One of the key comparisons made between 64 Studio and Ubuntu Studio is that the 64 Studio team was more selective in the applications added, and overall have worked harder at optimizing the "real-time" (RT) kernel to produce the lowest latencies in audio work. One of the problems I had recently with Ubuntu was the sound stopped working and sound is pretty critical for an audio studio. So far, the sound drivers are all working fine with 64 Studio, I just had to adjust the ALSAMixer the first go to get the correct channel unmuted.
But 64 Studio has yet to be completely trouble-free. For whatever reason, the latest kernel build 2.6.29 was not picking up my Ralink wireless network card. I did a little research and found someone else had this same problem but fixed it by rolling back the kernel to 2.6.26-1. I had to get creative with the network cables in the house to get them to stretch, but once connected to the WEB, I found that the commands: apt-get install kernel did not work right away, but somehow I eventually got it to work after running the update manager and installing a couple hundred other packages first.
I rebooted into the new kernel and sure enough, a wireless network option was now present in the network configuration dialog. Then in the course of an hour, I somehow picked up the wireless signal (rather quickly as I recall) and then later lost it and could not retrieve it. Somehow having success initially and then ending up back where you were feels worse then just failing at the outset!
I decided to upgrade to UbuStu 9.04 and I set up the following partition table:
12 GB: /
2 GB: swap
6 GB: /opt
60 GB: /home
Anyway, I was excited to try out my new UbuStu system but after just a few minutes of uptime the screen went black and the system could not be revived! In fact, I had to kill the power-supply to shutdown as the power switch was even unresponsive. This has happened 3 times in a row now and needless to say, I'm somewhat discouraged. Now I face the choice of reinstalling UbuStu 8.04 or otherwise testing out a different "DAW optimized" linux distro. Giving some consideration to the latter, I started doing a little research and found there are a few serious contenders: 64 Studio being one of the top recommended. Another that I came across is called AVLinux which (like 64 Studio) seems to be fairly stripped down and specialized just for audio work. Either way, this approach may be the best if I want to get serious about a DAW. I can use a different OS (probably a Puppy variant) for my more standard workstation.
However, now that I have released ChemPup and accumulated a whopping 41 downloads in just 2 weeks, I was, for some reason, prompted to take a look at a few other puplets which I decided I will continue to do and log my findings here.
First up is PupItUp Music Lab. The idea here is, as indicated by the name, to have the power and flexibility of Puppy Linux running a suite of music software that enables a mid-power computer to become a useful music composition and music education tool. 5 stars for concept, and still 4 stars for execution! The author (eztuxer) made several nice decisions for inclusion in this puplet which features numerous music software packages: AMUC, Audacity, Jack, LMMS, Muse Score, Qsynth, Rezound, and TK Solfege. The full description as well as links to download are available at pupitup.org.
After downloading, I had no trouble in booting up pupitup, however, upon shutdown and generation of a pup_save* file, I found pupitup did not load this save file on reboot! In general, I don't think you usually need to install Puppy Linux to utilize the pup_save* file, however, in this case a frugal install to /pupitup412/ and adding the pup_save* file to the same directory in the end seemed to be the cure. Since I run a fairly old laptop and have an interest in music composition, I was happy to add pupitup to my grub menu!
For now, my wife is very happy to be able to record YOUTUBE music using audacity for the purpose of learning. I briefly took a look at the LMMS sequencer and was impressed with its simplicity and usability. I'm also very interested in testing MUSE since I want to work more on my staff music composition. I will be testing it out a bit more and report here later.
Being in post-secondary school studying chemistry and biochemistry now for about 11 years, I should have developed an analytical mind...and I have, though probably not well enough to solve really tough problems. Despite this, I can appreciate a valuable analytical tool, and after setting up google analytics I was immediately impressed with the level of detail in a variety of metrics analyzed.
Categorically, google analytics is made up of 5 major sections, 3 of which are absolutely impressive: Visitors, Traffic, Content. The other 2 are Dashboard (overview) and Goals.
The Visitor category compiles data regarding visitors' demographic, spoken language, frequency, loyalty, depth of views, duration, bouce rate, what browsers they are using, what OS they are using, what network connections, and a bit more.
The Traffic Sources category lets you know if people are redirected to your site from a link on another site and what that site is, or if they are coming from search engines, or an e-mail client.
