WikiWikiSandbox

I had a little free time this morning to explore the applications in puppy4.2 and found one called DidiWiki - a personal wiki app. Like most, I have had nothing but positive experiences using wiki sites for valuable [surprisingly] accurate information and thought it would be nice to learn a little more about using it and editing myself. The introduction gave me some places to visit to get started, one of which was the sandbox. I added some text and wanted to save but they require you enter a code word. The 'help' on this explained that if no code word is given, there is a community word used and to try peer-to-peer...whatever here:

"We created the code words to discourage robotic attacks. Both the code words and the code word mechanism are subject to sudden change. Our code word policy is to not have a policy. Should the site become subject to systematic abuse, the code word mechanisms will become more stringent. Announcements appear on WikiWikiSystemNotice. When a code word is presented, you may use it to save edits. This serves the role of a very simple CaptchaTest which probably only works because the rewards for breaking it are so small. There is a MozillaFirefox plug-in that will type the code word for you. When no code word is given, you may use an alternative code word that floats along among trusted users. There is no way to apply for this code. Try your friends-of-friends network. Remember that this code and the mechanism itself will change if abused. This server employs a number of self-protection mechanisms which are summarized in MoreAboutWikiAccess. -- WardCunningham."

Okay so if anyone knows the floating code word among trusted users I would appreciate the tip. I already tried "open sessame."

TuxType on Puppy 4.2.1

I have been trying to get a fun typing program to teach my nephew how to type on the panasonic toughbook running Puppy4.2.1 that I gave him. I had previously tried an older version of TuxType that was readily installed on DSL using the DSL apps utility and it worked straight away. Nevertheless I wasn't too happy or surprised that this wasn't equally as easy on Puppy4.2.1. I guess I'm still discovering the "paths of least resistance" for configuring my puppy. At one point I found this great review (here) of 3 different typing tutors where the author/father subjected his 13 y.o. to each one and asked him to spend time testing them and then report his observations. In the end, TuxType was found to be fun, but too advanced for teaching from scratch and another app. called Klavaro was the favorite. Well I could only get Klavaro as an i386.deb file and I spent a bunch of time trying to get my puppy to install it and have yet to succeed. From the puppy package manager I found pb-debianinstaller which I had tried out on an earlier puppy and got to work, however, now on Puppy4 there's problems with the web-server configuration....which I know nothing about.

So I finally found a TuxType.pet from this site (http://pupweb.org/desktop/) which I was hyperlinked to off the Puppy Jumping off page stored locally at file://localhost/usr/share/doc/home.htm. However, this newer version is a significant enhancement over the one I used on DSL and required the SDL libraries... so after a bit more searching I found a .pet for those at the almighty puppy forum. Finally I at least have a working program to encourage my nephew to learn....when he's not too busy playing online flash games, building bionicals, pokemon card games...wishful thinking on my part.

Maintaining Office Productivity: Virtually Solved

Currently, my "job" is school.  I am on a research assistant-ship pursuing a Ph.D. in physical organic chemistry.  Part of my degree program has involved learning the "art" of computational chemistry / molecular modeling.  Given the inherent toxicity in chemistry and my general aversion to odors, I really enjoy doing chemistry in silico.  Having made a fairly substantial leap to a linux desktop has presented a number of challenges in this regard.  First there has been the obvious struggle of losing some 'compatibility' with MS Office, but I believe this to now be a non-issue.  The real struggle is continuing to use niche chemical software: Cambridgesoft's Chem3D, ChemDraw, E-Notebook; Wavefunction's Spartan; Gaussian's Suite of Programs including GaussView; SciFinder Scholar etc.  Only Gaussian has a suitable linux version, but that has been difficult to obtain.

