Sunday, 7 December 2008

iPod won't sync photos

I've just had a problem syncing my iPod Touch. I would get an error mid sync "The iPod "iPod Name" cannot be synced. An unknown error occurred (-50)."
I've done a lot of Googling for explanation and a fix, it took quite a while, so I thought I'd share.
The crash always happened when syncing photos. So after not getting very far with the usual suggestions I ignored all causes and fixes not relating to photos. The problem seems to have come from me replacing my iPhoto library with a different one since my last iPod sync. The solution (for me) was to delete the iPod photo cache folder.
  1. Find your current iPhoto library in the Photos folder
  2. Right (ctrl) click and select 'show package contents'
  3. In the new window delete the folder iPod Photo Cache
Tried syncing again. It told me that I had my iPod synced to a different library and did I want to delete all photos and sync with the current library. Yes! Sync worked fine after that.

This link helped more than any other.

Wednesday, 15 October 2008


I was investigating using GMail as online storage space today. It gives 7.2 Gigs of space now! I haven't decided on this or tested anything, but I came across a curious warning on the Gspace FAQ site. It said to be very careful that you put not if that was your address otherwise your files could potentially be sent to someone else's account!

I was momentarily panicked, thinking about all the mails I had been missing- I use both interchangeably when giving my email address. After a bit of testing (sending emails to both addresses from a different account) it turns out this is absolutely false. Both just work. I remember when I signed up it gave me the address but does exactly the same in all emailing and logging on options I have found.

Maybe there is some complex situation regarding the specifics of Gspace that I haven't appreciated but in terms of direct access to my mail account the two addresses seem identical. I'm considerably more relaxed now, but I still think I will set up a second account if I do decide to use it as a file server mostly in case uploading activity causes the account to be temporarily blocked.

Sunday, 28 September 2008

Zotero under fire

Zotero the excellent, free, open-source reference manager is under fire from its closed source competition via a law suit. Thomson Reuters the makers of the unstable and expensive market-leading Endnote software have sued George Mason University, the developers of Zotero, for "violating its license agreement and destroying the EndNote customer base" (Courthouse News Service). The complaint comes primarily from the fact that the latest version can import Endnote styles. I picked up on this from Neil Saunders' blog post who puts it really well
"Here’s my simple, black-and-white view of the world. The greatest achievement of the internet is the potential to set information free. There are free-thinking, forward-looking organisations like GMU who see this potential and act upon it. There are also organisations who see only threats to their corporate interests. Publishing corporations no longer control the flow of information to consumers and some of them seem to be struggling to accept this, adapt and move on."
Our support should definitely go to George Mason University who have moved the world forward and improved it with not just a piece of software but a great implementation of the open-source idea. This is software driven forward by users, in this case initially at the GMU's Center for History and New media. Comically there is also a claim that "GMU reverse engineered Reuters' EndNote software to create Zotero". I don't see any signs of that, thankfully they are not very similar in any meaningful respect, Zotero is generally much better. Zotero works nicely from within a web browser, Endnote works when it feels like it.

Zotero is not alone however. There are a growing number of free (though often not open source) web based reference management systems. Maybe Thomson Reuters are just trying to mark out some territory and delay the inevitable a bit longer. Ultimately they are going to fail, I just hope their lawyers don't hurt Zotero too much on their way down.

Saturday, 20 September 2008

Mobile Blogging

I'm trying out blogging from my iPod touch. I just downloaded the free app life something. Quite straightforward to set up.

Don't yet know the important details like if I can save drafts or edit posts or what the app is really called (it doesn't say on this page and i've forgotten). Will press "Done" and see what happens! LifeCast, that's it.

Posted with LifeCast

Google for pirates!

Apparently today is international talk like a pirate day. Google are always keen on adding languages and today added Pirate to their list of interface languages. Good.

Friday, 19 September 2008

How to migrate away from WordPress

Well it wasn't as straightforward as I first imagined. Google-searching found a lot of stuff, but it was almost all to move in the opposite direction. My reasons for moving back to Blogger are outlined in my previous post, maybe I was a bit naive to expect all the good stuff in the free version, plus I am becoming a huge Google fan and just feel good about being back at Blogspot. Ok not quite so many features in some places, but more in others, and much more reliable in my experience.

To try and import my previous posts from WorPres to Blogspot I chose to use the wxr2blogger python script found here. It worked quite well after two fairly obvious (in retrospect) modifications. First remember to prefix the command with "./" (this may be specific to Mac?). Secondly I needed to use the workaround detailed in the README file. After that, and repeating from the beginning, the conversion to something that blogspot could import was complete.