The Content category displays which pages are being viewed how often and for how long as well as which pages visitors are leaving the site from (exit page).
To many people, after reading this entry, you are probably thinking "welcome to the 21st century!" as this tool has been around for the better part of a decade now, but nevertheless, this is a new discovery for me!
Uploaded Agora Forum for Joomla! 1.5 but having some problems. Seems that Agora is coded in PHP5 and my server host is configured for PHP4. When trying to post to the forum the following message appears:
Parse error: parse error, unexpected T_STRING, expecting T_OLD_FUNCTION or T_FUNCTION or T_VAR or '}' in /home/content/r/p/k/rpkopreski/html/CHEMTOOLBOX/components/com_agora/helpers/emailprocessor.php on line 5
I had originally a similar error even dealing with syncing to my user list with Agora and found a solution on the agora forum. However, it appears there are going to be a slew of problems associated with forcing Agora to play nice with PHP4 so I called GoDaddy and found I can change my server to run PHP5 by going to:
Hosting Manager --> Content --> Add On Languages
However, this may destroy every damn Joomla! site I am currently hosting. And I'm not sure yet how it will play out so I need to track this carefully. Takes up to 24hrs to propagate on the server so more to come....
Okay, that was fast! So far it looks like the posting problem is instantly fixed! Of course this may have broken something else somewhere, but I will have to wait and see!
-remaster ChemPup-0.2.6 and re-upload (note diffs)
-generate MD5 checksums for ISOs
-trim the fat on ChemPup-1.0.1
-start a proper changelog
-build axs ChemPup kits
-produce multisession DVD
Puppy Remaster Rubric:
1. copy /tmp/root/.mozilla and /tmp/root/.gftp to /tmp/
2. delete /tmp/root
3. copy /root to /tmp/root
4. copy .mozilla and .gftp to /tmp/root
6. delete /tmp/etc/xdg
7. copy /etc/xdg to /tmp/etc/xdg
9. edit puppy***.sfs file to chempup**.sfs file
10. create then rename .iso
ChemPup-0.3.0 is bothersome. I am very excited that I got Avogadro to work!!! However, at a bit of a cost. First the success story. I downloaded a copy of Barry K's UPup which includes the ubuntu-debian repositories in his powerful new package manager. This was accomplished through project "Woof" which is essentially a project aimed at making puppy buildable/extendable with any existing linux repo. Very cool! I used UPup to download Avogadro, analyze it's dependencies and add them as obtainable and install everything automatically. I had to deal with one "lib" problem (I wish I had documented it earlier) and then had Avogadro running in UPup in about an hour. Then I had an idea....prompted from some research at the forums. I saved my UPup session and then renamed the .2fs save-file to the standard pup_save* format so ChemPup (based on Puppy 4.2.1) would read it. I then booted ChemPup-0.2.5 (the devx version) and loaded the new save-file and voila! I had a new version of ChemPup with Avogadro working.
However, after testing several other programs, I found everything worked except one: BKChem. Grrrr. This is not an acceptable trade-off in my view as BKChem is by far the best 2D structure editor I have found for linux. I believe the problem lies in the python libs added with Avogadro, since BKChem runs with python. I spent a couple hours trouble-shooting this but since I am not a trained CS-guy (i.e. self-taught) I have yet to correct the problem. In the mean time I am thinking of offering both versions and explain the deficiencies in each. Essentially, the addition of Avogadro is very beneficial for people that want to do computational chemistry and JChemPaint is still available as a 2D structure editor. However, for those who want to produce higher quality 2D structures for use in documents or publication, the BKChem version is better.
1. Fix the BKChem/Avogadro incompatibility issue
2. Find a silk-screen CD package
3. Find/Buy 3D glasses
4. Work on a multi-session DVD
5. Assemble packages and make sell-able on chemtoolbox.com
6. Make donations page on chemtoolbox.com (remember to show $flow)
Once we made it past boot-up, I found that I had serious desktop icon arrangement problems depending on the size screen I booted on. Now I know why Barry K arranged all the icons to the referenced upper left hand corner so it would remain the same no matter the screen size. I made the adjustment. I also changed the GTK them to "stardust" which offered a "windows-like" icon set. Finally I tweaked the main menu, removed unnecessary programs, added descriptions the the chemistry programs and changed the location of the "home" folder.
