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January 31, 2004

GATech Thesis package (cont'd)

I happened to be able to install the gatech-thesis LaTeX package on a Mac OS X machine without incident. You should have the tetex/latex fink package installed to have this work. Get fink from http://fink.sourceforge.net, then in a Terminal app as root, do an "apt-get install tetex". The following is what I did. I first downloaded the tar.gz file. In a terminal, I unpacked the tar.gz file with "tar zxvf gatech-thesis-1.6.tar.gz". I sudo'd as root with "sudo su" (or "sudo -s" will work as well). Then did the following:

1. I copied the files to the following locations. If the directories were not there, I made them first before copying; e.g. with "mkdir ":


  • /sw/etc/texmf.local/tex/latex/gatech-thesis/gatech-thesis.cls

  • /sw/etc/texmf.local/tex/latex/gatech-thesis/gatech-thesis-patch.sty

  • /sw/etc/texmf.local/tex/latex/gatech-thesis/gatech-thesis-losa.sty

  • /sw/etc/texmf.local/tex/latex/gatech-thesis/gatech-thesis-gloss.sty

  • /sw/etc/texmf.local/tex/latex/gatech-thesis/gatech-thesis-index.sty

  • /sw/etc/texmf.local/bibtex/bst/gatech-thesis/gatech-thesis.bst

  • /sw/etc/texmf.local/bibtex/bst/gatech-thesis/gatech-thesis-losa.bst

  • /sw/etc/texmf.local/makeindex/gatech-thesis/gatech-thesis-index.ist


2. I then ran "texhash" which refreshed the database.
3. cd into julesverne/basic.
4. Run the DO_pdf.sh script to test the installation (i.e. type "./DO_pdf.sh"). And you should have a resulting pdf file that you can view.

On the Mac, the fonts look exceptionally good. Of course, for your use you will have to change /sw/etc/texmf.local/tex/latex/gatech-thesis/gatech-thesis.cls to your liking; however for me, not much change was required.

Posted by johnvu at 03:55 PM | Comments (1)

January 30, 2004

Thesis/dissertation LaTeX document classes and packages

LaTeX Class File for a Georgia Tech Thesis. After painstakingly trying to tweak the "report" document class that comes standard with LaTeX to produce a document that fits my graduate school requirements, I decided to throw all that work out! I wanted to start fresh with a whole new document class for my thesis and began searching. I came across a class file that is currently actively updated by Charles Wilson at Georgia Tech. The files are distributed as GPL and seems to fit the bill for my graduate school requirements as well (well, almost fits it with very minor modifications).

I don't think the 1.6e patch is implemented within the current 1.6.tar.gz package file that is available for download. I wish Charles left an email or some contact info for me to ask him whether it is included or not. Also there are no instructions on how to apply the patch. Anyone out there know how to patch it to 1.6e? Could you care to tell me how to do this?

You can use the LaTeX package for your thesis, but would have to change "Georgia Institute of Technology" in the gatech-thesis.cls fle to the name of your university. The reason I am probably going to use this LaTeX package as opposed to the many other thesis packages is because it is closest to the requirements for my university and because it appears to be actively updated. Of course, YMMV.

I installed the package on my Debian Linux box, here's how I did it:

1. I copied the files to the following locations:


  • /usr/local/share/texmf/tex/latex/gatech-thesis/gatech-thesis.cls

  • /usr/local/share/texmf/tex/latex/gatech-thesis/gatech-thesis-patch.sty

  • /usr/local/share/texmf/tex/latex/gatech-thesis/gatech-thesis-losa.sty

  • /usr/local/share/texmf/tex/latex/gatech-thesis/gatech-thesis-gloss.sty

  • /usr/local/share/texmf/tex/latex/gatech-thesis/gatech-thesis-index.sty

  • /usr/local/share/texmf/bibtex/bst/gatech-thesis/gatech-thesis.bst

  • /usr/local/share/texmf/bibtex/bst/gatech-thesis/gatech-thesis-losa.bst

  • /usr/local/share/texmf/makeindex/gatech-thesis/gatech-thesis-index.ist


2. Luckily, my Debian /etc/texmf/texmf.cf file already came standard with the line of text "TEXMFLOCAL = /usr/local/share/texmf" so I didn't have to add that in. But if you're distro doesn't have that, add it.
3. I then ran "texhash" to have the latex system re-index all package files. Charles mentioned something like "initexmf -u" to refresh the database, but I couldn't come across any program with that name.

I don't see why the same procedure couldn't work in say Mac OS X or any other *NIX latex system. Read the INSTALL file to find out how to refresh the database after copying the files in a MikTeX system in a Windows environment.