There were sill quite a lot of things to do however and I started to wonder if it was worth all the effort. On balance I still feel it was.

Images migrated, but as links back to the original post images. I didn't like that, they didn't look quite right, text didn't wrap, so I exported them all to my desktop and reimported them to the new blog.

Comments migrated perfectly! I wasn't expecting that. Unfortunately some spam comments also carried over and needed to be deleted. Strange really since they weren't visible as comments on the WordPres site.

The script unfortunately exports posts in small batches, since apparently blogspot refuses to import large batches of posts. It took a while to import, check and post everything. Many "posts" were created that were blank, and I had to delete. I had about 4x as many posts after using the script as I actually had on Wordpress.

Anyway, all done now. Thought someone might find my experiences useful.

WordPress no more

This is my first genuine post on All the previous posts were imported from the WordPress version of the blog. I wanted to try WordPress because of all the really nice looking blogs I had seen. It never really worked for me though.

None of those nice templates are available on the free version, nor can you import templates.

There was always weird stuff going on. The font would change on different days. Why? At least one link just evaporated.

Most annoyingly of all WordPress intercept me trying to log on and redirect me to a screen persuading me to set up a second blog. Entering the same url a second time however does get me on. Anyway that bit of marketing was the last straw.

Sunday, 17 August 2008

iPod fix

I recently had a problem with my iPod touch where some (but not all) applications would refuse to launch or immediately crash back to the main screen. Downloading them a second time did not change anything. I'm running version 2.0.1 software. I didn't find anything useful when searching the web yesterday. One of the reasons to post on this blog was to add to the Google searchable pool of stuff that is out there. I followed a link to the iPod touch troubleshooting page, and decided to restart the iPod by holding the top sleep/wake button until the red "Restart" slider appeared. After restarting everything worked just fine, some applications for the first time. Yet another triumph for the turn it off and on again strategy! It hadn't actually occurred to me that I had NEVER retarted my iPod, only toggled it between wake and sleep.

Amazing things the iPod touch (and iPhone). I almost never put the headphones in, just use it as a mobile internet device. Typing is very quick and very intuitive. The screen quality is sensational for photos. I use Google notebook, Evernote and Zenbe lists as productivity devices. Gmail, Google reader, and Safari web browser are excellent too. Email yourself a PDF and you can browse it at leisure, even if offline. Yes the screen is big enogh for this. Lots of new (often free) applications appearing daily, it reminds me of how Palm was years ago before they fell asleep.

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.

Sunday, 29 June 2008

Dropbox- realtime file syncing

Dropbox is a multi-platform solution to syncronize files across machines. I'm not going to review it here, check out the website. Its in beta invite-only release now. 2GB of free storage. The point of this post is that I have 10 invites to give away. Email me if you want one (see the About button above for my email).

Friday, 27 June 2008

PDF manipulation

Some journal publishers (e.g. Science) put a really ugly and uninformative cover page on downloaded PDFs. I have been looking at writing a script to either delete the first page of a PDF or to shuffle the first page to the end. I particularly wanted to do this because I use the excellent application Papers to manage my PDF collection. This gives a preview of the PDF by showing the first page- fine unless that is the cover sheet. There are a couple of command line options to manipulate PDFs including pdftk. I was thinking to turn the script into a droppable application and then I could keep it on my desktop and just drop PDFs onto it to convert.

Now just this morning I have realised that this is really easy to do in Preview, Apple's integrated PDF viewer. Just view the thumbnails of the pages and drag the first page to the last. Or select it and delete. I guess it would be good to have a script to batch process lots of PDFs, but this is very straightforward indeed.

I can't believe I didn't realise this before. This is especially useful since Papers has an "open in Preview" command.

Thursday, 19 June 2008

Zotero- have I upgraded too fast?

I might have spoken too soon about Zotero the bibliography tool. Although it looks great in Firefox3 when I actually came to use it today after a while of only thinking about writing stuff I discovered that I had broken it. I upgraded to Office 2008 (OS X) a couple of months ago and the Zotero toolbar only works with the previous version of Word. Also in the past when I have been using ISI Web of Science a beautiful little import button has appeared in the title bar when viewing records and just clicking it imported the reference in to Zotero. Now its gone. WoS has gone through a website update this year and maybe that killed it. So I exported all my references from WoS (in several formats) but couldn't get them in to Zotero. I could see how to get references from other bibliographic tools but WoS no way. I'm sure this used to work for me. The excellent forums didn't help me much on this occasion.