Notes on making the puplet:
I had difficulty figuring out how to retain most of the aesthetic settings like desktop wallpaper and icons, and additions made to the menu. I sort of cheated and simply renamed the puppy-fun module to "Chemistry" in /etc/xdg/_root_.jwmrc and /etc/xdg/menus/jwm.menu but I left the rest of the settings pointed to puppy-fun.menu. Then I simply edited puppy-fun.menu to read name "Chemistry" I removed all categories listed and replaced with "Chemistry." Afterwards I needed only generate appropriate .desktop files for each new program added (just like with ubuntu/debian) and I was in business with all my chemistry programs added to the main menu.
During the "puppy remaster" process I then had to make sure to copy /etc/xdg over to the /tmp/etc/ folder at the appropriate time. Likewise, in order to preserve the rest of the desktop configurations, I copied any files I thought would be "config-like" from /root to /tmp/root at the appropriate time. By this procedure, I save all desktop configurations but do not jeopardize any Xorg, keyboard, video, mouse settings for the next user who will likely have a different hardware configuration.
I played around with burning a multi-session DVD or CD and although initially successful, it seems that I only can change the settings once and save to the disk which then closes the session. So now I believe I will offer ChemPup on a CD or a 2GB ext2 flashdrive and encourage CD users to save the personal file and ChemPup.sfs to a flashdrive as well. As such, I took my own 2GB flash drive, dual-partitioned into a 1GB vfat32 and 1GB ext2 to which I installed ChemPup-0.1.5. I selected mbr.bin for the master boot record step since I had done a complete reformat.
I am now working to set up www.chemtoolbox.com to be a mostly functional site that will at least a) not look hideous and b) host the ChemPup-0.1.5 .iso file as well as a few other support documents.
Office Productivity: (Default Puppy Linux)
Abiword - word processor
Gnumeric - spreadsheet
mtPaint - image editing
SeaMonkey - web browser
Periodic Table Wallpaper
Nomen - generates 2D structures from chemical names
WebMolCalc - web utility to calculate formula weight, combustion analysis, and isotopic distribution
BKChem - 2D structure editor
JMol - 3D molecular viewer
ChemPupDoc - documentation on using above programs.
OpenOffice.org-3.0 - full office productivity suite compatible with MS Office
JabRef - reference manager that syncs with OOO3
SeaMonkey - web browser
ChemPup-lite programs +
GElemental - periodic table packed with information on each element
Avogadro (if I can get it working some day)
OpenBabel - chemical file-type converter
SciFinder Scholar (maybe) - must have site.prf file added from school administrator
ChemTool - spreadsheet template with useful chemical equations
MassCalc (need to write) - molecular mass calculator
ChemPup-0.1.2 has been developed from Puppy Linux 4.21 running with 512 MB ram in a VBox machine on Ubuntu-9.04 and so far includes most of the packages I have envisioned in this first generation build. The following is the list of added packages:
Office Productivity Suite:
GElemental - a gtk+ periodic table of the elements with loads of information on each element
MoleCalc - a molecular weight calculator (runs in WINE)
BKChem - a 2D structure editor with .mol and .odt (openoffice) export capabilities
OpenBabel - a command line molecular file-type converter that handles over a dozen formats
WinDNMR - a dynamic NMR simulator (runs in WINE)
A suitable 3D molecular viewer (I want Avogadro which includes a force-field minimizer)
Plan to Make:
A slick spreadsheet template (OOCalc) that has useful conversions (mole to gram etc) and equations
Detailed documentation to maximize usage of the system (since most US Students don't know Linux)
Additionally I need to figure out what programs I should cut out to save space, if any, considering OOO is adding most of the extra weight. I will probably remove devx.sfs.
Building in the existing packages (listed above) was fairly straightforward....I needed to install Python, WINE (which I found as a .pet on the Puppy Forum) and a few other package dependencies that I cannot recall.
Update: In order to run BKChem it needs python 2.3 or later and after checking with > python --version <> ./configure; make; make install. Unfortunately these programs must be installed before python so I had to reconfigure python and went ahead and downloaded the upgraded 2.6. Python is a bit large so I removed the old version...2.6 also took several minutues (10 ish) to compile and install. Afterwards bkchem.py runs from command line with > python bkchem.py < in the working directory. I then easily created a bash script to start the program, made it executable with chmod 777 and added it to the desktop with a logo icon to make a simple point and click execution.
