MacResearch

Yup, I just started using journler too, a few weeks ago. The only thing it won't do for me is export attached files when I export entries. Journler is scriptable so I should be able to make my own export format with an AppleScript, but I haven't gotten around to it yet.

Notebook (Circus Ponies) and DevonThink (Pro and Office) should probably fall under your gaze. DT Office has OCR in it which is nice for those papers that are PDF bitmaps.

On another note--I would be careful to not select something that uses a file format that might become unsupported at some time. You might not be thinking of it now, but for a person whose career spans decades this is a very serious consideration. I wrote my dissertation as well a whole lot of other things in FullWrite Professional (still the greatest word process of all Mac time). Fun while it lasted, but I still need to look at some of those old files (letters to patent attorney, e.g.) and OS X on a G4 is the last gasp because the Intel processors do not run Classic, as I understand. (I wish I could figure out how to write a script to automatically convert them all to Postscript rather than do it all manually.)

I now have an aversion to single-source file formats. Some of these notebook programs store their goodies in a package so you can still get at them, but who wants to convert GB's of data by hand when the developer dies or loses interest in his program? Also, many of them can export as a web site which is pretty nice, and maybe all you need in the long run, but again, that's a gamble.

As for your original question (what notebook) I'm holding out hope for the Finder in 10.5--it is supposed to have a preview feature. What I'm hoping for is that Apple has the sense to provide a plug-in feature so that app makers can write a preview plug-in for their non-standard files. In the meantime, Path Finder has a decent preview feature for some file formats.

I'm sure many people would be interested in hearing about your efforts.

The issue of proprietary file formats is a concern, not just for the notebook but also for all those diverse applications that scientists like to use. Whilst some have open standards many are closed binary formats. In a project I was involved with we ended up having a print to database that saved a pdf version of the output. Not ideal but it was hoped that in the worst case it could be read and rekeyed if needed. MacOSX was rather nice in that it was easy to install in the PDF button in the print dialog.

You might consider some of the Wiki options available. Gina Trapani makes the suggestion to try installing your own Wikipedia (which supports LaTeX) or Instiwiki. See Hacks #4 and #5 from Lifehacker (Chapter 1).

There are also lots of TiddlyWiki options developed explicitly for this. TiddlyWiki is light weight, simple, flexible, and can be stored on a flash drive. Oh, and because it's all done in JavaScript accessed via any modern web browser, it's portable. These TW lab notebook options often include the jsMath plugin which allows LaTeX to be used within the Tiddlers.

One old favorite is TiddlyWiki Student Edition (SE), which may or may not be useful for general lab note taking.

If you do more TiddlyWiki searching, you might find lots of options that work for you.

All of that being said, there's also the OpenSource Electronic Lab Notebook.

--
Ted Pavlic
http://www.tedpavlic.com/
http://phaseportrait.blogspot.com/

You might try the CERF-Notebook™, which runs great on Mac OS X and Windows. Made by Rescentris, it offers all the features you ask for as well as full 21CFR11 compliance, audit trails, etc. It's in use by many academic as well as commercial (pharma) organizations.

I agree completely with you Albert -- that's one reason that the "Teams" features in Leopard server look so compelling. You can set up group calendars, wikis and blogs very quickly for yourself or the research group.

As soon as Leopard server is released, I'll have a walk-through of setting up a group wiki for my group. A few key additions to your list for a good lab notebook or wiki IMHO:

- Attachments (i.e., being able to attach graphics, data files, program archives, source code, etc.)

- Authentication: one key requirement for paper notebooks as well as electronic lab notebooks is authentication and signing (e.g., for patent or legal requirements).

But as you said, a wiki is great for collecting information and keeping it organized. Being able to link between multiple entries is very useful.

If you have experience with LaTeX, try the labbook package (http://tug.ctan.org/cgi-bin/ctanPackageInformation.py?id=labbook).

Copy and paste is a given and since files are stored in ASCII text, they can be reopened for millennia to come. If you use pdflatex to publish the lab notebooks, you can use all of the metadata associated with a pdf. You can also take advantage of link creation for pdfs to link to older notes/graphs.

You'll have to take care of your own backups, but if you use an automated backup system that task isn't too onerous. Finally, you can use Disk Utility to save files in an encrypted DMG.

Matt Kizerian
Systems Engineer
ReliOn, Inc.
www.relion-inc.com

I have just prepared a new E-Labbook system. It's and integration between Wordpress (for Lab Blog) and phpBB (for labbok).
You can find some information at my site www.francescocimino.it
Actually my siste is under construction so just few information are reported. However I'm just preparing an HOW-TO build an e-Labbook.

Francesco