synergenerator

Twitterpated with Tweetdeck

2010-10-25T08:46:00.003-04:00

As I have recently acquired my third diploma, I am currently in the market for a career...sort of. I know this friend of the family who happens to have substantial experience in "human resources," who has enlightened me regarding corporate recruiting in 2010. According to her wisdom, corporate recruiting is accomplished 95% through online social networks such as twitter, linkedin, and of course the mighty facebook. There are often new jobs that have not been advertised, instead they are filled through active corporate recruiting. As a result, it is imperative that today's professional, entry-level or otherwise generate a personal "brand" that is polished, accurate and consistent over multiple web-points. Therefore, despite my distaste for social media and how it is routinely utilized for false advertising, "bait-and-switch" tactics, hurtful defamation of character, rumor propagation or as a sounding-board for idiots; despite this, I must embrace it, harness its power and conquer it!

Hoopla aside, I was directed to the following article (click) which has sufficiently motivated me to push my linkedin account to 100%, make my fb profile a little more professional (i.e. remove the suspicious gas-mask) and actually start tweeting, or microblogging or updating my status or what-have-you. But, woe-is-me who has very little interest in this to begin with to have to update all these social-media sites so regularly. Can't I just have a single program where I can follow the updates and when I make an update it will syndicate it to all the social media sites I subscribe to? Well I went searching and settled on the first thing I found (a lot like how I ended up with my wife) ping.fm which is a website that accomplishes this syndication very easily. However, thanks to publicizing my interest in this syndication business, I was turned on to Tweetdeck, which is a superior tool for posting and managing multiple features to all these subscription sites. I also am really impressed that they are completely cross-platform (Michaelsoft Binbows, Macintosh Apples, and Linux) and I have it installed on my Kubuntu box at home, my wife's ubuntu netbook remix (though there I had to separately install Adobe AIR first) and my "business machine" running 7. Anyway, check out tweetdeck at tweetdeck.com

Rockbox for Sandisk Sansa e280 v2

2010-10-22T17:20:00.003-04:00

About 2 years ago a colleague at UNH told me about this free full featured firmware (oooh alliteration) for mp3 players called Rockbox (http://www.rockbox.org/). It has loads of themes that can be explored, simple playlist manager, and intuitive interface. For the Sansa e280 it also retains the FM radio functionality. Furthermore, it doesn't overwrite the mp3 player's existing firmware but is sort of a dual-boot. The problem for me was that the developers of Rockbox had not ported it to the Sansa e280 v2 at that time, only v1. Since then, I have checked in on the project every few months and after only a couple years wait, I finally got the opportunity to try it out (I guess at least grad-school taught me patience). The only quirk I have noticed is that the "back" button must be depressed when connecting the device to the computer by USB in order for it to mount on my Kubuntu box.

pour l'amour de la musique

2010-07-05T12:21:00.002-04:00

My newest obsession has to be Ampache. Shortly after I upgraded my hosting plan to "unlimited" I decided to use the storage to back-up my digital life (in case of fire/flood/toddler toilette experiments/etc). Since then, I have uploaded approx. 40 GB of media, most of which is home videos and music. I must admit I don't have a very impressive music library compared to many-a-cohort. Still, I always wondered if I could easily manage this lot with a web utility so I didn't always have to carry my external hard-drive around or copy my library whenever I get a new computer. I also like the idea of having it centralized since I'm not too good at keeping up on redundancy with media coming into possession using one of two laptops, home and work desktops, friends, and so on.

Introducing Ampache. Ampache has a lot of functionality that I am not able to exploit, designed for a server that you have total control over, which is not the case with my shared hosting service. However, I have successfully uploaded the PHP based installer, created a database, and configured it...and I'm not that smart so it has to be easy! The only problem that I haven't yet solved is increasing the maximum time my server will allow an Ampache PHP script to run. The default is set to 30 s, which is really not enough to catalog my entire library. My current work-around is to break the library up into many catalogs.

Nevertheless, I am happy with the user interface which allows me to either download a playlist .m3u file which then lets a media player (I use VLC) to stream from the web-server, or there is also a local flashplayer (xspf). I would prefer to use the xspf player since it is one click playback and has a nice interface which displays album art, however, lots of my music is in .ogg format which won't play. So I'm working on converting to .mp3s.

Independence...Really?

2010-07-05T11:46:00.004-04:00

It has been some time since I have posted, and I have the day off today, the missus is out to brunch, the twins in a nap, and their big bro chillin with dad, some goldfish snacks and peanut butter sammies. An unlikely coincidence that allows for some writing. I guess I should get it done!

First, I should mention that I was not looking forward to the local yahoos setting off their shitty fireworks at odd intervals all night long in my "quiet" town. I don't mind fireworks, I just think they should be controlled by local fire stations and light-able by authorized individuals. I decided, however, that "you can't beat 'em...so join 'em." Although I think I would prefer to exercise my patriotism at a time of day more amenable to my schedule, like when the kids wake up at 6am. Perhaps next year I will set up my 2 2x12"/2x8" monster purple cabs powered by my 800 Watt junky Crate mixer outside and rip out some a shitty version of "America the Beautiful" (I should think it's easy with YouTube to find a rendition by an 8 yo girl at her first recital!) followed by a Sousa March (you know the one, the really patriotic one) at 6am to kick of the 4th with a real bang! Better still will be the reprise on the 5th. I can't think of a better cure for a hangover.

That being said, I actually had no problem listening to this racket at 10pm this year since the kids easily drowned it out during our routine bedtime ritual. Maybe the extra helping of cake and blueberry pie at my friends pig roast played a role. By the way, I would not recommend bringing 3 kids under 3 to a friends pig roast unless you are hell-bent on being a spectacular circus side-show for all the other guests. I think I managed to say "hi" to like 3 people out of 30, not that I knew many of them. Let's just say watching two adults chasing around midget tyrants who are busy swinging croquet rackets, screeching, falling, stomping on flower beds, etc. is the closest my friends have been to the Ringling Bros.

Additional updates:

- I somehow inadvertently rejoined Facebook - I really don't know how to use the internet. My wife is convinced that my profile picture is damaging to my career.

- I celebrated the anniversary of this blog quietly as I was driving in to work on the 30th of May. That was a while ago, but I thought it deserves mention regardless

- I am looking into a Postdoctoral Fellowship at Texas A&M. Very few members of my family have been initially supportive, but they should come around.