The real trouble has been with Avogadro. This is a nice, intuitive 3D molecular viewer and force-field minimizer program that I test-ran on Ubuntu and was quite happy with, however, unlike with Ubuntu, I do not have a prepackaged .deb (.pet) for Puppy and will have to build it from source. Avogadro has several package dependencies, some of which I am having trouble with building as well: Qt4, Eigen2, CMake, and OpenBabel are all required before you can compile and install Avogadro. I installed OpenBabel and CMake okay (I think), and Eigen2 supposedly only need to be unzipped and it is ready to go (although they don't say to which directory it belongs so I stuck it in /usr/local/bin). Qt4 on the other hand has proven very difficult and I also found that I had the wrong version of CMake!! These programs (OpenBabel, Qt4, and even CMake) took a long 20-30 minutes of compiling time each. So long as I can get a user-friendly 3D molecular viewer I will be satisfied with this first release.
At a family get-together, I was recently asked by a war veteran who saw me tinkering with my hp pavilion laptop whether or not I knew "how to fix them things?" I asked what his problem was and he noted the last time he tried to boot his laptop it wouldn't start. His was also an hp pavilion. I told him to drop it off and I would see what I could do.
Upon initial investigation I found that the laptop would POST and the XP logo appeared as the OS began start-up, but then it suddenly would reboot...just as he indicated. So I decided to boot up Puppy Linux and see if I could access his hdd. I found I needed to boot with puppy pfix=ram (or something like that) since the Puppy startup script would hang when searching for the pup_save.sfs file. This was the first indication of a problem with the hdd. Once booted, I clicked the sda1 icon at the bottom left of the desktop and found (after futzing things up and a few reboots due to impatience) after about 120 seconds an error box indicates a problem with the drive and then after (no exaggeration) 20 minutes the ROX window finally opened and displayed the contents of the drive. After this initial wait, it took a mere 2 to 5 minutes for subsequent directories to open. It seemed as if the drive was spinning at only 10x or so.
Only 3 or 4 hours later (yes I was working on other stuff also) I had transferred the files that the owner cared to save to my external hd and started the reformatting and installation of my copy of XP. An hour after that I had XP installed and later at home I finished up with transferring his important data back. Success!
I wanted to give crunchbang another chance and so far I'm really happy I did. What is it? It's a non-official Ubuntu distro that uses the openbox desktop manager and gtk+ apps. The install did not natively support my broadcom wireless adapter, but after connecting via eth0 wired and editing my sources list according to the list of Salimane Moustapha, I used the "restricted device manager" to identify and install the appropriate driver and crunchbang I was online with wireless! Then I spent time making several of the suggested updates and installs on Salimanes extremely helpful ubuntu blog and since then I've just been exploring what this distro has to offer. In general, it is a clean, dark-themed desktop which I like. But most important is it is actually quite fast (really rivaling Puppy so far) and comes with all the support of the ubuntu community.
Crunchbang comes stock with loads of well-chosen lightweight apps that provide a very full-featured system. Internet tools include: firefox, liferea feed reader, pidgin IM client, gpodder Podcast catcher, transmission bittorrent client, gftp client, skype, gwibber microblog client. Audio/Video tools: VLC player, rhythmbox, audacity, kino vid editor, and more. Other apps include abiword, gnumeric spreadsheet, gimp, inkscape, xfburn CD/DVD creator.
I went ahead and added a frugal install of Puppy 4.2.1 to my /home partition of crunchbang. I set it back up the way I wanted it with xmms player and I finally figured out how to get the openoffice.org .sfs file to work. I know I will keep working with puppy, but crunchbang is nipping at its heels at this point....
Here's a list of links I'm compiling for my Digital Audio Workstation set-up:
Reviews for Linux Music Produciton
Linux MIDI Software Collections
Ardour on ubuntu
Configure Rosegarden MIDI
Ex-Research Chemist School Teacher Linux Musician:
OpenOffice for puppy is distributed as a .sfs "squashfile." I found a list of available versions at this Doku Puppy site. It seems that the easiest implementation is to place the .sfs in the appropriate /mnt directory and on reboot OpenOffice will run. However this is only true for a frugal install as noted here. I spent some time trying to figure this out, and then more time to determine what to do if you have a full install? I finally got a great tip from an IRC puppy channel member on xchat who gave me this link to using a .sfs with a full install.
