Monday, April 28, 2008

Update on cb2Bib

On Ubuntu Hardy, I had to install the bibutils package by hand to get better functionality of cb2Bib: try this link. Bibutils compiled nicely, but didn't make a deb package. I had to install tcsh to run ./configure.

Bibutils is found here

Sunday, April 27, 2008

Bibliography tools, continued.



This is a very interesting package. It means "clipboard to bib." Does make picking up references much easier off of web pages. It apparently can do things automatically if one teaches it how, at least some things.

As it is, it right away picks up what it can, like journal name, pages, and volume, then I have had to select the title, or authors into the clipboard, and it asks me what's the category. Very nice.


Got it working with Firefox 3 b5 on Ubuntu. Very nice. I'm still a bit puzzled. I was able to save some snapshots and links, and use cb2Bib to massage them into bibtex database entries.

How to get the pdfs on my system integrated, and downloading pdfs? I know kbibtex and JabRef can do some of this.

Saturday, April 26, 2008

Zotero w/ Firefox Beta 5

How to get Zotero working w/ Firefox Beta 5 (Ubuntu Hardy Heron)

I've been wanting to test Zotero for more serious research. FInally I have it working. Here are the steps, pretty easy: (28 April 2008)

  • Download THIS FILE. (right click, yada yada)

  • Open that file with Firefox (File > Open File)

  • Restart Firefox

I can now add tags. Zotero looks more polished.

Friday, April 25, 2008

Ubuntu Essentials

In this space I will outline several essential tweaks, installs, and configurations that FOR ME have improved my experience with Ubuntu. I am writing this on the day that Hardy Heron has been released. My productivity has improved with Ubuntu. I don't have to spend so much time tweaking and configuring, as I did with Gentoo. [Gentoo is still probably better, but some things I never could get to work w/ Gentoo work perfectly with Ubuntu out of the box].


Rule # 1. Learn to use the VC, which means virtual terminal, and the command line. For a plunge off the deep end do "Ctrl-ALt-F1" simultaneously.

Rule # 2. Set a root password.

Rule # 3. Make a separate /home partition if you use your machine for valuable work (writing, programming, correspondence, artwork, you name it). You WILL have to reinstall the system at some point---in days, or in years. Avoid being a victim of the "it's time to reformat your hard drive" people at the local windows shop.

Rule # 4. Immediately set your repos. System -> Administration -> Software Sources.

Rule # 5. Don't believe all the rules you hear.

Issues with Ubuntu

I am crazy about Ubuntu, but I do have some issues. For starters I will do a "mind sweep" off the top of my head:

Emacs is not installed by default.

Tracker, the search tool, is a pig: it took me several days to figure out where my CPU cycles were going, and how to turn Tracker off (the Daemon and the Client).

Slocate is crippled out of the gate, and needs to be opened up.

/etc/fstab in the new Ubuntu is a thorny knot with hidden pitfalls for the unwary, and, yes, for the wary as well.

Even though I have taken pains that VLC would be the default DVD player and *avi player, etc., the gnome default keeps popping up.

Gnome does not allow me to tweak enough. Some of the nags I have cannot be solved (at least easily).

The installer makes it all too easy to make partitioning mistakes. Most importantly, it is too easy to overwrite a /home partition, and too easy to wrongly partition a favorite directory. Another issue: I have often had to start up sfdisk in a partition to recall which partition I wanted to call / or /home.

About /etc/fstab again---there is a serious bug that shuffles the identities of paritions. It moved an ide drive into /dev/sda and the former /dev/sda (for years) became /dev/sdb . Major bork. It is so confusing, I am never sure when /dev/sda means what. I am very afraid.

It's pretty hard to get to the point of compiling packages. This is a long standing Debian issue with me.

XEphem is not installed by default.

I'm a bit intimidated by Ubuntu's online docs. Gentoos docs are thousands of times better. Well, with Ubuntu you can find what you want, but it's more confusing, and you will find some advice that is best not followed, from well-meaning users who don't know better. Keep this in mind. That being said, I have found some really excellent HOWTOs on line for Ubuntu. Skepticism is well rewarded.

Coolness of Ubuntu

Gnome is working really well. Feels right.

Wireless access is as simple as pie.

Printers (at least HP) are installed before installing them.

Thunderbird "just works" for Gmail.

Even complicated applications, for example for video editing, are working for me out of the box. This was not the case 2 or 3 years ago. I was afraid of this, but I have been pleasantly surprized.

Important Steps on a new Install

$ sudo su

# passwd

(Add a password for root). Now I can run su in a terminal when I want to. This works for me. I am actually becoming more friendly with sudo anymore, though.

Get rid of Tracker.

Edit slocate configuration and enable indexing of more directories.

Install Emacs.

Put a terminal launcher on the panel.

Add repos and update. Can take "forever".