I would like to add that sadly, my university is not as up-to-date about creating thesis templates for their students like GA Tech appears to be. Kudos to GA Tech for helping out their students. For those of you using this package, good luck, and good writing. And if you come up with any useful hacks to this document class, please let me know about it. Come to think of it, I'm sure Charles Wilson would like to know about the hack as well, if you can find his contact info.

Posted by johnvu at 12:02 PM | Comments (0)

January 29, 2004

LaTeX and the lab notebook

The TeX Catalogue OnLine, CTAN Edition. This appears to be a promising LaTeX class file. If you're a grad student actively doing research, take a gander at learning LaTeX if you haven't already done so. It will do wonders for you in the long run -- i.e. when writing your dissertation. And if you just started out in the lab, you're just in luck, try out this labbook class. It has some interesting features in attempting to keep a lab notebook organized, but alas, there are many pitfalls in using solely LaTeX (yes, I admit, LaTeX is not an end-all, be-all) -- for example, what to do with all those flow cytometry data files? Or your Excel or FlowJo data files? Or your DNA sequence files or chromatograms? You get the picture.

Posted by johnvu at 11:11 PM | Comments (1)

January 28, 2004

My favorite part

MSNBC - No more┬ kishka? What about tripas?. If you happen to be a Pho connoiseur, you'd be sadly disappointed to hear that "sach" will have to be removed from the menu. For those of you who don't know what this is, it could be made from beef small intestine. However, the article is actually not really correct. "Sach" happens to be typically made from stomach, not small intestine. It's very thinly sliced in pho. Also, "tai" in pho is the thinly sliced steak meat, and there is really no such thing as "tai" stuffed "sach" as the article seems to imply. There is a dish known as "doi" (the d is pronounce like a y) which is a Vietnamese sausage that definitely should be banned. Come to think of it, if they're banning these organs to begin with, why not just ban the whole cow? Yikes, that means no more pho for me.

Posted by johnvu at 05:47 PM | Comments (0)

January 27, 2004

The publishing revolution continues

The Chronicle: 1/30/2004: The Promise and Peril of 'Open Access'. Wow, this is an extensive and informative article by Lila Guterman. Read it just to gain perspective of the kind of numbers involved in stocking a diverse biomedical library. If big research universities like those in CA and Duke University are having trouble paying for the journals used in their library, how do you think the smaller universities fair? I particularly liked the following paragraph:

In 2002, PLoS received a $9-million start-up grant from the Gordon and Betty Moore Foundation. Using that money, the group recruited a respected staff, including Vivian Siegel -- who had been editor of Cell -- as executive director. It also bought publicity, including a television commercial that ran during The Simpsons and The Late Show With David Letterman last summer.

I had no idea that lots of scientists watched "The Simpsons." You'd think they'd get more coverage with shows like National Geographic or something. But then again, I rarely watch National Geographic.

Posted by johnvu at 12:34 PM | Comments (0)

January 23, 2004

Ties to industry

Scientists with Industry Ties. Here's an interesting database -- the title says it all. The information provided here was collected from scholarly publications, news articles, rÚsumÚs, industry bulletins, federal agencies, corporate and university websites, conference programs, and direct contacts. Because we cannot independently verify all of this information, the accuracy of the list cannot always be guaranteed. We have reported information obtained from reliable sources but users are urged to independently verify all information.

Posted by johnvu at 04:36 PM | Comments (0)

Medsearch standalone tool

Download file. As promised, my port of an old tool of mine called Medsearch. It needs wxPython installed in addition to a working Python installation, of course. Run it on the commandline "python medsearch.py". It has the same search limits as what you would find on the PubMed website. I know, I know...I need to learn about and implement containers to make the form look better than it does now, but that's the best I can do at the moment. This is GPL'ed software -- do what you like with it, but stick with the GPL. I will try to add a checkbox to save the file as an XML file rather than a text file so that users can import into JabRef, if they so choose.

Posted by johnvu at 12:35 AM | Comments (0)

January 22, 2004

Java reference manager

JabRef: Java GUI for managing BibTeX and other bibliographies. I stumbled upon this via a posting on the pybliographer newsgroup. Looks like a promising bit of software. Perhaps for some of you it's worth a look-see. If you're still stuck in the MS world and need to organize your BibTeX references for a LaTeX document (the best way to write your dissertation by far), this might be the answer for you.

In other news, I've just ported my Medline search tool using wxPython -- as an exercise to see if I could do it and run it in Windows. It works for my purposes (in Windows XP) but is fairly rudimentary in function. It will however save your search result as a Medline file so that you can import into pybliographer if you ever so choose. I'll be releasing my port shortly, even though I think most of you will probably not need or want to use it. Now for trying to get the pybconvert function of pybliographer to work in Windows....might work, haven't tried it yet.

