Monday, December 14, 2009

Backups that just work.

After all the drama with the KSODs that I experienced in Vista and Win7, I’ve decided that it is high time that I put together a good backup system. Here’s what I’ve come up with.

I have a primary backup system that continuously backs up data, and a secondary system that images the computer every other week.

My primary backup program is called Rebit. The company tagline for the product is “Ridiculously Simple Backup” and for the most part, this is true.

Rebit is a bit like Time Machine on the Mac, sans the cheesy user interface, working quietly in the background using the Microsoft Volume Shadow Copy Service to backup everything to the Rebit appliance.

The software supports revisioning, so you can back up and access multiple versions of files like you can in Time Machine.

There are virtually no settings to configure – it just backs up everything -which adds to its simplicity. However, this can be a little frustrating to techies who want to be able to verify backups or apply backup filters to exclude large VMware images, for example.

So far, everything has worked smoothly with the 1TB Seagate Desk external USB hard drive that I bought for the Rebit. The installation and activation of the software went smoothly, and creating the first system image took overnight.

Subsequent incremental backups took much less time. If Rebit is plugged in, it seems to echo file changes pretty quickly, but also creates a new incremental system image daily. If it is not plugged in, Rebit automatically will catch up with all the file changes the next time you plug it in.

My secondary backup program is Paragon Backup & Recovery 10 Free Edition. Paragon Backup is free for personal use.

I was very pleasantly surprised by how full featured it is for free software, supporting archive verification, boot USB & CD creation and even incremental backups. 

I use this program to create a drive image every other week.

I should mention that both Rebit and Paragon Backup are compatible with Win7 64-bit. I haven’t tried to restore from a backup from either system yet, but will report back when I do.

Incidentally, Rebit for some reason just would not work with an older 640MB Western Digital Caviar Blue hard drive that I had put in two different USB enclosures. At random times it would freeze the computer which wouldn’t recover until I turned off the external drive.

However, the WD HD is working fine as a Time Machine drive in Meike’s Mac Pro. Perhaps it likes Macs better.

Tuesday, December 8, 2009

ImageJ “Import Using QuickTime” requires 32-bit Java &

The open source image analysis program ImageJ by the National Institutes of Health is a fantastic free tool for scientific imaging. It can do cool stuff such as this.

However, I’ve discovered that it natively supports only the AVI 1 specifications which limit your video imports to 1GB, even when using virtual stacks to open larger files.

The workaround I found was to import the video using the “Import Using QuickTime” feature under File > Import > Using QuickTime.

Unfortunately, this add-in doesn’t work when called from a 64-bit Java environment. So I reinstalled the 32-bit version of ImageJ.

It still didn’t work. I finally tracked it down to some instructions that I had missed here.

Basically, the fix involves copying the file from “Program Files (x86)\QuickTime\QTSystem\” to “Program Files (x86)\ImageJ\plugins\Other-Plugins\” which did the trick.

I don’t recall doing this previously before I switched over to a 64-bit OS, but this procedure fixed my installation and I can happily open large video files once again.

Monday, December 7, 2009

Windows 7 Backup fails with 0x8100033.

Quick note: I have been having problems with the Windows 7 Backup program creating a system image. It always fails with 0x81000033 error, and a quick search on the Internet reveals that other people are having the same problem too.

The most common theory is that the hidden System Reserved partition installed by default with Win7 has too much “data” in it, causing the Microsoft Volume Shadow Copy Service to fault out because it does not have enough working space on that volume.

Sneha, the Microsoft representative in this thread on believes the problem is due to the USN journal setting for the partition being changed by third-party software, eating up space on the hidden volume and causing Backup to fail. Backup requires

The last post by Sneha in this thread was only 19 hours ago and unfortunately he doesn’t have a solution other than to turn off the system image option in Backup. This is an unacceptable solution.

Hopefully, Sneha will return with a definitive solution on how to fix this. As of now, I still have no good backup solution, but I will try to reinstall Rebit on my new external hard drive, since I could never get it to work with my old HD.

Side-note: If Sneha’s theory is correct, could Rebit have changed the journaling settings for the System Reserved partition? I have been able to perform a system image backup successfully with Windows Backup *once*, and this was before I installed Rebit. Hmmm…

EDIT: I found this solution on the web. I haven’t tried it myself, but it seems reasonable. Just make sure to backup your system first before messing around with the System Reserved partition:

Thread Title w7x64rc backup fails with error code 0x81000019
Started by: david.wells

Reply: A Workaround Without Repartitioning:

When trying to make a system image of Windows 7, I got error 0x80780119.  After searching this thread (plus others), I found my 100 MB System Reserved partition had grown a large USN journal.  I assigned it a drive letter.