- I am brewing all-grain (details here)

- I have discovered a great web-tool to enable me to play my music library from the web (see later post)

Home Studio Upgrade - mobile workstation

2010-06-12T13:56:00.004-04:00

I recently made 2 purchases to allow a more flexible, complete, mobile solution to my DAW. I now have the ability to take my studio on the road and use my Sony Vaio.

First I have added a simple E-MU XMIDI 1x1 USB interface ($25) so I can use my midi keyboard with a USB port.

Secondly, I needed a USB audio interface / preamp. After some research I found an excellent solution that offers a substantial "bang-for-your-buck" using an ART USB Dual Pre ($80) which does not require any drivers. When you plug it in you will find "USB audio codec" added to your sound I/O hardware options. However, you don't have to select this for your system if you run most of your studio software on top of JACK. Instead, just change the input and output preferences in the JACK setup and you are good to go!

I also found software designed to be a guitar effects simulator called Rackarrack which also has an on-board tuner and can route your guitar notes to midi events. Although it has limited sensitivity, this may be a good way to score midi data for someone (like me) who plays guitar/bass better than keyboard.

bash scripting

2010-06-01T12:15:00.002-04:00

I wanted to put together a simple bash script that would take a wildcard argument from the command-line and send the output to a text file (g03data.sh *.log > output.txt)

I needed to add the following (found here) to the top of my existing script:

if [ -z "$1" ] then     echo $0: usage: $0 filename     exit 1 fi

while [ ! -z "$1" ] do     # do stuff to $1     shift done
exit 0

MSWord Reference Range

2010-05-20T13:30:00.003-04:00

I had some trouble figuring out how to use MS Words simple footnote/endnote reference tool with regard to adding a range of references. I found help here: http://word.tips.net

In summary, I found it relatively easy to create the macro (below) and then I could highlight the numbers in the middle of the range and format them to be hidden with a hyphen in their place.

Macro:

Sub RefListToRange()

Selection.Font.Hidden = True

Selection.Collapse (wdCollapseEnd)

Selection.TypeText Text:="–"

End Sub

Ubuntu 10.04 media trouble

2010-05-13T21:13:00.002-04:00

Random (20 min to 1 hour of play) video errors:

vlc loses audio and movie player loses audio and video stream.

error from movie player: pa_stream_writable_size() failed: Connection terminated

Refurbing a Toshiba A45-S150

2010-05-10T16:40:00.003-04:00

My friend asked me to fix his laptop as it seemed to have a virus on it. Well after a boot I found not only virus trouble, but lots of out-dated, useless software (mostly AOL crap that I know is painful to get rid of). He said I could do whatever was needed, so I decided the easiest path would be to reformat with Puppy using gparted and then perform a reinstallation. I decided to partition the HD to allow installation of XP (ntfs) and linux (ext3) so after doing this with gparted, I proceeded to install an old copy of XP I obtained. It had a license key with it that was supposed to work :) but alas I have had to find a workaround.

A bigger problem with this job was losing all the toshiba drivers including those that run the network adapter. I spent a few minutes searching and finally came across this forum thread:

http://laptopforums.toshiba.com/

Which pointed me here:

http://www.csd.toshiba.com/

This was critical as I was S.O.L. with most of the hardware on this machine without these!

So now I just need to get any other drivers deemed useful, deal with the activation, SP2 and SP3 upgrades, WGA issues and all that jazz. (yes windoze is a pain).

After the couple hours needed for all that, I'll take 30 min. to do a Ubuntu 10.04 LTS (lucid lynx) install just in case the other system goes to shit!

p.s. I figd out activation (FFX Madman), however it may have interfered with installation of MSOffice 2007.

Soft Studio Solved?

2010-05-05T13:10:00.003-04:00

Whilst the misses was away (Vegas Wedding - 4 days) I made it a goal to upgrade my system: 1. Upgrade to Ubuntu 10.04 LTS on new HD 2. Reconfigure my software studio. I had just purchased a WD Caviar Blue 160 GB HD (ultra quiet!) and installed Ubuntu 9.10. Eventually I will get smart and make a remaster of my system so I don't have to reconfigure everything when doing something like this, but it is rare that I have to move to a new HD. Still, I had to start rebuilding my software suite. I can manage this to 95% completion in about 2 hours which I banged out early one morning.

I accomplished a network upgrade to 10.04 (lucid) in about an hour, however I had to troubleshoot a few bugs, two of which were related. The login screen lagged a very long time and my USB drive would not automount on boot like it used to. Searching the web, I found a fix and after deactivating the floppy drive (I don't even have one) in the BIOS settings this was corrected.

After installing my standard (and more) suite of software, I made my "Studio" menu and fired up JACK, Qsynth, and Qtractor to test things out. Unfortunately, I was unable to record midi from my keyboard! After racking my brain a bit, I decided to uninstall Qtractor and build it from source. Although this is always a non-trivial task (although getting easier), it fixed the problem. I also installed LinuxSampler, and the front-end GUIs Qsampler, and Jsampler (see earlier post 3.10) from the CVS repos.

I had hoped that the LinuxSampler engine would eventually be my "go-to" for running multiple samples on different channels simultaneously. However, I cannot figure out why the GIG files (or any samples for that matter) sound lousy, bad, terrible, fuzzy, etc (keywords!). Really annoyed after having built Gigedit, LinuxSampler, and Qsampler from source. I decided to play with Qsynth (.sf2 soundfont sample handler GUI for FluidSynth).

After some digging and tinkering I believe I have a solution. Use Qsynth with Qtractor and Hydrogen (on top of JACK of course) to build all my MIDI files in real-time with a MIDI keyboard and then record into Ardour. The breakthrough was figuring out how to play multiple samples (.sf2) from Qsynth simultaneously. Here is how:

Qsynth loads audio "engines" and you can set up several at once. However, you only need one!
In setup I select alsa_seq as the midi driver, and jack as the audio driver. Then under "Soundfonts" tab select each of the soundfonts (.sf2) files you want to have available for your Qtractor piece. Then edit each entries "offset" so they are different (0, 1, 2, etc). This sets the "stack" with different banks. Save and leave "setup." Then select "Channels" from the main Qsynth interface. Right-click the channel of interest and select "edit." Then you can select different "banks" and assign different soundfont samples to different channels! Now give your neglected 2 year-old a high five!