I have used Endnote since my PhD, but it has always been very buggy and unreliable on Macs (unlike PCs I believe). I got to a stage a few years ago where it was almost unusable, and I saw no signs of them updating the Mac version. I bought a copy of Bookends, which was great, but decided not to pay to upgrade to the new version 10 because I saw Zotero as the way to go. I still do, but wish it just moved a bit faster. I may have to spend the money on Bookends though as I can't live without a working bibliography tool. Sad, I see so many really good aspects to Zotero, but maybe I'll have to abandon it until the next major upgrade.

Wednesday, 18 June 2008

Mind Maps from

There's quite a lot of software out there for creating mind maps (those diagrams of linked text bubbles). Generally they are great for brainstorming and seeing the big picture before launching into a project. I have used them very little (at least electronically) because the software tends to be feature-rich and cost money, be very very ugly, and make it difficult to synchronise brainstorms between my home laptop and work machine.

I recently came across which I appreciate. It is a free, simple, but well thought-out web application. There is a good real-time help pane, but it is hardly necessary it is so intuitive to use. Since it is web-based there are no issues in failing to sync. I'm not sure if it would meet the needs of power users but for the rest of us it is definitely worth looking at. If you want to keep maps between sessions you will of course have to set up an account. There is also the option to just click and try it without logging on.

Firefox 3 and Add-ons

I really love the new Firefox3 release. I've had beta version before but just updated and all my add-ons are also updated and are working nicely. The firefox Add-ons page can be found here. I previously managed to seriously confuse my bookmarks by upgrading and then downgrading to Firefox2. Don't try this.

I have also now swapped to using the social bookmarking site. This has really nice integration with Firefox3, adding buttons to quickly bookmark a site. The best thing for me is that the left panel where bookmarks are typically listed in a browser can now toggle to display bookmarks complete with a searchable listing of tags. It is really slick. Very quick, well designed and much much more useful than tradiational bookmarks. I had got to the stage with Firefox2 where I was Google searching for sites that I knew were in my bookmarks because it would be faster to find them that way! The tag-based approach to data is so powerful I just groan when I see programmes not supporting tags.

Also in my add-ons is Zotero. This is an extension to help collect, manage and use bibliographic information. I'm an academic and spend a lot of time collecting journal articles. Zotero deserves a post by itself, soon I hope.

Lastly is Google Notebook. I don't really use this as a notebook for manually typing information (I use Journler). But Google Notebook has a great web-clipping function. OK this is also found in other software too but Google's implementation is pretty fool-proof.

Sunday, 15 June 2008


Parsers is a graphical user interface for text parsing operations. Developed by the same guy as produced the excellent Journler software is is likely to progress well. Although much of the functionality is usually accomplished by scripting and langages like perl manage this very well that approach isn't for everyone. The GUI is nice and the functionality looks good. The application is described like this
Parses is “drag and drop text parsing and data mining”. The app is designed to help you preprocesses data so that you’re left with only the information you need in a format you can easily apply elswhere. In a visual environment you create and test re-usable, rules based documents for parsing well formatted text.

For example, let’s say you want to download your local weather information from an online feed. The temperature, conditions and forecast change by the hour but the html in which that information is contained otherwise stays the same. That is, the relevant information or variables change but the format remains constant. Parsers helps you extract the temperature, conditions and forecast from the feed so that you can use the information elsewhere, in a widget, your own webpage or a spreadsheet for example.
I haven't had much chance to play with it yet, but it looks interesting for small repetitive tasks.

Why blog?

I am starting this blog to post computer/ software/ web and tech related stuff. Yes there are millions of blogs out there that do this already, but thats the point. When I can't find out how to do something I Google it and often hit someone's blog that describes a little bit of tech-trivia really well. I hope that I can do the same for someone myself.

Also, blogs are a good place to organize your thoughts and keep a record of how you solved challenges that are good for future reference.

I already have a blog for work-related stuff called EvoPhylo. I realized (from reading other people's blogs) that mixing disparate topics is not a good strategy so I thought I'd start this to keep things separate. I also wanted to try out WordPress too.

What I intend to post about and what I actually will do may not be identical, but here is how I see it at the moment
  • Web solutions; I'm starting to discover a lot of nice web software and data-managemnt tools that probably fall under the web 2.0 moniker
  • Productivity; Getting Things Done (GTD) and the like
  • Software (OS X); biased towards information organization
  • Google stuff; Documents, Notebook, Sites etc etc
  • Technology; hardware, not all of it, biased towards info storage and web access
Lets see how it goes...