Fsutil usn queryjournal F:

Then I ran this command to clear and disable the USN journal on my System Reserved partition:

fsutil usn deletejournal /N /D F:

This freed 48 MB.  The USN journal on my System Reserved partition remained disabled after a reboot, which I verified by re-running the query.  Subsequently, I was able to make a system image without error.

Look here for details on FSUtil:

Mancer, MCITP-EA

Thursday, December 3, 2009

Seven Excel 2007 tricks and tips for data analysis.

When taking data for simple scientific experiments, typically you have built in replication so that you can calculate the means, standard deviations and the 95% confidence intervals at each setting of interest.

But it’s always such a pain to massage the format and order of the replicated data so that you can perform the statistical magic.

Here are some Excel tricks and tips that help me when I perform data analysis. You can find more information in Help or on the Web:

  • Sort: The sort function in Excel is your friend. Use it to sort the data in numeric order from smallest to largest.
  • Consolidate: This magical Excel function takes a list of data with replication and outputs lists of averages and standard deviations for each unique variable in the left-most selection column of the Reference area. From these, you can calculate the 95% CI with ease and plot the data with error bars.
  • SHIFT + END + RIGHT and SHIFT + END + DOWN: These two key sequences select cells from your cursor to the right-most-end and bottom-most-end of your data block respectively. It is so much more efficient than click-dragging down through pages and pages of data.
  • DOUBLE CLICK the Fill Handle: This auto-fills a formula down to the bottom of the list, referencing the size of the column to the left of the formula – no need to click-drag this either. The Fill Handle is the black dot at the bottom right of the cell.
  • F4 toggle: This toggles the cell reference between a relative reference that moves with the cell and an absolute one that stays fixed (the cell reference has the dollar signs in the address).
  • VLOOKUP: This command allows you to find values using a lookup table. Use this to code/decode your data or to calculate the value of a function using a lookup table approximation.
  • Error Bars Add-In: This free third-party add-in from Jon Peltier allows you to set error bars in both x and y directions easily from a single dialog box. You can set this to the 95% CI column to add meaningful error bars on your graphs.

Excel is a wonderful tool for analyzing simple experimental designs. For more more complicated experiments including DOEs, Response Surface Analyses, I would recommend using a statistical package like Minitab, SigmaPlot or the Statistics Toolbox in Matlab.

Monday, November 30, 2009

Cuda 2.2 / Visual Studio 32-bit to 64-bit suckiness.

I have been working with nVidia’s Cuda SDK to speed up execution of my Monte Carlo photon transport simulations.

However, after the switch to 64-bit Win7, I’ve discovered that the 32-bit programs that I compiled previously don’t run in Win7 64-bit, even though WoW is supposed to let you run 32-bit programs in the 64-bit OS.

To make matters worse, I can’t get the 64-bit version of the Cuda 2.2 Toolkit and SDK to recompile the programs in 64-bit in Visual Studio 2008 (64-bit).

This is going to take some time to sort out. Grrr…

Visual Studio 2008 and nVidia CUDA.

I had to search for this again to configure Visual Studio 2008 to play nicely with CUDA.

For those who aren’t familiar with CUDA, it is a framework from nVidia that allows you to write programs in C to harness the extreme parallel processing processing power in modern GPUs for computation.

Anyway, this blog has some nice tips on how to get syntax highlighting, building and Intellisense in Visual Studio 2008 to work with CUDA source files.

Saturday, November 28, 2009

Print to OneNote 2007 / Win7 64-bit workaround with SnagIt.

Running a 64-bit OS means that all my technical computing programs have access to much more memory than previously in a 32-bit OS. And Windows finally can see all 4GB of RAM in my laptop.

But Microsoft requires all the device drivers to be 64-bit as well, which unfortunately broke the ever-so-useful “Print to OneNote” feature that came with Office 2007.

One solution is from OneNote guru David Rasmussen who has developed an open source workaround called XPS2OneNote:

However, for some reason this failed to work on my computer.

I’ve discovered that SnagIt, another little program that I bought some time ago, also has a virtual printer that you can send output to from any program.