Sony Vaio MotionEye Drivers

2010-05-01T16:03:00.004-04:00

Somehow I managed to get the "motioneye" webcam working in windows 7 pro. I originally recieved this laptop with Vista installed and upon upgrading the webcam was not working. Basically I installed all the updates and then went to Sony's "esupport" page and searched for the model printed on the bottom (PCG-5K1L) which returned a different list of models. I chose the one with "EN" at the end and then installed the "Cam" driver for Vista (but I'm running 7? Right!) and it worked after that.

Now I am curious if I can make the webcam run in Ubuntu Linux (while I'm waiting around for a network upgrade to 10.04 LTS). I ran lsusb and found the driver info:

Ricoh Co., Ltd Visual Communication Camera VGP-VCC6 [R5U870]

Now I think I may be able to get some headway according to this site:

http://www.arakhne.org/ricoh/

back for an update...

Update:

Installation of 10.04 took ~2 hours over a wireless connection (a bit slow, but I had other things to do anyway). It will take some time to see what kinds of advantages, upgrades, etc it really adds, but I expect to be fully satisfied.

After that I installed the following files from the above URL.:

ricoh-webcam-r5u870_0.11.4-0arakhne1_i386.deb
ricoh-webcam-r5u870-firmware_0.11.4-0arakhne1_i386.deb

Then I tried "cheese webcam booth" software and verified the motioneye webcam works!

VT-NMR Simulation Calculator

2010-04-26T13:10:00.013-04:00

Enter Temperature (T) in Kelvin and the rate-constant (k) from the simulation (see H. Reich's WinDNMR).

Contstants: Gas (R), Boltzmann (kb) & Planck's (h) constants.

Your browser does not support iframes.
Visit Encalc Online Scientific Calculator for the full calculator.

Download Buttons and Better xspf player

2010-04-09T10:35:00.005-04:00

I wanted to know how can I have a "cyber-button" that upon clicking will get your browser to start a download from my server. Here were some useful answers to start:

How to Create an HTML Download Link

Self Extracting Zip File (1) (2)

I also found a website that used a xspf player that included a "shuffle" feature. I thought this was neat and had to have it! I found one with instructions here and here, extracted and uploaded the .fla, .as, and .swf files and presto-blamo it worked.

Don't Call Me Doctor...

2010-04-07T23:41:00.004-04:00

Not because I failed. I passed, I just don't yet feel comfortable with the way it sounds. My dissertation defense took place at 2 pm on April 6, 2010. I presented 46 slides which took 45-50 minutes after which I took 4 or 5 questions from the general audience. Following a 5 min. break I entered a private session with my 5 faculty committee members which was a "round-robin" Q&A lasting 2 hours. I botched a few answers, but in the end the committee was satisfied.

Regarding my presentation, I ended up exporting my OOO3 Impress presentation to a PDF and running a slide show with evince! Very fast, hardy solution. Of course I was not able to run my x-ray crystal videos embedded or from a macro. But I had them both queued up in totem and running in the background during the presentation so I could easily pull them up without losing momentum.

So now I just have about a weeks worth of corrections to make to my dissertation and I will submit the final version to the graduate school. I plan to attend a hooding ceremony at commencement on May 22.

PhD Defense Presentation

2010-03-31T17:30:00.003-04:00

I would like to expand some on this later (after the defense) with reflections etc.

Now I just need to get down the procedure I used to make a quality MPEG of a rotating crystal-packed molecule that I can call from OOO Impress.

To make an MPEG from PyMOL I first needed to install the FreeMol addon pack:

1. Download FreeMol "trunk" tarball from svn repo here.

2. Follow install tips from here.

I moved the FreeMol "trunk" directory to /opt/trunk/ and then cd into each package within /opt/trunk/src. Then I ran < ./cofigure ; make ; sudo make install ; make clean > within each package directory. I had to install the GNU fortran compiler (from synaptic package manager) for one to work.

After you "save as" your MPEG movie you can call it from OOO Impress using a macro command.

1. In OOO Imress go to -> Tools -> Macros -> Organize Macros -> OOO Basic

2. Create a new module within the standard library following these instructions.

I deviated somewhat by using this in my macro command:

Sub Main

Shell("totem --fullscreen --toggle-controls /home/me/chem/movie/movie.mpg",2)

End Sub

New Discovery - It looks like I should be able to embed an AVI file directly into my Impress Slide. From OOO go to Insert -> Movie & Sound and select the .avi file. May need to install a codec (libavcodec?) first...verification needed. Also to convert the MPEG from PyMOL to an AVI format install ffmpeg and then run
> ffmpeg -i file.mpeg file.avi

A video toolbar comes up when you click on the embedded box where you can select "repeat." The AVI video will automatically start playing when you advance to the slide and continue until you move on.

PhD Dissertation - The End is Near

2010-03-25T07:21:00.007-04:00

I thought maybe it would beneficial to document some of the process of writing my dissertation since I went about it a bit nontraditionally (not just taking too long to do too little) using predominantly open-source software.

Disclaimer: Although writing a chemistry dissertation with open-source software is readily accomplished, it is probably unwise to make a switch from MS Windows after already starting your writing. It is recommended that you make the decision a year-ish early and write at least one hefty report to acclimate :)

Software Used

OpenOffice.org 3.1 Office Suite:

OOO3 Writer - Word Processor

OOO3 Draw - Drawing Program - I used this to prepare all of my Figures and Schemes saving each one separately with a unique alpha-numeric identifier for easy renumbering at the end.

OOO3 Calc - Spreadsheet - Used to generate tables and graphs

JabRef 4.2 - Java-Based Reference Manager - Fast and flexible, however there is a bit of a learning curve (maybe a few hours) associated with using the "style file," a template that formats your bibliography. I know there are several others out there, but JabRef was easy enough that I could get started with it right away and it is very robust. Documentation on their web site is good, and you will find there the critical plugin for syncing to OOO3.

SciFinder Scholar - Chemical and Biological Database Search Engine - SciFinder Scholar is sooo expensive that you shouldn't have to pay for it. Your institution will likely have a site-license (mine has one with only 3 seats or simultaneous users for a student body of 12000) and you need only download the Windows executable and obtain a copy of the site.prf file (a key granting you access) from the school (check with the library). Yes it is windows only, but again I found it to run nearly flawlessly in WINE for Linux.

BKChem 0.13.0 - Python-based 2D Chemical Structure Editor - BKChem is far from perfect, but for my thesis it worked great. This may in part be due to most of the chemistry I do is with flat polycyclic aromatic hydrocarbons, however anyone looking for open-source 2D structure editors should have good success with BKChem (also look at JChemPaint). The only major set back I had was in resizing objects as BKChem would crash. Otherwise very robust. Since BKChem exports a scalable vector graphic (SVG) to OOO2 .odg format I had no resolution trouble with resizing in OOO3 Draw.

