Sunday, 27 July 2008

Summer typin'; switch to the dark side

I've just learned how to swap my display to a negative image (OSX 10.5.4). This provides a really great way to use your laptop in the garden on a sunny day rather than going to work.

System preferences -> Universal Access, then check the radio button marked White on Black (in the Display section). The keyboard shortcut is ctrl-alt-cmd-8 (the 3 buttons to the left of your space bar and the number 8). It looks freaky, and is really useful in bright light. Unfortunately I haven't yet worked out how to take a screenshot for this blog (this picture was borrowed from the Apple site). Screenshots look great until you turn the screen back to normal (press the same 4 buttons) then you realize that the screenshot didn't reflect the negative image, it just looked like it did.

Anyway if you have an issue with screen brightness or contrast or just getting tired eyes from working in front of a big white page this might be useful.

Thursday, 17 July 2008

Fink and ftp proxies

I have being trying to use the fink program to install other applications. Fink describes itself like this
"The Fink project wants to bring the full world of Unix Open Source software to Darwin and Mac OS X. We modify Unix software so that it compiles and runs on Mac OS X ("port" it) and make it available for download as a coherent distribution. Fink uses Debian tools like dpkg and apt-get to provide powerful binary package management. You can choose whether you want to download precompiled binary packages or build everything from source."
Although I had fink working well on my previous iMac, it has been refusing to work for a while now on a range of new computers. It just fails to make a connection.I had 2 hypotheses- (1) the Univesity have introduced some unseen security that prevents it from connecting (they don't like ftp) or (2) I had messed up some setting.

Something I saw in fink FAQ this week rang some alarm bells and made me go back to check my settings.

Issuing a fink configure command allows you to change lots of settings including proxies. I knew that I would have to go through proxies for both http and ftp. It turns out that my ftp proxy was not prefixed by ftp:// -instead only the address was given. I suppose I had assumed it would fill this in since an ftp address MUST begin ftp:// but no. Actually the fink instructions at this point give an example address beginning http:// which should also be ignored.

Stupid really in retrospect, I should have spotted this earlier. Anyway this solved the problem.

Web of Science and Zotero

I don't want to turn this into ZoteroBlog, but since reference managers are major productivity software for me and Zotero is changing and improving very rapidly here is another installment. Some of my previous worries about Zotero not coping well with Web of Science have been fixed. The handy little import this reference or this collection of references buttons are back in the Firefox URL bar.

Also I now understand how to get references out of WoS and into Zotero by export/import. To do this mark the references you want. Then go to the marked reference list and tick the info to export (ie check the abstract button). Select BibTex from the menu at the bottom and Save. BibTex is imported very well by Zotero.

Wednesday, 9 July 2008

Turn it off and on again

I said below that Papers (the PDF management tool) may or may not be playing nicely with dropbox synchronisation. I investigated some more and discovered 2 things. Firstly dropbox had stopped syncing, I don't know why, so I restarted it. It lept into action and updated my Papers folder and others from changes I had made last night at home (and had clearly made it onto the server). Secondly I noticed that it had partially mangled my open Papers database, but only for the records that had changed. So for 3 or 4 records I had the info in my local Papers copy (work) but had updated the records at home. It now said that these PDFs were missing. I restarted Papers and now everything was perfect, all PDFs were found, all modifications for records (whichever machine I had made them on) were sensibly amalgamated. Obviously this isn't an ideal situation but at least the tried and tested "turn it off and on again" is a very simple solution to occasional problems.

Using Endnote bibliography styles in Zotero

I just downloaded and tried installing an Endnote style. It worked beautifully. Although how to do it seems obvious to me now, it didn't 15 minutes ago, so here is what I did.
  1. Go to Endnote styles page and download the styles you want.
  2. Open Zotero and open the preferences pane, choose Styles from the icons at the top
  3. Click the + button at the bottom right corner
  4. A window appears allowing you to select and import the style from wherever you just saved it

It should then appear in your style list. I just did this for BMC Evolutionary Biology which you can see in the window screenshot given here. I haven't yet investigated whether you can batch import files.

Zotero 1.5 Sync preview

Zotero 1.5 Sync preview is an update to the mostly excellent Zotero reference collection and management software. The big change here is that your references can now be synchronised across machines via the Zotero server. I haven't experimented very much with it since the launch yesterday but after a quick look it seems excellent, a very helpful addition. Another big change that was mentioned is the ability to use more than 3000 Endnote bibliographic styles to format your citations. I couldn't quite see how to implement this, but I only really played with Zotero1.5 for about 10 minutes last night so it might be in there. It requires Firefox3. Now if they could only get Microsoft to fix MS Word 2008 to accomodate bibliography tool bars again we would be there. I saw a blog recently (forgotten where) with someone saying that an institutional licence for RefWorks is around $10k. Zotero is free, and does all the same things, often much better, than RefWorks. It is also a community driven open-source project and needs supporting for that reason alone.

Dropbox in action

I've been running dropbox on my home laptop and work desktop for a few days now. It seems to be working amazingly well. Very user friendly, very quick. I have moved my data folder for Things (a GTD application) to the dropbox folder and after pointing the application to where its data had moved to it has worked flawlessly. My home and work machines are perfectly in sync. Now there are many other sync options but this one has the advantage of not having to remember to do anything, ever. The application at home and work are always in sync. I do not have to remember to press "sync" or close an application or anything. Remembering to sync before going home has be the cause of the failure at all previous sync strategies using a variety of sync software. Dropbox syncs continuously though in realtime.

I have also synchronised my Journler application. It has worked flawlessly again, even though I have the application open on 2 machines simultaneously (although I am only modifying one at a time obviously).

Papers has not been so smooth. I still need to investigate whether it is syncing properly or whether I am just imagining that some things are not updated. It could be that the application doesn't write some data until it is quit, that would certainly cause problems I guess. More experimentation required.

I have also moved my folder of perl scripts to the dropbox folder. Not only does this sync between home and work but includes a versioning protocol. So if I modify a file I can go back and examine previous versions of that file and revert to one if I have messed things up. I know that svn etc do something similar but this has been idiot proof and has not required all the messing around to install that subversion seems to take.