Then you can easily route these printouts into OneNote by using the SnagIt / OneNote output accessory which is available here:

Although it is not free, SnagIt also allows you to perform some cool graphical edits and annotation before sending the content on its way to OneNote. Info on SnagIt can be found here:

Friday, November 27, 2009

DRM sucks and only punishes people who play by the rules.

I have been rebuilding and reinstalling programs on my computer the last two days and I’ve run into digital rights management problems twice already!

The two programs that complained are Adobe Creative Suite 3 Standard and Mindjet MindManager 7.

In both cases, reinstalling the program and trying to activate it resulted in errors indicating that I had tried to install the programs too many times.

In the case of CS3, you get two activations so that you can install it on two different computers,  but in my case I guess that it counted both Vista (my original OS) and Win7 32-bit (the upgraded OS that died). I rebuilt my system with Win7 64-bit which set the counter over the limit.

You can deactivate one copy before moving it to another computer, but that is hard to do when your OS fails before you can deactivate CS3. And now I can’t even install the second copy because it has counted the same computer THREE times.

MindManager is even more limiting with only one activation available. And I couldn’t find any way to deactivate it from the menus within the program.

Anyway, in both cases I was able to call customer support, explain the situation and then activate the programs on my rebuilt computer.

Still, it feels wrong that I had to pay a lot of money to have the privilege of running into these DRM problems, while someone who “found” torrents of these programs wouldn’t have to deal with the DRM at all.

What happens when these programs become abandonware in this age of planned obsolesce?

Will these companies still stand by their part of the license agreement to provide you with working software when these products aren’t supported anymore?

Programmers need to make a living and be paid, which is why I buy software, but DRM is not the solution.

Upgrading Comsol 3.5a from a non-administrator Win7 account.

I ran into a problem installing the Comsol 3.5a hotfix to my installation of Comsol Multiphysics.

Basically, the symptoms are the following:

I followed the online instructions for installing the hotfix:

  • Download the update35a2_win64.jar file
  • Move it in to the COMSOL35a\updates directory
  • Run Programs > COMSOL 3.5a > Tools > Install COMSOL Update from the start menu using “Run as Administrator”.

I then ran Comsol to check the version number. But to my frustration it always displayed version instead of the updated

However, Comsol running from an admin account would display the correct version number

I tried copying Users\<username>\.comsol\ver35a\preferences.ini from the admin account to the standard account, but it kept getting replaced with the old version of the file upon launching Comsol in the standard account.

The solution I found was the following:

  • Temporarily give my non-admin standard account admin privileges by going to Control Panel > User Accounts and Family Safety > User Accounts > Change your account type
  • Run the update install tool using “Run as Administrator” and choosing the now-admin “standard” account
  • This is very important - run Comsol once using “Run as Administrator” and choosing the now-admin “standard” account
  • Close Comsol and take away admin privileges from the “standard” account

Running the update program from an admin account is pretty standard, but I think the key is then to run the program once using admin privileges.

I guess the update program only stages the changes so that the next run of Comsol can execute the changes. Or something like that.

This fix works for me. Good luck!

Wednesday, November 25, 2009

Computer crashes and whatnot.

Some of you may recall some months ago when my Vista computer was struck dead by the dreaded "Black Screen of Death" (KSOD to you technically inclined). If you Google around the Internet, you'll see that KSOD seems to be a relatively common failure, thought to be caused by a number of different issues but all of which result in a catatonic, non-functioning computer.

Like most things in life, it felt worse while it was happening than reflecting on it now, and in the end, I was able to fix it and even got my system into a better state than it was previously, being forced to stop my normal hectic life in order to recover, tidy up and get rid of dunnage in my computer.

Unfortunately, KSOD struck again this past weekend, and even the otherwise wonderful Windows 7 was not immune. It happened after what I thought was a rather innocent "chkdsk /f" to fix errors on my hard drive but resulted in it deleting perfectly good permissions in the NTFS file system access control list and leaving me with a dead computer.

Only this time, I don't have a good backup... more on this later. Ironically, I ran the disk checker in an attempt to fix my backup problem.

So once again, I am forced to stop the busy planning, running around, doing and yes, procrastinating in order to put back my computer into a working state.

Taking a step back to reflect on the situation, however, I can make two related observations. The first is how much of all the things I consider to be important in my life resides in that little digital homestead that is my computer. And the second is how much of my own identity and happiness I've permitted to be tied up to these material things.