I have been mulling this problem over for nearly two-weeks and made several attempts at either finding a replacement software for each of the programs or otherwise attempting a "virtual" solution.  I was able to install SciFinder in WINE which is a very nice "non-emulator."  As mentioned before, I have found a few incomplete solutions for ChemDraw (BKChem, XDrawChem) and I now have tried a few different molecular GUIs including Viewmol, PyMol, Gabedit, and Tinker's Force Field Explorer (FFE).  Pymol is powerful and has great aesthetic potential as a molecular viewer, but does not serve well as a molecular editor.  Gabedit has lots of apparent functionality working as a front-end to a number of computational programs (G03, MOPAC, GAMESS, MOLPRO) but its editor is very clunky and lacks the intuitive feel I've grown accustomed to.  Tinker and FFE I expect will eventually serve as a useful way to 'clean-up' structures with a force-field calculation, but it too has no builder!  

After contacting support at PQS (a computational chemistry solutions company for hardware and software integrated in a parallel computing environment) I was given some advice to transfer the working GaussView install on the cluster computer (running Novell SUSE) to my Ubuntu 9.04 desktop.  So far, that has not been a trivial task.

So somewhat at a loss, I have swallowed my new-found linux pride and installed XP on a virtual machine created through VirtualBox 3.0.  This too required about 3 hours of research, trials and tribulations, but it seems to be the most powerful solution.  There are lots of forums on the topic of this configuration, some of which are succinct and informative.  Here are the links:

http://www.virtualbox.org/wiki/Downloads

http://download.virtualbox.org/virtualbox/3.0.0/UserManual.pdf

Supposedly it is possible to use VirtualBox to boot an existing OS installed on a partition of your HDD, but this requires a lot more understanding and caution and still has many bugs.  Otherwise the process is quite straightforward:

1. Download and install VBox for your OS-distro

2. Create a Virtual Machine using the wizard: check the VBox Forums for discussions regarding set-up, configuring your virtual disk, etc:

http://forums.virtualbox.org/

3. Install a 'guest' operating system

4. Install "guest additions" from the 'Devices' drop-down menu of your window holding the guest OS

5. Set-up shared folders to allow file access between 'host' and 'guest'

That's as far as I am for now.  I have installed most of the ChemOffice Suite (just need E-Notebook, and a key-crack) but still need GaussView and Spartan.  The system runs quite fast, but I do have 4GB RAM on my 'host' and allocated 1024MB RAM for my 'guest.'  

What the Flux Ubuntu...

My journey for "optimizing" the performance of laptops I have on hand is nearly over. So far I have been happy with my choices for the Dell Latitude CPi (Puppy 2.16.1: 233MHz, 128MB SDRAM) and Panasonic Toughbook CF-37 (Puppy 4.21: ~300MHz, 192MB SDRAM).

My principle laptop is an hp pavilion ze5600 running a 2.8GHz Intel Celeron and 512MB RAM and although I am sure that any flavor of ubuntu should run fine on it, I wanted to try some medium sized distros out. So far the only one I have found/tried is Fluxbuntu. The idea here is your basic ubuntu install + fluxbox window manager - several non-critical daemons to give a very fast OS. It's true, this distro ran lightning-fast, but I was quite surprised to see I could not get either network adapters to work. I was mostly looking forward to having the support of a synaptic package manager added. Puppy doesn't have this, but I've read that the Puppy team (Barry really) is working on 'woof' which will be a basic package manager that gives you apt-get functionality.

So for now, I am running Pup 4.2 on the hp ze5600 alongside XP for my wife. I am considering a xubuntu install, but I will probably do some more digging around first.

Pupdate: Back to 2.16 on Dell Latitude

Okay, so it is true what they say..."it is better to have loved and lost than to never have loved at all." Unfortunately I was unable to solve the problem of getting sound on my Dell Lat. CPi with Puppy 4.21. I probably spent close to 6 hours on dealing with this set-back, and was a bit disappointed when I couldn't figure it out. I need to remember that I am still very new to linux and to cut myself a little slack. It's not like I have nothing else going on...3 kids in diapers under age 2, writing a dissertation...blah, blah, blah. I need to remain somewhat practical and focus on my discrete goals: I wanted to revive this ancient machine with a fast, light, practical OS that lets me surf the web, blog, listen to music, make simple edits to images and other light-duty work. Puppy 2.16 seems to manage this fine and should give me a bit more life out of this machine.