Avogadro 1.0 - Powerful 3D Chemical Structure Builder and Force-Field Minimizer - I can't say enough good things about Avogadro. It is my front end to all of my computational chemistry. It is easier to use than GaussView (almost as intuitive as Spartan's Builder), offers beautiful, fast graphics, implements MMFF, UFF and Ghemical force-fields, reads loads of file-types including Gaussian Cube files, displays MOs, cross-platform (YES Mac and Windows too!) and it's bloody free!! (I don't know how but thanks to Marcus Hanwell and his faculty advisor Geoff Hutchison).

PyMOL - 3D Chemical Structure Viewer and Graphics Renderer - Although a little clunky, PyMol's greatest strength is producing very nice graphics which are saved in .png format. I know it has many additional uses, however, I only used it to prepare beautiful 3D molecular visualizations for my thesis. It is only missing a "ball-and-stick" display style (which is available in avogadro) but the "stick" style is clean and the images do come out much sharper and scale well.

WinDNMR in WINE - Dynamic NMR Line Shape Simulator - Although not available for Linux or Mac, WinDNMR worked without any trouble through WINE for Linux. The program is free-ware, but the author H. Reich requires e-mail registration in exchange for an activation code. This program requires adequate knowledge and skill for proper execution but the manual/tutorial is available and thorough.

MestReNOVA - Advanced NMR Workup Software - MestReNOVA is not free, but a 45 day trial is available for Windows/Mac/Linux, giving the average graduate student enough time (I got a 15 day extension) to do the final workup of all NMR FIDs.

pdftk - PDF merge/split Command Line Tool - This little gem came in real handy to manage my dissertation in 5 parts. Splitting up the OOO3 .odt files allows for faster save times and handling. I didn't learn how to start page numbering from a different number than 1 until after I merged my 3 chapters and appendix into the .odt file which was a little frustrating to manage the 155 page document for final minor edits. Still saving each part separate and exporting as a PDF worked well and pdftk seamlessly merges one printable document. Most likely pdftk is downloadable from your package manager (that's what I did with Ubuntu) and type pdftk --help for a list of command options.

Hurdles and Lessons for Writing a Dissertation/Thesis with this Software:

The OOO3 office suite is nearly as powerful as MS Office but there are some significant differences, some advantageous. There is no way I can give a complete overview of these differences, but there are a few helpful points I may make.

1. Page Numbering in OOO3 is tricky. It is a good idea to break your document up into sections as it saves time in the end. However, this is only true if you learn how to number starting with a different page than 1 well in advance. OOO-Writer uses page "styles" to manage this information. For example to number your preface with Roman Numerals and then start Chapter 1 with page 1 (as is usually the case), the preface pages must be designated a separate style "preface" than the rest of the document which will probably remain "default." It is imperative to sort this out early with some test pages. Consult the following website documentation: OOO3 Wiki, Taming OOO3, OOBlog. I'm sure there are lots of other sites with this information, but the first 2 alone basically got me up-and-running (although a bit late!).

2. Build a detailed and "Advisor Approved" outline for your entire thesis. Use the Outline Formatter in OOO3 (usually defaults as you build) for this and you'll be happy you did. My outline literally became my headings and subheadings for each section of my dissertation which I could easily reformat numerically after I was finished using the Bullets/Numbering toolbar.

3. Use a reference manager to keep your bibliography organized. I used JabRef with an OOO-plugin (see above) and it worked well for me. I did the best with my "style-file" for ACS formatting and left it alone until I was finished the document before a final format.

4. Organize your Tables, Figures, Schemes and Componds with a well designed alpha-numeric coding system so you can use "Find/Replace" tool in OOO3 at the end to provide a final number. I used "T" for Table, "F" for figure and so on, followed by a 1,2,3 for which chapter the table or figure was in, followed by Roman Numeral designation for which part within the chapter it was in, followed by a capital letter. The trouble I ran into was when substituting C2II (the "I-th" compound of part I Chapter 2) with the number 16, compounds C2IIA-C2IIZ (compounds in part II of Chapter 2) became 16A-16Z!!! So don't do that! Use a better system and you'll be golden.

5. Export and test as you go. Your advisor will probably want to use your well-crafted figs, schemes, tables in journal submissions later on (hopefully) so you should save each one individually with a good systematic archiving method and export them into a format that will be useful for collaboration purposes (MS Word 2003 / 2007). Also deal with your text. I found exporting to .rtf worked well for keeping my text formatting, but my figures/schemes/etc were botched. It is useful to figure out a system that you know will work early on so you're not "stuck like chuck... cuz chuck was stuck" -MM.

Linuxsamplers: QSampler, JSampler

2010-03-10T10:27:00.010-05:00

Installing LinuxSampler and QSampler on Ubuntu directions here.

More significantly just follow the CVS instructions from here.

Note that to install from the cvs source you must first install:

cvs, automake, g++, and respective dependencies, all of which are available through synaptic.

In addition either libsndfile or libaudiofile with the 'dev' files must also be installed.

Installing JSampler/Fantasia found here.

wrote the following script to launch JSampler: /usr/local/bin/fantasia

with help from here.

#!/bin/bash

linuxsampler &

samplerPID=$!

java -jar /opt/Fantasia-0.8a.jar

kill $samplerPID

Configure linuxsampler for jack support with > ./configure --enable-jack

Tutorial on setting up VTPO virtual orchestra with JSampler/Miditzer in Puppy Linux!

I ALSA Don't know JACK about linux-rt kernel

2010-03-07T13:20:00.002-05:00

Okay, I thought I would quickly document the exact procedure to get JACK (via QJackCtl GUI) to play nice with ALSA and the Real-Time kernel (linux-rt) on Ubuntu 9.10.

1. Install linux-rt from synaptic

2. Install QJackCtl from synaptic or Ubuntu Software Store

3. Go to System -> Administration -> Users & Groups and add your user to the following groups: audio, pulse, pulse-access

4. Enter the following into your command line

> sudo su -c 'echo @audio - rtprio 99 >> /etc/security/limits.conf'

5. Reboot

6. Start QJackCtl and edit the following prefs:

Setup -> Settings tab: check the boxes next to Realtime and No Memory Lock

Setup -> Misc. tab: check the box next to Start Jack Server on Application Start-up.