Anyway, my new hard drive should be arriving by post anytime now and then I can start the lengthy process of reinstalling and reconfiguring Win7 and all my applications. Luckily, since KSOD results in a non-booting computer but doesn't actually delete data, ultimately I will not have lost much except for a lot of time and perhaps some pride.

It's also a good opportunity for me to install the 64-bit version of Win7, which I chose not to do previously coming from a 32-bit Vista system because I would have to reinstall all my programs. I guess I have time to do that now.

So anyway, some notes for people who have encountered KSOD and are frantically searching the Internet for solutions...

On KSOD causes and solutions:
A lot can be found on Google with the search terms "KSOD fix chkdsk". There seem to be a number of different causes including corruption of RPC server permissions, registry permissions, Event Log permissions and chkdsk-related permission corruption. This is a good page that describes a number of them with possible solutions:

Both times in my case (Vista and Win7), I believe that the KSOD was caused by chkdsk going haywire. In the Vista case, my computer had blue screened and crashed, and after restarting the system, Vista ran the mandatory chkdsk because "Windows wasn't shut down properly". In the Win7 case, I started "chkdsk /f" myself. Both resulted in chkdsk "Replacing invalid security id with default security id for file " and corrupting the ACL. Both cases ended up with KSOD upon reboot.

Microsoft has a hotfix for similar symptoms in Windows Server 2003, but not for Vista or Win7:

I don't know if this is the same issue, but it doesn't specifically mention Vista or Win7 and probably isn't compatible.

Althought the resetting file permissions post near the end of the KSOD thread on matched my symptoms and seemed promising, it didn't work for me and I couldn't get past the KSOD.

Also, because the file permissions are messed up, I still couldn't get access to the files after putting the hard drive in a USB enclosure and connecting it to a Vista system. I got arond this by booting into UBCD4Win/BartPE, which runs a modified XP system and doesn't enforce ACL. I suppose you could get Vista to read the hard drive by turning off UAC or trying to Take Ownership of the files, although I didn't try this myself.

On hard drives:
I ended up buying two drives - a 1TB Seagate FreeAgent Desk external USB hard drive, and a 500GB Western Digital Scorpio Blue laptop hard drive.

The FreeAgent drive is fantastic. It seems reliable so far and the industrial design is beautiful. I love how the white LED pulses through the perforated metal cover when the drive is in use. Stunning! And the power adapter is small and comes with both exchangable UK and EU plugs.

I bought the WD Scorpio Blue hard drive because it was available quickly and seems to be the default workhorse model that most people buy - dependable and robust.

Originally, I wanted to get a drive with a shock sensor built in, like the Seagate Momentus 5400.6 (ST9500325ASG), the Momentus 7200.4 (ST9500420ASG) or the WD Scorpio Black (WD3200BJKT). Seagate drives with the G-Force sensor end in "ASG" and WD drives with the freefall sensor end in "BJKT".

Long story short - nobody seemed to have any of the sensor-enabled drives in stock except the 7200.4, but a quick Google of "Seagate 7200.4 click problem" reveal that this drive might have a serious design fault.

On Backup solutions:
I have used both Aronis TrueImage and Rebit backup solutions.

While Acronis offers more features and capabilities, I never could discipline myself to make regular backups often enough to matter. Also, only the 2010 version supports Win7, although if you search the Acronis forums, it appears that Win7 users are having problems with restoring backup archives.

Rebit is meant to turn a USB hard drive into a backup appliance that you plug in to your computer and forget about it, like Time Machine for OS X. However, I never could get it to work right, although the second copy I bought for a friend works brilliantly for them. One suggested solution by Rebit to troubleshoot the system is to perform a chkdsk /f on the host drive...

Anyway, this post is much longer thatn I wanted, but I hope my experiences help those of you who found this page by searching for KSOD. In the end, none of the "quick" solutions worked for me and I am reinstalling my system and working on having better backups.

Good luck! Your data probably is fine and with a little peserverance, you'll be back up and running in no time. Take care.

Friday, November 20, 2009

Turn on the Bluetooth Radio before upgrading to Windows 7.

Recently, I upgraded my Dell laptop to Windows 7 and I have been quite pleased with the new OS. Microsoft has made numerous performance and usability tweaks that make the overall Windows experience much nicer and more streamlined in general.

One problem I’ve had with the upgrade though is that Bluetooth support broke.

I forgot to turn on the Bluetooth radio before uninstalling the driver and upgrading to Win7, and Windows did not properly detect the hardware and install support for it.