I recently handed off a Panasonic Toughbook to my 11 year old nephew and today swapped out DSL-N for Puppy 4.21. With only 64MB RAM it is a bit too sluggish, but I have a $15 128MB module on its way in the mail which should give it the boost it needs. Fortunately, the sound module worked immediately, requiring no configuration so he should be in good shape. My goal here is to catch him early to get positive exposure to linux in general. DSL-N was a little too challenging with its basic configuration to navigate the file-system and run progrmas so for him Puppy should be much more enabling...I definitely want to keep him excited about his new toy and not get overwhelmed or discouraged.

I Think I'm in Puppy Love

Puppy 4.2.1 is rocking my world!! I had originally chosen 2.16 based on a review that suggested it would be easier on a low-spec laptop. My Dell Lat. CPi definitely qualifies with 233MHz Pentium 2 and only 128MB RAM. However, I was struggling with getting my Linksys WPC55ag wireless network adapter running and thought, maybe its drivers would be included with Puppy 4.2. Well not only is this true, but this install is only slightly lagging in speed compared to the previous version.

Overall the benefits are far out-weighing the marginal slow-down. The desktop manager is enhanced by a widget toolbar, a useful 'disappearing' top toolbar and a menu refresher that manages newly installed apps. I suspect when Puppy 5.0 comes out with 'woof' package manager that will supposedly rival mature managers like synaptic, this light-weight portable distro will really start to make waves. I already can't wait and I don't really know anything about linux!

How Much Is that Puppy in the Windows?

Impressive...Very Impressive...

I'm of course making reference to 'Puppy Linux.' Right now I am posting this blog from an old refurbished Dell Lattitude CPi with a 233 MHz Pentium 2 and 128MB RAM. My wife bought it "refurbished" for $300 way back in 2004 and it was preloaded with Windows 2000. She could only use it for about 2 years before she couldn't stand its speeds any longer and has mostly sat by the wayside until I recently started tinkering with linux and computers in general. In my hunt for a lightweight OS I found only a few contenders. Obviously DSL and DSL-N were among the first I discovered. Although I liked both of them, they were not without their troubles. First, I couldn't get DSL to work with an 'acx' driven pcmcia network adapter that I had or a WCA55ag Linksys adapter. It had plenty of features to what I wanted out of a basic portable setup, but I don't even have a network adapter of any kind on the Dell and didn't want to shell out $$ on a new pcmcia just yet. Second, I had lots of difficulty getting it set up to save my desktop configuration and install to the hard drive. It was pretty fast however. DSL-N has a more mature 2.6 kernel with better driver recognition and sure enough the Linksys ran right away. I found the system to be just as fast and the boot times better once I did a HD install. I still had a bit of trouble saving my desktop configuration and although the MyDSL apps installer is a great idea and has a few gems, the lack of a proper package manager is a significant downside. Furthermore, it seemed like it would be a chore to install synaptic.

Then I discovered Puppy and so far it is a big winner...and I'm mostly talking about speed here. Barring boot times, it is much faster than the DSLs. I'm completely amazed, especially since it is running entirely from RAM. Right now I am running 2.16.1 which came with loads of network adapter drivers including the acx series. Strangely, where DSL worked with my Linksys adapter immediately, Puppy will not, and so far, I'm struggling a bit to get it functioning.

Puppy's desktop is nicely configured. Slick graphics for icons, a very fast desktop manager, and loads of useful apps. I have just started with it so I am sure I'll have a follow up on functionality soon. My final thought is that...oh yeah, it saves a configuration file to a location you specify and then searches for it on boot so everything is just as you left it. The only trouble so far is I haven't been able to install it to the hard drive, but it moves so fast, I'm not sure I should bother...so what if I need to keep a cd in it to boot?