Install a number of programs that I use commonly. In fact, this is where I'm planning to develop a script of other means of my own to get my important utilities installed. It took me a full 24 hours to get the current install up to minimal usefulness, and I had to remember each step, one at a time. Examples: enscript, gthumbs, texlive, ghostview or gv, for starters. Dillo, filelight, vlc, k3b, numerous codecs, amarok, alsamixergui. Some things few would want. These can be taken care of with an edited list made from "dpkg --get-selections"

Turn off unneeded services. (System -> Administration -> Services).

Edit the "Applications" menu and add a submenu for ME. Drop favorites into it.

Add numerous high end Directories to the Places "Bookmarks".

Install dict and many dictionaries.

Install build-essentials, and compile xephem from source.

Recovery problems I have known

I have to admit, the recovery problems have been getting fewer and farther between. That being said, they haven't gone away.

Borked desktop. It always takes me by surprize, the desktop won't work anymore. I have had to delete .gconfd .gconf and .gnome2, perhaps other dot directories, to recover a borked desktop. This is easier if you can log in as root form a VC.

Notable Packages

I am starting to like GNOME Commander. Hope it's not all show and no go.

Nautilus is worth learning to use properly. You can drag a directory onto the sidepanel. This has saved me hours and hours.

Synaptic is better than it used to be. A shopping trip is worth your time.

Things I'd Like to See

Filesystem / Partition icons on the desktop should show device names, not sizes. I tried to fix this, but go lost in /dev/fstab, almost losing the whole install.

Kudos to the Ubuntu team.

Saturday, April 19, 2008

Time Enough At Last?

If I'm going to write about literature, libraries, bibliographies, it is obligatory to begin with some specific mentions.
  • Time Again At Last, episode8, season 1 of the Twilight Zone, aired on 20 November 1959. Always remembered, this dramatic depiction courses through the streambeds of my life in a particularly haunting manner. A man who wants to do nothing but read, at last given all the time in the world, in the end is deprived, by the shattering of his glasses. Who could not forgive you for downloading this in any manner possible?
  • Johann Gotthelf Fischer von Waldheim. (Link to article in German) Steven Jay Gould wrote a piece about him. I named my third son, Thomas Gotthelf Fisher after him. In brief, as Steven J. Gould relates in one of his columns in Natural History, he built up a medical school at Moscow University, the entire library---and every one of his personal books except one---were burned when Napoleon entered Moscow. His appeal to scientists around the world netted a 20,000 volume library in, if I recall correctly, a year or two. In my isolation in Chuuk Lagoon I was brought to tears by the story. What is my personal interest in this story? Briefly, almost all of my books, scientific specimens, instruments, and whatsoever, were lost in Chuuk, to Typhoon and Fire. Most of it will never be replaced. Who cares?
  • Libraries have been a personal bugaboo of mine, for as long as I can remember. When I was a child, I remember almost always being late to return library books. I never received my University diploma, partly because over $1,500.00 in libary fines stood over my head. I had, you see, two faculty library cards in my wallet and I had been lax in returning the books I had checked out as a work study library researcher for these two professors.
  • I have recently been attempting to recover the literature for my MS Thesis research, begun in 1984 (24 years ago!). Most of it was lost in Chuuk. Who knows where it all went. I have been living in a purgatory of sorts, a well trained and competent library researcher, with no access to books.
In 2008, one can happily report, it is becoming easier and easier to access literature on the Internet. There are problems, however. The yield per unit of effort is abysmal, even still. And despite much good literature now being available free online, as pdf files, most of it is not. One's interests are necessarily forced by what is available to him.

Yet, in an endeavor such as mine---retrieval of specific important historical papers---the gates are all too often closed. Jstor tries to own the world---can't we attempt to bring a class action suit against Jstor when they attempt to charge 32.00 or maybe more for a paper that the publisher has available free on line? And to charge 52.00 for a paper written by a scientist who has been dead for 100 years? Gads!

So I am gathering together the references, getting what I can off the Inet, and trying to find other ways, perhaps through a friend. If I am fortunate enough to visit the North American continent this summer, perhaps I'll be able to do some diligent literature searches.

For now, I have started experimenting with various ways of handling references for bibtex, the bibliography component of LaTeX, the markup/typesetting macro language I am using for virtually all of my writing. I will forego the discussion of LaTeX. See the TeX User's Group site.

I have been experimenting with the following (not in order):
  1. a number of utility programs for manipulating bibtex citation data bases.
  2. gbib
  3. kbib
  4. kbibtex
  5. Jabref
  6. Referencer
  7. Emacs bibtex mode
  8. Pybliographer
  9. cb2Bib
I have been amazed at the outcome of these experiments; but as yet I have not been able to get my head around the best of them. They do more than I could have ever imagined, and I'm not sure how.

In future posts I will review mainly for the following:
  1. kbibtex,
  2. JabRef
  3. cb2Bib, and
  4. Emacs BibTeX mode.
Referencer is also interesting, but the file format is not as easily compatible. I will continue to experiment with it, but as it stands, it is not a serious contender.