However, I discovered that in order to turn on the radio, I needed a driver to talk to the hardware. But the original Vista driver refused to install under Win7.

So I was stuck up the proverbial creek without a paddle.

Fortunately, after a little searching with Google, I found this little Dell utility to switch on the BT radio, and although it didn’t specifically mention compatibility with my specific laptop model or with Win7, it worked fine for me.

Dell Support – R159805.exe:

After running the utility, Windows 7 immediately detected the hardware and rushed off to find and install the Microsoft Bluetooth drivers. After a reboot, everything works perfectly now, better than it did before with the original Dell / Widcomm Vista drivers, I might add.

So if you are having problems with Windows 7 detecting your Dell Wireless 355 Bluetooth 2.0 + EDR hardware, try this little utility and see if it helps.

Friday, August 21, 2009

Healthcare reform and the scientific method.

One thing about any scientific measurement is that the signal always is convoluted with noise. One tries to hone in on the signal by verifying the data with repeated measurements. The more measurements you make, the better you can characterize the noise and have more confidence in the signal.

This echoes the rule of thumb from my news reporting days at my university newspaper - always confirm information with a second source. Better yet, find a second source *AND* a third source.

It seems like there is a lot of noise out there in the health care / health insurance reform debate. Some of this is normal "noise" associated with debating complex issues. Health insurance reform *IS* complex and should be debated. But more and more in recent days, it seems to me like a lot of this noise has been injected into the debate for politically-motivated reasons.

A lot of it is plainly dishonest and not true, and although I'm sure these people truly believe in their causes, the arguments they make are not honest. Please, the ends simply do not justify the means.

Everyone is entitled to their own opinions and this should be respected. What we need is honest debate. So please make sure these opinions are informed ones.

Read the reform legislation and follow the money. See how your senator / congressman have voted in the past. Seek out the truth and see how it affects you.

And please make your own judgments. Our democracy depends on you.

These sites might help:

Mendeley: social networks for researchers.

It seems that social networks are being incorporated into everything now and academic research seems to be no exception. I recently tried out the new Mendeley Research Networks beta and I like it quite a lot.

It is a journal papers repository, citation manager and academic research social network all rolled into one. There is a desktop client that you can install on your computer which is integrated to a social network and cloud-based services that you can access through any web browser.

The client program and the web-based services are free, and the company promises to offer new advanced features in the future for a fee.

What about Zotero?

The first time I tried Mendeley was quite a while ago, and although the idea of sharing reading lists and finding out what other people in your field are reading was appealing, I deemed the early beta of the desktop client too slow and buggy to be useful. Instead I opted to use the fantastic open-source Zotero as my main citation manager.

However, Zotero is not without its shortcomings.

Although Zotero is quite powerful in capturing citations as well as just about anything else on the internet you can see in your browser, there always was a certain lack of polish in the user interface that made day-to-day use something of a chore, especially for retrieving information.

When I wrote my PhD transfer thesis using Zotero and the accompanying Microsoft Word plug-in for inserting 300+ references, it got the job done but it was slow and painful.

Each reference insert or edit would take tens of seconds to finish, and let's just say that during this writing period the word Zotero often would be preceded by another, not so flattering utterance that rhymed with "luck."

Mendeley - but is it any good?

Fast forward to today - the latest beta of Mendeley has improved its performance  tremendously, although crashes still happen quite often - at least once an hour over last couple of days, by my estimation. Compared to the rock solid 1.0.10 release of Zotero, this is a step backwards for me.

However, the interface is such a pleasure to use. Being able to not just sort but filter by author or publication is so great and helps me to find articles more easily.

Also, simple things like alternating the background color between each record helps visually to identify where each reference begins and ends. Little gold stars for favorites and green dots for unread papers that you can toggle on or off really add to the usability of this product.

Of course, there always were workarounds that you could implement in Zotero to do this - I had "unread" and "important" tags in Zotero for doing the same thing, but these little interface bonuses are so much better.

Mendeley also has a feature to let the program organize papers / PDF files for you that simply is manna from heaven. It works in a way similar to the "let iTunes manage your library" option, renaming and organizing files as you change the reference details. Simply brilliant!

The current beta does, however, lose track of PDFs once in a while and sometimes even deletes them, which definitely is not cool. Also, sometimes it refuses to match up PDF's with already entered citations. But as the program still is in beta, quirks like this hopefully will be ironed out before the 1.0 release.

