changes, being able to restore to a previously working point is an awesome safety net.  Since my netbook is not my primary computer, system restore is an extra application that takes up resources to periodically snapshot images of my system.  In addition, it requires a relatively large chunk of disk space.  So, I disable it.

1. Press the Windows key.
2. Type system in the search box.
3. Click on the System Protection link.
4. Click on the System Protection tab.
5. In the Protection Settings section, click on a drive.
6. Click on the Configure button.
7. In the Restore Settings section, click on the Turn off system protection option.
8. Click OK.
9. Once system restore is disabled for all desired drives, click OK.

With these tweaks, my RAM usage noticeably decreased and system responsiveness seems to be snappier.  Hopefully, they’ll produce a similar result for you.

If you’re already familiar with tickler file systems, skip the walk-through and read about the alternative.

A quick walk-through

Using the tickler file system is easier to describe with an example. The tickler file system consists of 2 sets of folders:

1. 12 folders labeled with the name of each month
2. 31 folders labeled from 1 to 31 for each day of the current month (enough folders for 28, 29, 30 and 31 day months)

Start with the day folders from 1 to 31.  Place the month folders in month order behind the day folders.  Let’s say today is January 1st.  You wake up with a slight New Year’s hangover and glance over at your tickler file system.  You notice the day 1 folder is empty, so there’s no reminders for January 1st.  Refile this folder behind the February folder.  The day 1 folder is now used to hold reminders for February 1st.

You just remember that you have a meeting tomorrow (January 2nd).  To remind yourself of the meeting, you put the agenda for the meeting in day folder 2.  The thinking is that when you look at day folder 2 tomorrow, you’ll be instantly “tickled” by the meeting occurring right after New Year’s.

After looking at your email, you notice the meeting is rescheduled for February 14th.  Day folder 14 is currently holding reminders for January 14th, so you place the meeting agenda in the February folder.  When February rolls around, you’ll need to go through all the items in the February folder and redistribute them among the day folders.

Weaknesses of tickler file system

The weaknesses of the tickler file system are many:

1. In a recent post at GTD Times, a GTDer asked about a “tickler lite” system to address their 43 folders (12 month folders + 31 day folders) frequently being empty.  Unless you have lots of reminders to tickle yourself about, this is one of the weaknesses of the tickler file system — multiple folders can go unused.
2. Making sure to check it everyday could also be considered a weakness initially until it becomes a daily habit.  However, I find that checking a system that is empty more often than not can easily lead to neglecting it.  For example, if you get email everyday, you’re more likely to check for new messages than if you get messages every few days.
3. One more weakness is the need to re-sort reminders stored in the month folders.  The necessity to re-sort reminders indicates that the reminder must keep track of its due date.

   If we go back to our previous example regarding the meeting agenda on February 14th, the date for the agenda must be somewhere on the agenda.  It might already be mentioned in the agenda or it could be a post-it placed on the agenda.  Because you’re putting off re-sorting the month day folder, you must remind yourself what date the reminder should be sorted into.

4. Additionally, you must remind yourself to do this re-sorting every month.  Doing it daily is another option.  However, you’ll be sorting and re-sorting other reminders in the month folder that are not quite ready to be sorted into their corresponding day folders.
5. After filing an item into the desired day or month folder, you’ll potentially search through 43 folders if you need to find the item before its “tickle” date.

An alternative

An alternative is it to leverage other parts of GTD to serve a similar function.

The tickler file is basically a date-based reminder that allows you to store a physical item. Instead of a tickler file, you could record a reminder in your calendar and then file away the item in your reference folders. The reminder could even tell you what folder to look in.  In this way, you could leverage your existing calendar and filing system and not have to maintain a tickler system that you rarely use.

The advantages of this approach are numerous:

1. No daily habit of checking your tickler file system, because your calendar is already something that you check everyday.
2. No re-sorting tickler reminders for the next month, because your calendar has entries for the whole year.  Just enter the reminder into its corresponding date in your calendar.
3. Only limited by your filing system rather than your tickler filing system.  Your filing system implementation is probably more robust than most tickler filing system implementations (large filing cabinet vs. expanding accordion files).
4. Depending on your filing system, items are categorized by topic or project rather than by date (as in the tickler file system).  Finding the item before its tickle date involves leveraging your filing system rather than possibly searching through all 43 folders.
5. No extra system to maintain and take up psychic RAM.

In a nutshell, the tickler filing system can be essentially re-defined as a reminder on your calendar that specifically references an item in your filing system.

UPDATE: A comment from Christoph Dollis points out the system is not limited to an item in a physical file system.  An item in your digital filing system could be just as effectively referenced from your calendar.