7. Restart QJackCtl and voila!

GCompris, TuxPaint on puppy linux

2010-03-06T12:47:00.002-05:00

These are fun for the kids, however, GCompris may be for 4+ not 2+ like advertised!

Here's the list of .pets you need to grab from here (reprinted from this forum thread):

Gcompris 8.4.13, and dependencies:
gnucap + gnuchess + python + pysqlite + pycairo + pygobject +pygtk + SDL + SDL mixer +tuxpaint

And

+sqlite 3.6.12
which you can get here

Also needed for TuxPaint: SDL_image-1.2.7-i486.pet + SDL_Pango-0.1.2-i486.pet + SDL_ttf-2.0.9-i486.pet + libpaper-1.1.23+nmu1-i486.pet from here as well :)

Note all the other goodies from the same site: Klavaro, Enigma, Childsplay, TuxMath.

RPM Challenge

2010-02-22T11:43:00.003-05:00

I registered for the RPM Challenge and I have been working on my music project called Nuclear Overhauser Effect (nOe) which I decided will be experimental and thus a learning tool to catalyze other musical endeavors. As of right now, nOe-i has 8 tracks with 2 more to record. I also want to doctor-up one or two of the existing tracks, but the RPM challenge deadline is Feb. 28, so I'm not sure if that will happen. The concept for this album is to use my iPod Touch to compose, record, and generate field-samples almost exclusively. So far I have been using the following equipment for this project:

Hardware:
iPod Touch-2G 8GB (firmware: v. 3.0)
Desktop PC (home-built) with Pentium IV 2.8 GHz, 2GB DDR RAM, Audigy Soundblaster Platinum with mounted breakout-box (operating system: Ubuntu-9.10 with linux-rt kernel v. 2.6.31.9.10)

Software:

- iPod -
Voice Recorder
Xewton Music Studio
i808
Flare (virtual turn-table)
Thereminator
Noise.io Pro
Guitar Pro
BassGuitar
GigBaby
RjDj
DrumMeister

*Ubuntu-Desktop*
JACK
Muse
Ardour2
Hydrogen
Qsynth
ZynAddSubFX

Now with just a little left to do and possibly not enough time to do it, I want to document a few ideas to add to the project:

- add theremin/scratch? to nOe-i06
- add noise.io synth/field-samples? to nOe-i09
- use field-samples for nOe-i10
- find noise cancellation software (audacity plugin?) for nOe-i08
- need artwork and liner-notes

Xewton Music Studio for iPod Touch

2010-02-14T14:16:00.003-05:00

Xewton Music Studio (XMS) is an amazingly powerful MIDI sequencer with a complete set of instrument samples for the Apple iPod Touch or iPhone. Despite several limitations, this app is quite powerful, very intuitive and loads of fun to use. It is well worth the current $15 list price. I am currently working on my first nOe album using this software almost exclusively for composition. It exports compositions as .wav files and has built in server capabilities which enables you to access the files from you desktop/laptop with a web-browser and download them.

Ubuntu Studio 9.10

2010-02-14T13:58:00.003-05:00

Shortly after I burned my first ISO of PCLinuxOS, I configured my first serious desktop with a dual boot of Ubuntu Studio 8.04 and XP. As I recall I had many growing pains configuring my audio with UbuStu, however, at some point I was successful and was able to recompose a song I wrote in high-school using Rosegarden.

At some point, I decided to upgrade to UbuStu-9.04 as I had been enjoying the usability of Ubuntu-9.04 (Jaunty) and 9.10 (Karmic) at school. Sadly, I had some major issues with this install that forced me to move to Ubuntu-9.10. I knew I would probably try UbuStu-9.10 when it was released with the hope that the earlier incompatibility would be corrected. It seemed to work okay, however I could not get it to work with my Ralink Wirless card. Also, I was frustrated that the UbuStu developers didn't include some of the slick upgrades (namely the Ubuntu Software Center) that is steadily improving the usability of Ubuntu. I had no way of accessing the web without "ruining my life" so I moved on to 9.10 and decided to go on a significant "shopping spree." I installed loads of science, education and music apps from the Software Center, as well as the kernel-rt from synaptic.

The most significant challenge was getting the JACK audio server to run and I eventually found that I had to add my user to the "audio" and "pulse" groups under System -> Administration -> Users and Groups. The follwing URLs were helpful for me:

http://ubuntuforums.org/showthread.php?t=600626
http://ubuntuforums.org/showthread.php?t=1336078
http://ubuntuforums.org/showthread.php?t=453486

and most significantly:
http://ubuntuforums.org/showthread.php?t=1143784

I still get the following error from Rosegarden however:

System timer resolution is too low
Rosegarden was unable to find a high-resolution timing source for MIDI performance.
You may be able to solve this problem by loading the RTC timer kernel module. To do this, try running sudo modprobe snd-rtctimer in a terminal window and then restarting Rosegarden.
Alternatively, check whether your Linux distributor provides a multimedia-optimized kernel. See http://rosegarden.wiki.sourceforge.net/Low+latency+kernels for notes about this.

Anyone ever heard of an online auction website?

2010-02-02T14:54:00.002-05:00

I finally sold some stuff on EBay. I have thought about unloading various collectibles, refuse-ables, doodads/trinkets/chotchkies, and "what-have-yous" for quite some time, and always thought "hey, what about EBay?" Well the time has come to overcome my fears and give it a shot. So far, not too shabby. However, I definitely see how small-fry sellers like myself could get burned. It is easy to be bamboozled.

To date, I have sold just a few items:

3 cell phones, and a graphics card.

And have earned a grand total of $180 which has nicely offset my recent purchase of a netbook for my wife (asus eee). She loves it, and I must say, I am quite impressed with how much power can come in a little package for pretty cheap ($250).

I'm sure I'll have Ebay updates in the near future!

Puplets: NOP, TEENPup, UPup

2010-02-02T14:29:00.003-05:00

Since my review of "Pup-It-Up" Puppy Linux Music Lab, I have tested a number of other puplets. I will give my best recollection and overall impressions of each.

NOP:
Probably my favorite puplet for general use would be Nearly Office Pup (NOP). Although I find it runs a little slower on my hp pavilion ze5600 laptop, that is probably due to a number of useful changes to the base Puppy, specifically xfce as a window manager and Opera for the browser. However, it is these two additions that make it a slick, user friendly system. Once adding the openoffice.sfs to the boot-up options, NOP is a clear winner for a desktop environment that even Grandma could use.