The killer feature though, in my opinion, is the inline PDF reader that allows you to highlight and annotate PDFs while tagging, taking notes and referring to referenced articles.

Previously, I did this in an open Acrobat window and switched back and forth between that and Zotero / Firefox, but having everything in one place is fantastic. Being able to open multiple documents at once, take notes and switch between them all from within Mendeley really helps to streamline my workflow.

However, the PDF reader function does seem to cause the program to crash a lot, but hopefully these bugs will be resolved soon.

Social research.

The other big aspect of Mendeley is the integration with the website, which provides online storage and access to your papers (500Mb per account), as well as access to aggregrate reading trends, shared reading lists, social tagging and collective citation editing of research papers. They describe it as for research papers.

Although the social network aspects are cool and interesting, it remains to be seen how useful this is to me.

The online storage of papers, however, is useful, although 500MB is on the low side for me. My current solution is not to have Mendeley sync my papers, but instead to put my PDF repository in my Dropbox where I have 3GB of online storage.

With this solution, only my laptop at home has the PDF's associated with the references, while the desktop at the University has the PDF's (via Dropbox) and references (via Mendeley) unlinked.

Hopefully, they will add a feature to link PDFs in a directory structure with citations in the Mendeley database - like how iTunes can relink tracks to mp3 files.

One interesting thing... Although papers written by others that you upload are accessible only to you, your own publications that you upload by default are downloadable by others, which makes for a clever and legal way to sidestep the giant journal publishing companies that tradtionally have served as the gatekeepers to all scientific information.

Hopefully this is used to improve general access to scientific information along the lines of PLoS and is not part of a hidden plan to monetize the site.

Overall, I really like Mendeley, enough to switch over from Zotero (although I will not be importing all of my citations over anytime soon - there is no easy migration path, yet).

It is a fantastic, streamlined, free (although currently buggy) solution for managing your papers and citations. The social network aspect also holds a lot of promise.

Thursday, August 20, 2009

Things are different when slow...

I uploaded a few slow motion films to YouTube. The clips were taken with a Vision Research Miro4 high speed video camera at frame rates of 1000+ fps and played back at a more sane 30 fps.

Things look quite different when slowed down, don't they?

Saturday, April 4, 2009

Tools to help you organize & simplify.

Image by Ian Lloyd. {Flickr photostream}

As I am now fully entrenched in the final phase of my PhD, I find myself reflecting more and more on finding the right balance between doing the massive amounts of work that is required to complete my research, and the other personal goals and simple pleasures that I have in life.

More and more I find that sleep and happiness seem to be a casualty of this struggle, and the result being that little things put me off balance. And yet the centering and focusing activities in my life that probably would be of most help - mindfullness meditation and yoga practice - seem to be the first to be sacrificed in order to get more done.

Ultimately, it's up to each of us to prioritize and figure out what we want to do with our lives. Still, a few things have helped me to organize and simplify:

  • David Allen's "Getting Things Done" which hopefully will help me to refine my personal GTD methodology.
  • "Getting Everything Done and Still Have Time to Play" by Mark Foster. Almost the perfect companion to GTD - reminds me that all these things to do are part of a bigger picture, a more fulfilling journey. As someone close to me once said, it's all about balance.
  • "The Alchemist" by Paolo Coelho. If you haven't read this wonderful story, drop everything and do it right now. It will make you feel good.
Software (not free)
  • Outlook 2007. Although the program still is huge and resource hungry, it has come a long way from the earlier versions of Outlook I stayed away from for personal use but was forced to use at work. This one actually is quite usable and I've grown to like it. This hotfix actually makes Outlook pretty snappy. It's nice to have everything in one place -- I've implemented all my GTD lists in Outlook Tasks.
  • OneNote 2007. This is the hidden gem in the Office 2007 Enterprise package that I bought through a student purchasing program. It follows an electronic notebook / sketchpad metaphor, but is so much more. I use it for everything from my research notebooks to personal notebooks and journals. It helps me get all the stuff out of my brain and into a searchable electronic form in my computer.
  • MindManager 7. For brainstorming or just charting out ideas and relationships, this mindmapping program is tops! I tried the open source program Freemind, but it was slow for large maps and the UI was not very friendly. I've found that it's worth paying for things that deliver good user experiences, especially if you are going to use them on a daily basis. And student pricing makes this package actually affordable.
  • SnagIt 9. This screen capture utility is really great, especially when used with OneNote and MindManager. A picture really is worth a thousand words.
  • Deskspace. A virtual desktop manager that uses a cube metaphor for desktop management, it is like Compiz Fusion for Windows. It allows me to separate email and IM windows on a separate desktop from work stuff to minimize distractions but still be accessible. I've stopped using this software because there is no easy method for moving windows from one desktop to the next. This feature supposedly is in development, but without this it is just eye candy that is not very useful.