So I'm still waiting for the .sfs to download and then to see how it all goes.
Note the inquiry began with this thread
I have tried PCLinuxOS in the past and found it quite user-friendly so I thought I would give it a go with one of it's derivatives: Phoenix (PCLOS Xfce).
Pros: Live CD works well and allowed me to test critical aspects such as wireless detection, available packages, etc. Wireless card was easily configured with a BCM ndiswrapper.
Cons: Still a bit too slow, a little faster after the installation. Very barebones on applications. Grub graphical menu only highlights the top entry by default, so on reboot I thought I would need to reinstall Grub to access my Puppy and Windows partitions...they were just hidden.
How is it PCLOS2009.1 can fit on a single CD and include many more office productivity packages, KDE, more multimedia packages, etc. Why can't this be more full-featured and use a faster window manager? I spent some time trying to get openoffice 3 to work and almost got there. I get the startup window when calling soffice from the command line, but none of the individual applications are launching, maybe they need to be installed individually.
"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."
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.
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:
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:
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.'
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.
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.
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!
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?
Since converting to linux (Ubuntu 9.04) at school, I have slowly been reconfiguring my chemical toolbox. I am using SciFinder Scholar (site licence from the university) through WINE and BKChem and xdrawchem for 2D structure creation. I still need a 3D molecular viewer and builder that would replace gaussview for windows. This has been a bit troublsome so far. The first challenge is simply to "test-drive" different programs available. After reading about some of the features of a few possible programs, I settled on taking a ride in MacMolPlt 7.1. However, just to get in the driver seat, I found myself sucked down a "rabbit hole" of dependencies. MacMolPlt relies on wxWidgets which depends on the GTK+ 2.0 development package which in turn depends on several libraries: ATK, TIFF, glib, pango, and cairo...all of which I apparently did not have installed. But like Alice, I was too enticed by the prospect before me and down I went.
Building from source so far seems a bit like making a birthday cake. Since I lack the skills of both a computer scientist and a master chef, in both cases I am having to make due with getting my ingredients "from a box." What Betty has done for millions of domestics, the Synaptic package manager does for me. Most times I try to follow the INSTALL instructions and read the README and usually my configure step will fail. I found all the libraries that I couldn't build from scratch using Synaptic and once installed, my configure step for wxWidgets passed. Still this took a couple hours with lots of trial and error. I later found wxWidgets for GTK in Synaptic also.
In the end, I fulfilled all the dependencies for MacMolPlt but still got a strange error in the 'make' step.
The real surprise came when I went back to work and as applications were being reloaded, all the text displayed in GNOME was turning to empty boxes!! After panicking a little, I tried to use the 'recovery' boot option and that didn't help. After rebooting I decided to try to use my web-browser alone to back-up my files. Fortunately I have GoDaddy server space and I was able to upload my Dissertation folder. I couldn't back it up any other way as even the terminal window was broken. I had older backups on a thumb drive and my other partition, but I would have lost a little more than a day of work....too much. When I reinstalled Ubuntu 9.04 (now more experienced) I made unique partitions for /root, /usr, /opt, and /home so I won't have to worry about losing my files or programs if I "break" my installation. I am now reinstalling all my software: Opera, BKChem, xdrawchem, Tinker, JabRef, WINE, SciFinder, Filezilla, etc and downloading my Dissertation folder from my server. Only lost about 3 hours....
As always, lessons learned.
Ridiculous! I never actively use my facebook account any more... and I have my reasons... regardless, I wanted to let people know that I'm moving on, past the "social networking" (which used to be something you did with people at a dinner party or on their porch with a beer and some crisps) websites, and I couldn't even accomplish this. Apparently facebook is so corrupt that you need to decrypt some obscure esoteric text and enter it into a box just to post something. Or alternatively listen to some garbled message and enter that instead. Furthermore, there are so many freakin widgets, photos, and crap that you need a speedy proc and connection to get it to move. The next paragraph was intended for my facebook cohorts...but alas, I gave up on posting it. I would send an email blast but I think that would be too pretentious. I doubt I'll be missed as I was never active in poking anyone anyway. Here's the message I intended to post:
I'm leaving facebook. Social networking sites are not for me. I stay connected to people I see face-to-face. Keeping touch long distance is easy with e-mail. Facebook is just too frivalous with all its "ice-breaker" gimicks, poking, time-wasters, etc. I enjoy annonymity and don't really want to know as much about others as they are often willing to share. I would appreciate if people asked permission before posting my image online or images of my family. I will, however, be hippocritically keeping my introvertedness public by blogging on topics that interest me. I will be deleting this (facebook) profile on July 4, 2009 to celebrate my independence. You may find what I'm thinking about/working on at my new blog:
Of course you can email me as well...