TEENPup:
My second favorite puplet as an all-purpose desktop would be TeenPup-legacy2009. Although about as "fat" as they come, this distro has a tremendous amount of applications with a "windows-like" feel and usability. I would keep it off of most old laptops, but it is a great choice to get the most out of an older desktop.

UPup:
Perhaps the most cutting edge of the puplets is UPup which is the current "pet" project of Barry Kauler (Puppy Linux originator). It is listed as "experimental" and in fact I remember finding some basic applications were broken. Simply put, UPup is a Puppy platform which readily installs debian (.deb) packages from Ubuntu repos. This makes it one of the most extensible, flexible of any puplets for a linux newbie like myself. My guess is this will be the future of Puppy Linux.

Snappy Holla-daze!

2010-01-02T13:48:00.002-05:00

I'm not so much a grinch as just a guy that could really give a rats-ass about the holidays. In the end I like what I like about it, and that's not much...mostly just the food. After Thanksgiving, I usually cannot wait until January 2nd...that's today. Anyway, a bit has happened since I last blogged and I will try to summarize as I am watching the kids.

At school, my French colleague and two of the Asians have left. Also my Vermont friend is gone to go teach ski racing to teens, but plans to come back to write his thesis in April.

Much of my time has been split between writing my dissertation and playing with the new $40,000 computer cluster. It was assembled and configured by a gifted 22 y.o. UNH undergrad who did a really nice job. It consists of a head node and 6 compute nodes running OpenSuSE, each with 24gb memory and the newest, fastest intel nahelem procs in a dual-quad core configuration. The nodes are networked with gigabit up/down cables. That's about the extent of what I can remember. Of course it has a slew of useful computational chemistry packages.

Although I don't have any training in CS, I managed to piece together a useful python script based on a similar one that I used as a template...though I added a number of useful bits for my own preference. Here it is:

#!/usr/bin/python

import sys
import os
import commands
import datetime

print "*************************************************************\n**See g03jobLOG in Home Directory for Log of Jobs Submitted**\n************
*************************************************\n\nEnter the Following Information for Your Gaussian Calculation:\n"

xyzFile = raw_input("Enter .xyz File Name (omit extension) > ")
uniqueID = raw_input("Enter Unique Identifier (no spaces; optional) > ")
g03root = raw_input("Enter Root Section (#) > ")
charge = raw_input("Enter Charge > ")
multiplicity = raw_input("Enter Multiplicity > ")
title = raw_input("Enter Title; optional > ")
queue = raw_input("Enter Queue (short (s) or long (l)) > ")

if uniqueID == "":
UID = ""
else:
UID = "_"+uniqueID

if queue == "s":
SGEQ = "short"
if queue == "l":
SGEQ = "long"

if title == "":
title = xyzFile+" / "+uniqueID

f = open(""+xyzFile+UID+".com", 'w')
f.write("%chk=/tmp1/"+xyzFile+UID+".chk \n")
f.write("%mem=20gb \n")
f.write("%nprocshared=8 \n")
f.write("%nproclinda=1 \n")
f.write("# "+g03root+" \n")
f.write(" \n")
f.write(" "+title+" \n")
f.write(" \n")
f.write(charge+" "+multiplicity+" \n")
f.close()

inp = open(""+xyzFile+".xyz", "r")
outp = open(""+xyzFile+UID+".com", "a")

for line in inp:
outp.write(line)

inp.close()
outp.close()

lines = open(""+xyzFile+UID+".com", "r")
list = lines.readlines()
lines.close()

del list[9:10+1]

fout = open(""+xyzFile+UID+".com", "w")
fout.writelines(list)
fout.write("\n")
fout.close()

print "Gaussian .com file ("+xyzFile+UID+".com) generated ... submitting"

jobName = "g03job"

f = open(jobName, 'w')
f.write("#!/bin/csh \n")
f.write("#$ -S /bin/csh \n")
f.write("#$ -N "+xyzFile+UID+" \n")
f.write("#$ -q "+SGEQ+".q \n")
f.write("#$ -cwd \n")
f.write("source /opt/g03/environment.csh \n")
f.write("g03l "+xyzFile+UID+".com \n")
f.close()

#command to submit
task = "qsub "+jobName
subJob = commands.getstatusoutput(task)
log = "/home/"+os.environ["USER"]+"/Computation/g03jobLOG"
cwd = os.getcwd()
now = datetime.datetime.now()

if subJob[0] == 0:
print(subJob[1])
f = open(log, 'a')
f.write("\n")
f.write(subJob[1]+"...\n")
f.write("Job Directory: "+str(cwd)+"\n")
f.write("Submission Time: "+str(now)+"\n")
f.close()
else:
print("...Failed : "+subJob[1])
sys.exit(2)

To Summarize - this script conveniently takes user input and edits an XYZ coordinate file to generate the appropriate Gaussian .com input file. It then writes a jobscript , submits it to the SGE queue, and logs (appends) the date/time and directory in a single file.

At home, I have enjoyed running ubuntu 9.10 and hope to do some recording with it soon.

64 Studio: A solid DAW Desktop....almost

2009-10-31T06:10:00.005-04:00

After the failure that was ubuntu studio 9.04, I thought I would look into any other possible solutions to my ultimate DAW desktop. Reading about the different choices, I settled on 64 Studio to try next, due in part to the fact that it is very similar to ubuntu with its debian roots. My first attempt at installation failed on one of the install steps, likely due to a bad burn/image download. I tried again, unscientifically adjusting all the variables: I downloaded the latest beta instead of the pronounced stable release (2.1) and I burned to a DVD-R instead of a DVD+R. The install completed.

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!

Up(down)grade to Ubuntu Studio 9.04

2009-10-24T21:56:00.004-04:00

I have been running UbuStu 8.10 since may 2009 and with the exception of having some trouble with the initial setup of sound, I have been very happy with it. Recently, after (I believe) a kernel update, the sound stopped working...and I haven't figured out the fix yet. I knew that eventually I would have to update/upgrade my system, and that when I did I would want to repartition my hard drive in a more logical fashion. So I figured now was as good a time as ever.

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.

Puplets: PupItUp

2009-10-23T12:36:00.002-04:00

It occurred to me recently that it is a bit odd that I had only obtained Puppy Linux 2.16 and 4.21 and learned very little about puplets other than that they exist before moving forward on creating my own puplet without ever having tried a single other puplet. I'm not sure if that indicates arrogance, ignorance, ambition, or sloppiness on my part...nevertheless interesting.

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.