Software (free)
  • Xobni. This Outlook plugin finds the social networks in your email. With 3rd party integration enabled, it also looks up the email sender in Facebook and LinkedIn. It helped me to discover a professor's secret alias on Facebook by matching up their profile with their email address! Data mining at its finest! My upgrade to Windows 7 disabled search across multiple .pst files, which was a deal breaker for me. Although I liked Xobni, the feature set did not offer enough to me to justify paying for it.
  • Flock. Not exactly a lightweight program, this browser based on Firefox does have hooks into all the social networks, tweets, blogs and rss feeds to give you a "mission control" style summary of the online world. And since I've centralized all my online social interactions in this browser, I can simply close the window to remove the temptation to see what's going on online. I liked Flock, but it was by far the the slowest of my web browsers behind Chrome and Firefox 3.5. Now I use Chrome as my default browser, Firefox for work and Trillian for keeping tabs of my social networks.
  • Trillian Astra. Great UI - kind of like an Adium for Windows. Still in beta, but great for centralizing IM interactions especially now that they support Google Talk and Facebook Talk in addition to ICQ, AIM, Yahoo! and MSN.
  • Skype. Brilliant P2P VOIP telephony. I subscribe to their computer-to-phone features and use this to reduce my London telephone bills and pay directly with American dollars (and save the currency exchange fees). Also, the free video phone calls are great, which helps a lot when you are a student ex-pat in a foreign land.
  • Spotify. Brilliant free and legal P2P jukebox. You actually can specify the song you want to listen to and it will play that song! In the free mode, it plays audio ads and displays visual ads its window, and uses P2P to reduce content distribution costs. Fantastic classical and jazz collection to listen to while you work.
  • TeamViewer. Excellent, simple to use remote control software that is free for personal use. I use it to farm out calculations to my work computer when I'm at home on my laptop. Still need to figure out the VPN features.
  • Dropbox. It's like having a USB memory stick on you wherever you go. The sharing and public folder features make it awesome!
  • Keypass. An open source password manager that works great! A Windows Mobile verision also is available so that you can carry your passwords securely wherever you go.
  • TrueCrypt. Keep private documents hidden and safe. On the fly encryption of volumes makes this open source program simple to use.
  • Switcher. Like Expose for Vista. Invaluable for when you have a gazillion PDF documents open.
  • Zotero (firefox add-on). If you have any need for reference management, this free add-on for Firefox is the best. The user interface can use some improvement, I feel, but for functionality and price, it is fantastic. I still have this installed in Firefox, but my reference manager needs these days are taken care of by the excellent and free Mendeley Desktop.
So those are my tools that help me organize and simplify. What tools do you use?

Wednesday, January 21, 2009

Hope and science.

Photo by Cayusa (Bart). {Flickr photostream}

For myself and for many others, yesterday marked the not only the end of the Bush Administration and eight years of failed policies and politics that I mostly disagreed with (the HIV/AIDS program in Africa is one of the few, overlooked succeseses of George W. Bush), but also the hopes for redemption and renewal with the inauguration of Barack Hussain Obama to the presidency of the most powerful nation on Earth.  

This election was special, yes, for all the reasons I'm sure you've read in a million other blogs and news articles, but also, on a personal note, because it was the first election I voted in while living outside of the United States.  And I witnessed first hand how people from all over - even here in powerful European Union nations - look to America for leadership and, yes, for hope.  

I started voting when President Clinton was in office but never have I seen such thirst and fervor for change, such high hopes, aspiriations and perhaps expectations placed on the back of one man.  

And while many cynics have prognosticated that this Presidency is bound to disappointment and failure precisely because no one person can hope to live up to such high expectations, I, for one, feel that these dreams can fuel "The Push" that Tavis Smiley commented is necessary to propel the President to become a Great President and achieve great things.

I hope it is not hubris to say that in some ways, I think that people who have not had the desire, the opportunity, or the education and the training to do science and engineering look to us scientists and engineers for leadership and hope when it comes to national and global policies that touch upon our respective research disciplines.

Science must not be political, but politics should be part of the scientist's life.  

