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.