Farewell Facebook, MySpace, Twitter, ...
So there it is. I also tried to delete an old MySpace profile of the same name as this blog and failed. I guess I'm not as computer savvy as I had thought...or is this just "the man bringing me down?" For real 'Networking' I am still entertaining the continued casual use of LinkedIn...until it becomes useless as well.
I have noted previously that I am a Ph.D. student writing his dissertation. Recently I've been having some saving problems in MS Word and I've lost a couple paragraphs of writing twice. I have reconfigured my school desktop to dual-boot xp and ubuntu (jaunty) and I started to determine if I could accomplish writing my dissertation within linux. I already have about 40 pages of what should be around ~150 page document including over a dozen figures, schemes and tables. One of the likely culprits is Endnote, a powerful bibliography database manager which seamlessly manages your MS Office Word citations in any format you need. However, it may be inturrupting Word in some ways and causing it to flake out on me on save. And yet it is too useful to discard so I wondered if their was an alternative for Sun's OO-Writer.
There is and it is called JabRef. So far, JabRef seems just as useful as Endnote only perhaps not quite as powerful. It doesn't imbed a widget toolbar in Writer and if you delete a citation from your text it doesn't seem to omit it from the references section. (Although I still need to spend more time learning its capabilities.) [Update: JabRef works great. I imported my endnote database with ease, although I had to do some manual edits. Also, there is a "sync" button in the plugin that deals with any edits you make. The only downside (documented on Alver's site) is that you must only use the style-file downloaded directly from the web. You can edit it at will but I wouldn't even try to rename it or copy it in anyway or you are "stuck like chuck"] It can import from Endnote, SciFinder and numerous other databases with various formats. To get it to integrate with Writer a plugin (written by Morten Alver) must be added. Alver's site (see below or click here) details installation and includes a needed 'style-file' which tell JabRef how to format your citations.
When I installed JabRef from Synaptic, I found it was not the most up-to-date version. When I installed the .tar.bz2 from the JabRef site, it did not make available an icon in the menu which is a nice feature for commonly used programs (I don't mind command line, but I just like the clean feel of a menu icon to start-up). Although I had no idea how to fix this I found enough information in this ubuntu forum thread to get the job done. Very Nice!
In addition to JabRef, I will need a 2D chemical structure editor to generate structures for my figures and schemes. I love CambridgeSoft's ChemDraw and have used it freely (at school) for years. At home I had a copy of Isis Draw which was a free windows tool. In linux I am not fully satisfied here. I haven't found a single editor of nearly the capabilities as these programs. However, I did find a well written review on several available programs which can be found here. Possibly by using a few of these you can have the power of chemdraw. So far BKChem is the favorite by a small margin. Fortunately I mostly work with flat polycyclic hydrocarbons so I think BKChem will work for me.
In summary: Although it requires a little more work to install and configure and lacks marginally in functionality, at least for now, there appears to be a viable alternative for serious chemical thesis writing. I will probably make the effort to convert.
For an extensive list in chemical software written for linux see this link:
When I was in High School, I took a music theory class with Bruce McCormick. He was an inspiration to every single student that had an appreciation of music and one of the hardest working teachers I've ever had the pleasure of knowing. This class spurred me to compose a 111 measure 5-part piece for voice...but with no lyrics. I spent many hours at a macintosh computer using software called Nightingale and entering notes with an attached MIDI keyboard. Upon completion, I assembled a group of vocalists to perform the piece at the annual spring concert my senior year. It was a significant highlight and achievement in my life. There was a poor quality video recording of the event but I do not posses a copy and I never made a synth recording or even saved an electronic record of the piece (not that I would be able to find a computer that could access it today since I believe Nightingale is no longer in use anywhere). For a decade now I have retained a single hard copy of the music and I am frankly amazed that it has survived the 5 times I have moved in 10 years. Regardless, I've always wanted to reproduce the electronic copy so that I could at last hear the piece again. Finally with my UbStu Linux distro I have that opportunity!
