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...