Betty Crocker Building Source Code

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.

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?

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

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

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

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

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.