Of all the various sequencers and recorders and notation editors I have come across so far, I'm most impressed with the completeness of Rosegarden. This software is incredible especially considering it is free! I have vowed to contribute to the authors as soon as I make some significant advancement in utilizing it to its greater potential...and as soon as I graduate and get a job.
Rosegarden runs on top of the Jack Audio Connection Kit (JACK) which is still a bit mysterious to me. The learning curve on Rosegarden has also been somewhat steep and I've spent close to 3 hours just in combing though the manual and Michael McIntyre's very useful on-line tutorial. I'm nearly half way through inputting my 'masterpiece' (I've yet to give it an appropriate name but had originally named it "Fortune Cookie") using the notation editor and so far I've figured out how to assign each track a synth sound from pre-existing libraries so I need only my computer's sound-card (Sound Blaster Audigy).
At this point I've spent a couple-few hours trying to figure out how to record my piece without success. I would like to be able to just use my computer's sound-card without any additional external components/keyboards/etc. It seems from the tutorial that this should be possible but it is not carefully described here so I will need to start search for information elsewhere very soon.
I've had interest in setting up a digital audio workstation (DAW) for about a year. A friend in grad-school turned me on to Reaper just a short while back. I have no experience here so the task has been formidable. I spent some time reading about sequencers, piano-roll, VSTs, etc., installed Reaper and played with it some. Meanwhile, I've also had an interest in "getting into a Tux."
A few years ago I fell into the world of computational chemistry and found myself at the helm of a "black-box" 4-node dual core cluster running SuSE. I didn't even know what a shell was. So I learned a bunch the hard way...the fun way by digging ditches and trying to get out. Around the same time, I needed a new desktop at home. I've always been given computers by my parents (specifically Dad who works with them a lot) and they were usually modest components, and ran the latest MS windows OS. Left to my own devices, I still needed to be thrifty so I bought a 2.66GHz Intel Celeron motherboard in a box pre-loaded with 1GB DDR. I initially dragged over my old hard-drive (Maxtor 12GB), and my father-in-law gave me a Seagate 7200rpm 120GB HD on which I loaded a copy of XP Pro that I borrowed from one of the non-networked instrument computers at school. I also installed my older CD-RW drive and a lousy CD-ROM drive. We were in the age of 2GB flashdrives so I didn't bother with a floppy drive. I recently upgraded to 2GB DDR RAM.
I recently acquired an old Creative Labs Sound Blaster Audigy Platinum (break-out box included) from my mother-in-law and decided this would be a great jump-off point for setting up my Linux DAW. I started by reading up on OSs and generated my first .iso image CD of an OS called PCLinuxOS2009. I don't remember how I heard about it, but when I loaded it up on a test-machine I was amazed at how easily it installed and how efficiently the package manager updated. I thought to myself "why have I never tried linux before?" I played with this OS for about a week and still like it a lot. However, as I started loading software to set-up my DAW, I started learning about a studio version of Ubuntu that had nice reviews. It came preloaded with all the DAW goodies and had a low-latency kernel built in. It also runs a "real-time" kernel which I think means it gives proccessing and memory priority to real-time processes. So I decided I wanted a "tri-boot" system. I started playing the partition game
I added a Western Digital 7200rpm 80GB HD to my rig and installed PCLinuxOS2009. I had a dual boot system. Success.
Prior to this some oddities had recently occured where MS Office files were no longer writable and other strangeness that I never documented so just a few days ago (concurrent with my upgrade to a dual-boot) I planned a reinstall of XP Pro. That's when shit hit the fan. I won't get into it all (as I don't remember it all) but I was unable to get a working installation of XP Pro from the disk I had used for the original set-up. Fortunately, I had obtained a copy of XP Pro Black edition from my French Pirate friend/colleague and after a few tries to reformat, I had an XP back up and running and all the important files saved.
