[Clutz]

Hey all,

I'm looking for some Wiki Software for OS X. I want to set up a personal wiki that I can use to as an electronic digital notebook for my lab notes. I'm slowly switching over to typing out all my notes and pasting them in my notebook from Word, but I thought this would be better- since its hyperlinkable this way. Ideally, I'd like to use something that uses an SQL or some other open source freeware database back end and that can run on Apache. Right now I just want to use it for myself, but if/when get my own lab, I'd like to implement this sort of a system for my entire lab, where the people in the lab enter their lab notes online everyday using a wiki-system where some pages can be closed for local use only, and others would be open for public viewing.

Any suggestions?

 

[jonathanjong]

Tiddlywiki?

 

[Clutz]

I've looked at it, but I want something with a heavier lifting back end- i need it to be a database. I'm thinking about forgetting Wiki altogether and just going with FileMaker Pro and developing something myself with it.

 

[blessingx]

Makes me think of DEVONthink (and it's AI), but not sure it's what you're looking for.

 

[Clutz]

A bit of background:

I'm a biologist so I have a lab notebook that I have to keep up to date. Every time I complete a procedure, whether it's completely routine, or totally new, I have to write down each of the steps of the procedure and take notes on it. If I make any mistakes- I take notes about the error- if I generate any data, it gets written down into the notebook.

Before I undertake a procedure, I first fill out my notebook describing each of the steps- then as I go through them I check them off. If I make any changes on the fly, they get written down in the margins. Normally this is all done in long hand and it goes directly into my notebook, but it doesn't actually work that well- for a bunch of reasons- terrible hand writing, it's not searchable, etc.

So what I'd like to do is be able to make an electronic lab notebook. That way I can type in the procedures I'm going to use. I can print them out and paste them into my lab notebook for working with on the bench, but I can also keep a digital copy on my computer. Any minor changes that happen while I'm following the procedure will be written into the printed notebook by hand, and then typed into the digital notebook after the procedure is finished. It'l be totally searchable, by date, by keyword, etc. Sometimes in the notebook I'll make reference to some work that was done days, weeks, months earlier- and it'll say "Turn to page 45 in notebook #3, date January 7th 2009". Then I have to haul that notebook out, find the page and look at it. This way, everything will be linkable- backwards and forwards.

I think that something like a wiki would work well for that, but because I want it to be completely searchable, I think it needs something like a sql backend. Right now I only have a few hundred pages of notes, but when I start to generate data, I'm going to fill up a lot more notes quickly.

I hope that accurately describes what I want to do. I Think there is a lot more I could do with it, but that's where I hope to start.

Brad

 

[jonathanjong]

Hm, sounds like some database software would be more suitable. That said, I'm using tiddlywiki for my PhD.

 

[D-EJ915]

Well one thing is to just try it out, apache, php and mysql are free why not give it a whack. There is tons of open source wiki software out there.

 

[Clutz]

Yes- that's what I'm looking for- suggestions for some wiki software that'd interface with apache, php, and mysql.

 

[thisbenjamin]

I would reccomend ubuntu-server as a platform, and either mediawikiManual:Running MediaWiki on Ubuntu - MediaWiki or the aforementioned wiki in an html file - it really is nice software.

It almost seems like you might want a specific app created for this task. It seems like something the biotech community should have developed open source by now, for free.

 

[Currawong]

MediaWiki runs in OSX as far as I know, you don't need a separate server, you just have to know how to set it up. MySQL can be downloaded an installed easily enough too. Also, you could run MAMP, which gives you a self-contained and more fully-featured Apache-MySQL-PHP install. You just have to make sure to back up the entire MAMP folder to back up all your data (but you're using Time Machine, right?). There are also wiki formatting toolbars for Firefox which should make it a bit easier.

The most basic wiki-like software you can get is VoodooPad, but it may not be featured enough for you. Filemaker is great for building your own database, if you take the time to build it, or build on an existing sample db. I think, regardless, you're going to be up for some serious experimentation before you settle on one piece of software, as they all have advantages and disadvantages.

 

[Clutz]

Quote:

Originally Posted by thisbenjamin /img/forum/go_quote.gif I would reccomend ubuntu-server as a platform, and either mediawikiManual:Running MediaWiki on Ubuntu - MediaWiki or the aforementioned wiki in an html file - it really is nice software. It almost seems like you might want a specific app created for this task. It seems like something the biotech community should have developed open source by now, for free.

Thanks for the suggestion, but I really want to run this on OSX. All my computers are Macs- although I will take a look into it. I could probably build a minimal desktop machine to run a ubuntu-server from. It'd need a pretty minimal processor- maybe 2GB RAM- and two smallish hard drives in RAID 1+0.

There is some specific biotech software for this, but I'm neither impressed by it, nor is it free. Biotech software tends to be extremely expensive- as most science / research software is, unfortunately.

Quote:

Originally Posted by Currawong /img/forum/go_quote.gif MediaWiki runs in OSX as far as I know, you don't need a separate server, you just have to know how to set it up. MySQL can be downloaded an installed easily enough too. Also, you could run MAMP, which gives you a self-contained and more fully-featured Apache-MySQL-PHP install. You just have to make sure to back up the entire MAMP folder to back up all your data (but you're using Time Machine, right?). There are also wiki formatting toolbars for Firefox which should make it a bit easier. The most basic wiki-like software you can get is VoodooPad, but it may not be featured enough for you. Filemaker is great for building your own database, if you take the time to build it, or build on an existing sample db. I think, regardless, you're going to be up for some serious experimentation before you settle on one piece of software, as they all have advantages and disadvantages.

I've looked at VoodooPad, and it isn't quite fully featured enough for me. I think I am going to try the Filemaker pro demo and give it a try, but the software Uncle Erik suggested also seems like it might be good possibility, but I'm worried that it's entirely proprietary. It is a pretty reasonable price thou $180 for the version I want, less 25% discount for academics. And it has scanner OCR support for old notes. Which would be awesome.

I'll take a look at MediaWiki and MAMP. Thanks a lot guys, this is exactly what I was looking for in terms of advice!