What is a tracing JIT?

Although tracing JITs are a complex technology, the core concept is about optimizing execution of the hot paths in a program.  The emphasis is specifically on hot paths that return to the start of a path which sounds very much like a loop.  However, the traditional definition of a programming loop is only a subset of these hot paths.  The broader definition includes code that spans methods and possibly even modules.  This broader definition of a loop is what’s called a trace.

Why use traces?

By JIT compiling the traces, code that is executed frequently runs faster.  Code that isn’t included in traces isn’t compiled.  The claim is untraced code would not benefit as greatly from JIT compilation since it is not executed as frequently.  The basic trade-off is the time needed to JIT compile and cache the resulting code versus the time needed to execute the code.

When does tracing happen?

Tracing takes place as instructions are interpreted.  Whether it’s Java, Python or Javascript, the code must be interpreted by a virtual machine.  It is during this stage that loops are detected and identified as traces.

How is a tracing JIT different from other JITs?

Run-time profiling for optimization and specific CPU and memory optimizations are done with most JITs to adapt the application for best performance.  However, non-tracing JIT implementations (Sun’s Java VM and Microsoft’s CLR) do this at the method level.  When code is determined to be “hot,” the entire method containing that code is JIT compiled and cached.  Tracing JITs do this at the trace level and may consist of a portion of a method (just a specific loop), multiple methods and even multiple methods from different modules.

Who is using tracing JITs?

The Mozilla Team uses a tracing JIT in the JavaScript engine for Firefox.  It’s codenamed TraceMonkey and is enabled by default in Firefox since version 3.5.  Adobe Labs has a tracing JIT called Tamarin.  It’s basically a JavaScript engine as well.  Technically, it’s an implementation of ActionScript which is based on ECMAScript which JavaScript is based on.  Tamarin and TraceMonkey are so closely related that they both use the same backend: NanoJit.

A Python interpreter called PyPy recently switched from being based on partial evaluation to a tracing JIT.  Microsoft is researching and prototyping a tracing JIT compiler (TJIT) for the common intermediate language (CIL) called SPUR.

Where can I find out more?

This post only scratches the surface.  There’s plenty more about tracing JITs!

• Andreas Gal’s blog
• Lambda the Ultimate thread on tracing JITs (highly recommended)
• Hacker News thread on tracing JITs
• Tracing JIT Notes
• Wikipedia entry on trace trees

How can Python interpret Python source code faster than an interpreter written in C?

The short answer is it can’t.  The long answer is that PyPy is actually two pieces of software:

1. an interpreter
2. a translator

The interpreter understands the full Python language.  The interpreter is written in RPython (Restricted Python).  RPython is statically typed which makes it easier to compile into more efficient code.  This characteristic is very important for the next step.

The translator takes RPython code as its input and translates it to a lower language like C.  Although the interpreter was originally written in Python (specifically RPython), the translator translates it to C which can be compiled into a much faster interpreter that could rival or even surpass CPython.

What’s the point of doing this in RPython?  Why not just code it in C like CPython?

The difference boils down to the perceived difference between hacking away at an interpreter written in RPython (PyPy) versus an interpreter written in C (CPython).  The claim is that an interpreter coded in RPython allows for faster experimentation.

Can a Python interpreter based on RPython code translated into C rival or exceed the performance of CPython?

At this moment (April 7, 2010), the answer is no.  Default CPython bests its PyPy-C equivalent on just about every benchmark.  On some benchmarks, the measurements are close.  On others, CPython is clearly the winner by far.

This is false advertising!  If CPython does better on most benchmarks, how can PyPy claim to be faster?

The answer is JIT!  The developers of PyPy created a JIT compiler for Python by adding a few hints to their RPython interpreter.  The PyPy JIT compiler just-in-time compiles RPython code to native code which is why it’s able to get such fantastic speed gains when compared to CPython.  PyPy-C-JIT crushes CPython on the majority of the speed tests at the PyPy Speed Center.

That doesn’t seem fair…  Of course native code will be faster than interpreted code.  What if CPython is coupled with JITting?

Turns out PyPy still comes out ahead.  CPython can be coupled with Psyco, a Python extension module that can JIT compile Python code.  The Psyco JIT approach differs from the PyPy approach, because the former focuses on partial evaluation and the latter on tracing.  I don’t know the difference yet (maybe another blog post?), but what we do know is this tracing JIT approach outperforms the Psyco approach.

So there it is…  PyPy in a nutshell.

UPDATE: It seems I’m not the only one interested in PyPy’s claims.  I came across a related thread on Stackoverflow: PyPy — How can it possibly beat CPython?