At the same time I was working to get my XP, Ubuntu Studio, PCLinuxOS "tri-boot" system up (the three stooges), but due to my newbie-ness (I will try not to ever use noob), I haven't yet gotten there. Instead I have Windows XP Pro Black Edition (XPBlack) installed on my SG 120GB HD and Ubuntu Studio 8.04 (Hardy) installed on my WD 80GB HD. Despite my success with configuring PCLinuxOS to drive the soundblaster, I decided to stick with this dual-boot for now and see what I could accomplish.
I then proceeded to get my sound blaster working for XPBlack by downloading the driver at support.creative.com. With PCLinuxOS the package manager set me up with the latest ALSA package (driver,lib,utils) and running alsaconf as root took care of the rest. Long story shortened, with Hardy, I went in circles before realizing that I needed to fully grasp the alsamixer utility instead of hunting for bug-fixes.
Now I have PCM sound from speakers and head-phones for both OSs.
1. I get audio CD playback from head-phone jack on break-out box only...no speaker sound yet
2. The system is not utilizing any of the 3GB of swap space allocated and even browser scrolling causes audio to skip.
3. Time to learn recording software (not really a problem)
Note: I have no idea if I will have enough resources available to accomplish midi sequencing with multiple virtual instruments given the current observation of swap-space and overall speeds.
The goal of this blog is mainly to keep myself on track with my life goals. Included in these are various projects which I will document here. May it also serve to provide some form of expression and the freedom to rant and rave as I see fit.
At the time of this writing, I am 28 years old, married to a lovely, caring, intelligent, passionate, driven woman named Elia who has given me 3 boys, the eldest Lucas (22 mos.) and the twins Ethan and Gavin.
I am currently in a state of slippage, redirection, and melancholly, quite possibly losing my mind, or at least changing it frequently. I am writing my Ph.D. dissertation on my work in physical organic chemistry. Although I have no working title, it's contents will enlighten the reader on the subject of polycyclic aromatic hydrocarbons (PAHs), specifically my work on the synthesis of a [4.4.4]Starphene as well as DFT calculations of large substituted acenes and a correlation of their HOMO-LUMO energy gap with their apparent photo-oxidative resistance (air-stability).
I used to be a musician; unafraid of expression, writing frequently, practicing often. I would like to restart the process: write, practice, record, learn.
I have a bit of a fancy for beer. I know, a bit 'cliche' whilst still in graduate school but I assure you I never completely went "off the deep end" by growing a full beard, touring breweries whenever possible just for free samples and turning my nose up at the award winning Pabst Blue Ribbon (their mommy put the blue ribbon ON THE CAN!)....okay I did that. Still, I have been lucky enough to acquire some great materials for homebrewing and better still, found some people who've shared my interest along the way. Again, I would love to "relax, have a homebrew" very soon. Did I mention the twins were born 3 months ago?
I used to ride a motorcycle. I've had my license since I was 18 and rode every year. My Dad pulled my first bike out of the dump, made it run (and pass inspection), slapped me on the back and said "don't kill yourself." It was a 1971 125 cc Honda Rebel and frankly I'm surprised I lived to tell about it. I remember cruising down the highway (litteraly down-hill) topping out at 80 mph just to push it (sorry Mom) and it was rattling so hard I thought the handlebars might come loose. I slowly upgraded from there: 1979 450cc Kawasaki rebuild; 1985 500cc Honda Magna V30; 2002 750cc Honda Shadow VT750. Last July my father-in-law lost his life on his Kawasaki. It's almost June this year and I've just registered mine and got it out of storage, it needs a chain and sprockets, I'm not sure if it will get them. I've got a lot of babies to look after.
So summer is here, I'm plugging away at my dissertation, looking for a job (hopefully a well-suited post-doc) and trying to find projects that will help maintain my sanity. I've been thinking for a while about trying a linux os at home and using it as a digital audio workstation. Why? Well it's a two-fer. I'll get to bang my head against the wall learning something that's not chemistry for a change. Linux is hard enough to get started in but I really want to compound it with the world of DAWs, sequencers, digital effects, samples, synths, VST plugins, etc. I sang bass in a college chamber choire. I played sax in the pep-band and guitar in the jazz band in high-school. I've been writing "singer-songwriter" crap for about 15 years (although a bit dried up for the past 5). I don't know much about any of that, but I don't know anything about digital composition and recording. Thus, this is the start of my blog.