Our logical and evidence-based investigations into and our intuitive understanding of scale-spanning phenemona from the smallest mechanisms of biology to the grandest nature of the physical universe puts us in a unique position to elucidate and explain in lay terms to the general public and to policy makers how and why certain things work the way that they do, and why some things should be different.

So often, I've seen friends and colleagues perpetuate a sort of isolationism, blaming politics and politicians for bad policies but not doing anything about it, resigning themselves to simply concentrating on surviving in their little corner of the world.  

Yes, "it is the politicians' job" to sort out these things, but we, in addition to being scientists and engineers, are citizens of our communities, of our nations and of the world.  Simply complaining about it all the time really is just a waste of energy.  

We have to weigh our desires for change against the sweat and tears that it might require, and then, if we so choose, work to create the change that we want to see.  It won't be easy and may require untold sacrifice, but if it's what you want, then the journey will be worth it whether you succeed or not.

I hope.

Wednesday, January 14, 2009

The New Year and Getting Things Done

Photo by Meredith Farmer. {Flickr photostream}

Well, we are well into the new year and usually it is just about now, two weeks in, that one's resolve to keep new years resolutions starts to be tested in earnest. That's why I prefer instead to make many, smaller, actionable resolutions on a smaller time scale. So instead of resolving to exercise more in the new year, I promise myself that I will go to the gym or the yoga studio at least two times next week. With a bit of persistence and discipline and constant resolution making, this can become part of the normal routine in which it feels weird not do to what one set out to accomplish.

In theory...

Unfortunately for me, this type of self-motivation and goal-setting seems to work only for things that I really, really enjoy, and not-so-pleasurable things that need to be done at work or at home always seem to be put by the wayside, languishing in the hidden corners of my mind. Yet these unfinished tasks do get they revenge, so to speak, as with each passing day of undone-ness, their numbers and power gather in strength and manifest themselves as stress and anxiety over what things I haven't finished and what tasks I've forgotten about.

Which is why I was very pleased to come across "Getting Things Done" by David Allen. It's an organizational system that has been around for quite some time now and has achieved a cult status amongst some practitioners that rivals the Cult of Mac. And although I haven't read the book yet -- I have too many other things I want to finish first! -- I've come across enough summaries and discussions of it on the web to have gotten the general idea of the system.

The general hypothesis is that we have too many things in our mind to keep track of, and that all this clutter impedes our ability to get things done. So if we could get all this "stuff" out of our mental buffer and onto paper, index cards, a computer notebook, whatever, then we could free up our mind for actually doing these tasks.

For those of a computer science mindset, this might be akin to moving all the "keeping track of stuff" processes and data from active memory to the hard drive so that there is more memory for "getting stuff done" processes.

The actual implementation of this in real life is quite mechanical and algorithmic, which suits me quite well as that is my normal approach to work anyway, but I can imagine it to be quite foreign to people who are of a more intuitive mindset. Still though, if things aren't getting done, this might be a nice approach to try.

I'll save the actual details of my implementation of GTD for a later post. Suffice to say that it seems to work better for me than my previous approach, as I organize tasks and projects in Outlook, OneNote and MindManager. I'll also let you know how I'm getting on with this system, if it's actually increasing my productivity or just adding overhead.

On that note, here are two thoughts that I think are useful counterpoints against blind adoption of anything without a clear intention in mind:

My problem (or maybe just the way I feel) is that a lot of people (myself included) get so caught up in the tools, that we loose track of what the end results should be. Maybe it's the tools that I've used, but I don't feel that they promote anything other than collecting and organizing "stuff".

- unknown, 43 Folders group, Google Groups

We can get a lot of stuff done with to-do lists, and they are a very helpful tool, but using the lists alone will leave us feeling unfulfilled because we end up chasing after a never ending to-do list and forget to live our lives.

- Tina Su, "How to Design Your Ideal Life,"

I think the key insight for me is that GTD is meant to be a tool for achieving what you want, rather than the answer to the meaning of life, a lifestyle or even a solution to procrastination. Like many things, change must begin with oneself and we must initiate, take responsibility for, and see through to the best of our abilities and desires the change we hope to achieve. There really doesn't seem to be a substitute to good old fashioned hard work. (Believe me, I've looked really, really hard!)

I know I have been guilty of sometimes being more fascinated with the tools rather than what I could create with them. Keeping that in mind, we'll see how I progress with GTD in getting my research done.

Anyway, hope everyone is well and Happy New Year!