DISCLAIMER: I have not used PyPy — just very curious about the problems it solves.

Python in the Browser, Jimmy Schementi
Using Python in the web browser leverages Microsoft’s Python implementation.  The goal is to use Silverlight/Moonlight with IronPython as a client-side browser language.

State of PyPy, Maciej Fijalkowski
PyPy is an implementation of Python written in Python.  But why?  (UPDATE:  What is the purpose of PyPy?)

Python 3: Next Generation, Wesley Chun
This talk went through a laundry list of new features and bug fixes in Python 3.

Unladen Swallow: fewer coconuts, faster Python, Collin Winter
Unladen Swallow is Google’s Python implementation branch of CPython.  It claims significant speed improvements.  Currently, the interpreter is a virtual machine with a JIT built using LLVM.

Understanding the Python GIL, David Beazly
Discussed key issues with the global intepreter lock (GIL).  It seems improvements in Python 3 solve some problems associated with the GIL, but create new ones.  Beazly goes over how difficult the problem is, and how he feels it can be solved.

Easy command-line applications with cmd and cmd2, Catherine Devlin (a.k.a. PyOraGeek)
The talk title was a bit deceiving.  She prefaced the talk with a disclaimer, because the topic was actually command-line interpreters.  This is more along the lines of applications like the bash shell or Python’s REPL.  cmd is Python’s class for line-oriented command interpreters.  cmd2 is Devlin’s enhancements to cmd.

The rest of the talks I attended were about software testing!

Why not run all your tests all the time?  A study of continuous integration systems, C. Titus Brown
Brown compared continuous integration systems: Hudson, Buildbot, CruiseControl, Bamboo, Bitten, Pony-build (his project).  Despite this possible bias, a strong recommendation was give for Hudson (Java-based).

Tests and Testability, Ned Batchelder
Batchelder discussed testing lifecycle: test isolation, harvesting output, dependency injection and mocking.

Rapid Multi-purpose Testing, Holger Krekel
Krekel’s py.test is a command-line tool to collect, run and report about automated tests.  It supports test skipping, test running modes, parametric testing, test discovery, and multi-cpu testing.

New and Improved: Coming changes to unittest, the standard library test framework, Michael Foord
These changes will be new for Python 2.7:

• New assert methods.
• No more fail methods, standardize on assert*.
• Better multiline string testing.
• Unit test discovery.
• cleanup() method cleans up in reverse order (improvement over current tearDown() method).

Backported to Python 2.4, 2.5, and 2.6.  Check it out at unittest2.

What were the findings?

The genes responsible for the responses below are very strongly associated with smokers:

• Alcohol detoxification/response (2 genes)
• Inflammatory response (3 genes)
• Oxidative stress response (2 genes)
• Cholesterol homeostasis (2 genes)
• Bile acid binding (1 gene)
• Organophosphorus response (1 gene)
• Immune response (1 gene)
• Toxin response (1 gene)

How is this related to smoking?

• Alcohol detoxification is strongly expressed and could be correlated with ethanol and a number of other alcohols found in cigarettes.
• Inflammatory response and oxidative stress are very highly correlated with cigarette smoking.
• Cholesterol homeostasis is needed possibly because HDL (good cholesterol) is lowered by cigarette smoking.
• Bile acid binding could be associated with bile salt concentration being increased by cigarette smoking.
• An organophosphorus response could be the result of organophosphorus found in pesticide which is used on the tobacco found in cigarettes.
• Immune response is suppressed by smoking cigarettes.
• Toxin response is triggered by smoking cigarettes.

How was this done?

The bulk of the analysis is done using R.  Before loading the dataset into R, some pre-filtering is done to remove the annotations.

Using R, outliers are processed using a correlation plot, cluster dendrogram and a CV versus Mean plot.  To further filter the genes, two approaches are taken: remove genes with an average expression value less than 50, and remove genes with a coefficient of variation in the lowest quantile (5%).  A t-test with multiple test correction is used to do feature selection.  Principle Component Analysis (PCA) is used for dimensionality reduction.  A Scree plot shows the effectiveness of this approach.  Using the previously identified PCA components, quadratic discriminant analysis (QDA) is used to classify the samples into their respective smoking or non-smoking classes.

The filtering, feature selection and dimensionality reduction focused our analysis from the original 7,129 genes to just 23 genes.  Finally, using fold change, the 10 most discriminant genes are selected.  This is defined as the 5 genes with the greatest positive fold change and the 5 genes with the greatest negative fold change.  The result of this analysis is summarized in the findings above which correlate these 10 genes with smokers.

Here is the R code and PDF presentation.