And for unrelated news that doesn't affect most, if not all, of you -- I just found out that my graduate office will gladly submit my dissertation as an intact PDF file to UMI for archiving. Thank you!

Posted by johnvu at 10:53 PM | Comments (0)

January 21, 2004

New Mass Spec online tool

MassSpectator. For most of you this is probably old news. NIST has provided a tool that may be helpful for those of you doing mass spectroscopy. Here's the Eureka alert link for it: http://www.eurekalert.org/pub_releases/2004-01/nios-oci011604.php.

Posted by johnvu at 12:46 PM | Comments (0)

January 08, 2004

Pybliographer release 1.2.2

Pybliographer - Release 1.2.2 is out. New stable release of Pybliographer is available, starting today. Additionally, there is a new Arch repository for the source code. Having read that some users are trying to install pybliographer in Mac OS X (and their difficulty in doing so), I realized that pybliographer could break out and be a highly used program if it was ported for other OSes. To this end, I wonder if the main developers would be receptive to porting it using wxPython? Shadow's experimental bittorrent client was developed in wxPython and tons of other software use it. Just a thought.

Posted by johnvu at 02:21 PM | Comments (2)

January 07, 2004

Presidential promises schhmomises

Howard Dean for America: DFA. Surfed upon this page via the Scientistsfordean.com page (or should it be deanforscientists.com? -- you know, you scratch my back...) Read what Dean said:


Under my plan, we cover all kids and young adults up to age 25 -- middle income as well as lower income.

That's a bold, very bold statement. I have a very hard time believing that it's possible. How many presidents have you known made similar promises of universal healthcare? How many do you know have been successful? I rest my case. Sure, it's easy for past presidents to blame it on Congress, or something else, but at the end of the day, err, term, what does he have to show for the effort? Those of you who really know me, know that I'm a fairly optimistic, gung-ho type of guy, but for whatever reason, in this situation, I'm a big critic, very skeptical -- I don't think it can be done anytime soon. I really really really hope I eat my words on this, though. Because if I'm wrong, I know my son will be covered until he's 25 (as per Dean's promise). Oh, wait? Dean didn't outright promise this? He calls it a 4-point "plan" and not a promise? In my eyes, it's still a promise. I hope he lives up to it if I and the rest of the voting population gives him the chance.

Posted by johnvu at 01:15 AM | Comments (0)

January 03, 2004

Possible New Year's Resolution: starting a webpage (free)?

Is one of your New Year's resolutions to start that webpage or weblog that you've always wanted (and to get it done right) without paying too much? I found this deal advertised at Techbargains.com for free webpages with no banner ads, nothing, at 1and1.com. Well, free for 3 years and who knows what they will do with it after that. Use their service at your own risk; however, the features sound pretty awesome. But I am also fairly skeptical this will last for long -- or even for the 3 years they advertise. Why? Well, the accounts provide you with access to your site via ssh. Sounds like a shell account to me. Who knows what kind of havoc a 133t h@x0r will do if certain scripts were allowed to run on the server. I can't say for sure what executable access is allowed until I sign up for an account, but if I do sign up for one, I'll let you know.

What's the advantage of going this route and starting a blog on your own website rather than going with the cookie-cutter style of Xanga and the like? Well, customization is, in my opinion, the reason why you should go with personal blogging software like MovableType (MT) or Wordpress (the new development arm of the highly popular b2 blog engine). The nice thing about the account from 1and1 is that it also provides all the nice backend database tools like MySQL and scripting languages like PHP so that you can install MT or Wordpress in your site. You can ensure your site is strict XML compliant or Transitional XHTML compliant. Don't get me started on why web standard compliance is important (although I still have yet to make my site fully compliant). The sky's the limit in terms of design elements. And best of all, you control the advertising on your site. Want to make a little money on the side? Provide some very useful information and then apply for Google's new service called Adsense -- ooh, wait, I'm giving away all the secrets. After all, the more people who sign up for Adsense means more diluted advertising payouts to those already in it, right? I think not. In the best case scenario, all the content providers who are not really in it for providing good content but rather a quick buck from Google, may end up finding their site denied from Adsense.

So please, go ahead and start that site you've always wanted to start. You probably also want to get a unique domain name to go with that site of yours. You can purchase cheap domain names nowadays from lots of different registrars -- check out Dotster, Verisign, Register.com, Godaddy.com. If you happen to start a site that provides information about life science, scientific publishing, graduate school, etc., please comment here about your new site (if it's an obvious attempt to bring traffic to a spam site, I will delete your comment). Good luck with your venture and if you happen to blog, please blog often, blog well, and stick with it -- I've seen too many blogs put by the wayside (understandably so, since I will eventually have to retire this site sometime in the future when I am no longer able find time for it).

Posted by johnvu at 02:34 AM | Comments (1)