Google Analytics

2009-10-20T13:42:00.003-04:00

It was over a year ago that my wife first told me about google analytics and I didn't listen too much...I had other motivations at the time I guess. However, with the launch of chemtoolbox.com, she mentioned it to me again and this time I dove right in!

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!

ChemToolBox.com Agora Forum Troubleshooting

2009-10-16T13:23:00.003-04:00

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!

ChemToolBox and ChemPup ToDo's

2009-10-10T22:33:00.003-04:00

-add new screenshots and update ChemPup features list
-upload ChemPup-1.0.1
-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
-test shopping-cart
-build axs ChemPup kits
-produce multisession DVD
-

Puppy Remaster Checklist

2009-10-10T21:58:00.004-04:00

I need to be more meticulous with the remastering process for puplets. As such I will need a "rubric" to follow each time I remaster a puplet so I do not miss a critical step. Starting Now!

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
5.GO
6. delete /tmp/etc/xdg
7. copy /etc/xdg to /tmp/etc/xdg
8. GO
9. edit puppy***.sfs file to chempup**.sfs file
10. create then rename .iso

ChemPup-0.2.6 Released at ChemToolBox.com

2009-10-09T10:43:00.004-04:00

So I have a functioning web site (www.chemtoolbox.com) with a download manager called remository that is pretty easy to use and tracks download totals. To date, ChemPup-0.2.6 has been downloaded 8 times since its release on 10.7.09 (2 days). I posted a forum thread at the official puppy linux forum (http://www.murga-linux.com/puppy/) and have 85 views in just 2 days. I am hoping for feedback and may ask for some when my downloads total reaches ~20.

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.

TO DO:

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)

ChemPup USB boot

2009-08-31T16:09:00.002-04:00

Ideally ChemPup would be delivered on a 2GB USB flash drive that had a small (128MB) windows readable (VFat or NTFS) partition that has the ChemPup user guide, quick-start guide, tech support info etc. Then upon reboot, the flash drive will already be inserted and the bootable ext2 partition with ChemPup will boot up and they will know exactly what to do for the initial boot. Well it seems that this is very possible, but not necessarily fail-safe and instead depends on the hardware configuration. I am unsure if it is important which partition be "first" on the drive, but on initial test it seems that windows is only happy reading the first partition. Likewise I had trouble on at least one older computer to boot ChemPup from the second partition, but when first in line it was okay....meanwhile, at school I have found ChemPup on partition 2 boots without any trouble. So I am encouraged, but again, I will need to have "back-up" plans that can be rapidly deployed if a user has trouble with older hardware.

ChemPup-0.2.0: Wife Tested...trouble in paradise

2009-08-29T19:41:00.002-04:00

I had my wife try to do a first boot of ChemPup-0.1.5 and get through it without any instruction or interference....it didn't go the way I had hoped but nevertheless was a very valuable trial that lead to several improvements. She had significant trouble with the initial Puppy boot since it asks a couple tough questions about hardware configuration: mouse type, and monitor type. It's true, once a windows only user I can attest that determining my screen size and resolution presented some challenge when I first tinkered with DSL. So the first critical change is to provide step-by-step documentation on the initial boot that can be read and printed from the users current Windows OS or otherwise sent as a hard copy.

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.

ChemPup-0.1.5 ready for beta testing

2009-08-27T16:46:00.002-04:00

I now have a ChemPup "full" version that I am happy enough to beta test. The .iso is 454MB which is kind of in the middle for a puplet based on my survey of the official puplet page, though most attempt to be smaller than 100MB. However, I decided to leave devx.sfs which adds some extra but will facilitate growth for now, and of course as mentioned previously the "full" version comes default with openoffice3.0.

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.

ChemPup-0.1.3

2009-08-24T10:17:00.003-04:00

I have temporarily abandoned implementation of Avogadro in my ChemPup project. I was wasting too much time for a "proof-of-concept" product. Now I am thinking of dividing the project into a ChemPup "full" and ChemPup "lite" set. The difference will be that ChemPup "lite " will be released as a downloadable puplet (hopefully under 400MB) that I will host on a basic descriptive website. ChemPup "full" will be at least 700MB (I think) and will be burned "open-session" to a DVD (I hope). The full version will come with extra documentation, and OpenOffice3 will be bundled in along with several other features (see below). I also am hopeful to put together a useful spreadsheet template that will have relevant (solvable) chemical equations with descriptions. I also hope to write a simple program to calculate molecular weights since I haven't found a quick-and-easy one yet. So here is the list of features for each:

ChemPup-0.1.3 "lite"

Office Productivity: (Default Puppy Linux)
Abiword - word processor
Gnumeric - spreadsheet
mtPaint - image editing
SeaMonkey - web browser

Chemistry Programs:
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.

ChemPup-0.1.3 "full"

Office Productivity:
OpenOffice.org-3.0 - full office productivity suite compatible with MS Office
JabRef - reference manager that syncs with OOO3
SeaMonkey - web browser

Chemistry Programs:
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

2009-08-15T16:54:00.005-04:00

I recently had the idea to assemble a Puppy Linux "Puplet" that would be configured with software useful for an undergraduate chemistry student. Considering I know nothing about programming and I am still very new to Linux, this is proving to be a challenge...but I have had success so far.

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:
OpenOffice.org-3.0

General Chemistry:
GElemental - a gtk+ periodic table of the elements with loads of information on each element
MoleCalc - a molecular weight calculator (runs in WINE)

Organic Chemistry:
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)

Need:
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.

Puppy Rescues Windows

2009-07-31T16:20:00.006-04:00

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!

installing debian packages to puppy

2009-07-26T00:16:00.003-04:00

For the first time, I installed a .deb package (a space adventure game called epiar for my nephew) in puppy 4.2.1. I had to use the tips found in this puppy forum thread. I haven't figured out how to add a menu entry yet... but I would think it to be similar to how I can do it in ubuntu. It is after midnight so I reckon I'll tackle that another day.

#!CrunchBang!#

2009-07-17T23:11:00.003-04:00

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....

Linux Resource Links

2009-07-15T12:27:00.001-04:00

Linux Admin for Noobs

http://linux-newbie.sunsite.dk/index.html

Excellent Ubuntu post-install configuration procedure

http://theindexer.wordpress.com/

DAW Links List

2009-07-15T11:37:00.005-04:00

Here's a list of links I'm compiling for my Digital Audio Workstation set-up:

Audigy2: review/drivers

Creative Labs Audigy2 Sound System Review

http://www.linuxquestions.org/

http://ubuntuforums.org/

http://www.alsa-project.org/

Reviews for Linux Music Produciton

http://createdigitalmusic.com/

Linux MIDI Software Collections

http://linux-sound.org/

http://www.linuxlinks.com/

http://tldp.org/

http://www.linuxjournal.com/

http://freemusicsoftware.org/

http://www.openstudioproductions.org/

Ardour on ubuntu

http://ubuntuforums.org/

Configure Rosegarden MIDI

http://ubuntuforums.org/

Kubuntu Studio?

http://kubuntuforums.net/

http://bmccosar.wordpress.com/ (jack)

http://bmccosar.wordpress.com/

Ex-Research Chemist School Teacher Linux Musician:

http://bmccosar.wordpress.com/

http://www.jamendo.com/en/artist/bruce.h.mccosar

OpenOffice for Puppy?

2009-07-15T00:28:00.005-04:00

This is still a work in progress.

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.

Added gtkPod to Puppy Linux

2009-07-15T00:20:00.004-04:00

gtkPod is an ipod-ready app to manage your music list from your mp3 player. Here are the useful web pages I found to install gtkPod. First I installed all the "lib" .pet files from here, then I installed the main gtkPod.pet from here.

That's it!
Note the inquiry began with this thread

PCLinuxOS Phoenix Test Run

2009-07-14T08:34:00.003-04:00

Still looking for a more complete workstation for my laptop (although if I get openoffice working on puppy I may just stick with it). I think GNOME and KDE might still be a little sluggish with only 512MB RAM (though I've ordered another 512MBs so then it should be fine). Fluxbuntu and Crunchbang were very fast desktops featuring the Fluxbox and Openbox window managers, but I could not get either to work out-of-the-box with my wireless card (BroadcomBCM94306MP).

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.

WikiWikiSandbox

2009-07-13T07:36:00.002-04:00

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

2009-07-12T07:38:00.002-04:00

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

2009-07-08T15:37:00.005-04:00

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...

2009-07-06T08:16:00.005-04:00

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

2009-07-04T23:00:00.003-04:00

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

2009-07-04T00:54:00.003-04:00

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?

2009-07-02T05:47:00.004-04:00

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?

Betty Crocker Building Source Code

2009-06-29T11:20:00.006-04:00

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.

Goodbye Facebook.

2009-06-21T09:30:00.004-04:00

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:

http://synergenerator.blogspot.com.
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.

Writing my Dissertation: Linux or Windows?

2009-06-21T07:47:00.007-04:00

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.

Links:

http://jabref.sourceforge.net/index.php

http://www.itk.ntnu.no/ansatte/Alver_Omholt_Morten/jabref/OOPlugin.html

http://groundstate.ca/chemdraw

http://ubuntuforums.org/showthread.php?t=225390

For an extensive list in chemical software written for linux see this link:

http://www.redbrick.dcu.ie/~noel/linux4chemistry/linux4chemistry.py

Reproducing My First Masterpiece

2009-06-18T00:00:00.003-04:00

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.

Moe, Larry, Curly and Grub

2009-06-16T16:34:00.004-04:00

I have so far stuck with my XP Black/Hardy Studio dual boot and been very pleased. Linux has been a refreshing source of daily learning and many challenges. I suppose I've grown accustomed to challenges and enjoy those that have no deadline or serious consequences.

At school, however, I decided to pursue my 3-boot system...I don't know why I get so enamored with frivality. My desktop (on loan from UNH) has a huge excess of storage that wouldn't be filling anytime soon (around 120 GB free of a 160 GB drive) so I thought it safe to manipulate. However, unlike my home pc, I only have the one hard-drive to work with. I was a little intimidated by the prospect of destroying my 6 years of Ph.D. work sooooo..... I copied my "important" files to a networked computer and then downloaded a .torrent of partition magic.

Partition Magic had lots of scary read-me documentation that is likely to thwart the plans of the timid or ignorant. I narrowly escaped...nearly thwarting myself! I did a disk cleanup and defragmented the drive as suggested. At some point I recall scrambling to find the recommended floppy disk back-up but I couldn't find any working floppy diskettes in the department!! So I ignored the advice and continued anyway. It worked flawlessly. I was very pleased with the results of using Partition Magic and would recommend it to anyone that wants to partition their hard drive. (Just make sure to back up!)

I first installed PCLinuxOS2009 on one of the 30 GB partitions I made and it ran without a hitch. I got my first big scare when I tried to boot back into XP. Instead of booting the OS it went to some utility that ran a full system diagnostic scan. Not really sure what I was looking at, I figured I'd run the scan and then perhaps it would pass on to boot. 30 minutes later and just before I had to go home...no boot. When I closed the dialog box, the whole machine rebooted back to the PCLinuxOS grub boot loader. I had a conference to attend the next day and dwelled on the problem. Then it occured to me that I saw a tiny sliver partition at the front of the drive when I was running Partition Magic. I guessed that the grub boot loader menu item for Windows XP defaulted to hd(0,0) and that this was the location of the DELL Utility that ran. After editing this to hd(0,1) in menu.lst in grub the problem was solved.

I still had a roughly 30 GB partition set aside to load ubuntu studio 8.04 (UbStu) but I wanted to keep the nice graphical boot loader splash page that came with PCLinuxOS. So during the installation I skipped the grub set-up. However, I wasn't quite sure of the hd location of the install. So the lesson learned is to carefully note your partition table as you partition your drive. Where is what partition and what is it called. After I fiddled with the menu.lst file in grub for a while, I finally got ubuntu studio to load. Success!

In summary: I learned a bit about partition tables, installing multiple operating systems on a single drive, and configuring a grub boot loader (Including creating a personalized splash screen).

To Do:

1. Write about my experience thus far with Rosegarden/JACK

2. Figure out how to record MIDI tracks in Rosegarden with only my soundcard

Problems:

1. Cannot record my MIDI sequence in Rosegarden

2. Audacity and Rosegarden freeze my system (complete lock-up) when run together

3. Still not sure how to manage my swap space.

Notes:

The last time I ran UbStu my swap space wasn't even loading and I couldn't get it to load with a >swapon -a. However, I ran a few memory intensive programs and my system memory peaked at about 25-27% so I guess I just have way more memory than my celeron processor can handle. The processor was maxed out.

SoundBlaster Audigy, Ubuntu Studio 8.04, XP Black

2009-05-31T08:37:00.007-04:00

Synopsis:

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.

Problems:

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.

Introduction

2009-05-31T07:48:00.006-04:00

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.