My tag, my label = defining myself

Wordle from my publications.

6"x4" digital print comparison

Comparing digital photo online printing

I have only compared the price of 6"x4" (15cmx10cm) digital photos here and included the all important delivery charge which usually varies more than the actual printing prices.

No. of prints	1-4	5-49	50-99	100-149	150-199	200-299	300-499	500+
Photobox
Price	£0.10	£0.10	£0.10	£0.10	£0.08	£0.08	£0.07	£0.05
Delivery charge	£1.49	£1.49	£1.49	£2.49	£3.99	£3.99	£4.99-£5.99	£7.99
Jessops
Price	£0.25	£0.19	£0.12	£0.12	£0.07	£0.05	£0.05	£0.05
Delivery charge	£1.49	£1.49	£1.49	£1.99	£1.99	£0.00	£0.00	£0.00
Snapfish
Price	£0.09	£0.09	£0.09	£0.09	£0.09	£0.09	£0.09	£0.09
Delivery charge	£0.99	£0.99	£1.49	£1.49	£1.49	£1.49	£1.49	£1.99

Postage is additive for Photobox if you order a mix of calendars and posters or any type of mix. At Jessops, you can pick up your photos from your nearest store free of charge.

An the winner is Jessops for orders above 200 prints and Snapfish for orders below 150 and it is a close call between Jessops and Snapfish between 150 and 200 prints.

I will hopefully make a spreadsheet so that it is possible to calculate where you can get the best deal based on what you want printed. More of that later.

iPhone App to identify a bird song in the field

Image by nixam via FlickrWouldn't it be cool if you could use something like Shazam to identify bird songs out in the wild. Doing a quick Google search, I found a few websites with mp3s of bird songs, for example xeno-canto. Shazam might already work with bird songs but I wouldn't know because I don't have an iPhone. I would get one though if I could use as a bird song identification tool.

UPDATE 30/07/2010.
I've found a few interesting posts and comments on this topic:
http://originalprojects.com/projects/shazam-for-birds
The comment by the user 'nature' is interesting http://www.tuaw.com/2009/02/09/this-iphone-app-is-truly-for-the-birds/
An education app http://itunes.apple.com/us/app/chirp-bird-songs-usa-lite-v3/id352826689?mt=8

UPDATE 05/05/2011

This blog posts explains in a neat way how Shazam works:

http://www.soyoucode.com/2011/how-does-shazam-recognize-song

Rod Page's Talk Science at the British Library

Podcast of Rod Page's presentation for "Talk Science" at the BHL.

Mendeley profile and BiomedExperts

Mendeley definitely seem to be on the ball, they have actually bothered to comment on my blog. They also seem to be very open about their future plans and about making certain aspects of their software flexible for use by the users (i.e. formatting of your own citations styles).
What I think would be a cool thing to do, is to use the information from the My Publications to automatically create peoples profiles.
In BiomedExperts, I only needed to select my publications to have a profile generated with keywords that define the organisms, concepts and ideas I work on. It also used my co-authors to create a network of collaborators and addresses from my publications to create a GeoNetwork.
My profile is bare at the moment except for My Publications. It would be nice if it could be self-generating.

Mendeley

I have been doing a bit of a comparison between Mendeley and Papers recently because I haven't used Endnote for a while, actually since my last post on Reference managers. People suggected Zotero and EndnoteWeb to me, but I didn't like either of them.

I must say, I really love Mendeley as a social tool. It is great to be able to share pdfs with collaborators and to be able to access my references as easily at home and at work, especially since I have a PC at home and a mac at work.
Creating collections with all the associated metadata for publications is great. I haven't yet used the word plugin, so I will let you know shortly what I think of that. The down side with Mendeley is that you only have 500Mb of space online at the moment.

Papers is cool too, especially the fact that you don't need to open up a pdf reader as a separate program, you can do Google Scholar, ISI, Pubmed etc searches within Papers and automatically download pdfs if your instituion has access. You can highlight words in the pdf and do searches on those or highlight the doi and get all the associated metadata. Unfortunately, it only works and macs and doesn't have all the social networking aspect that Mendeley has.

Endnote, Connotea and GoogleScholar

What's good about Endnote:
It helps to format bibliographies in 100s of different styles
It provides easy access to your bibliography
What's bad:
What's the point of downloading stuff to Endnote, it takes for ever. Wouldn't it be best to leave it on the web.
It's a pain to sort your bibliography, you end up with loads of different libraries and often want to merge libraries or split them.
It's a pain to add book references as you usually have to do it manually or any other non-journal references for that matter.

What's good about Connotea:
Easy to add new references, you just need a doi or URL.
You can reference anything that is on the web.
You can tag your references and see you else (how many other people) have that reference in their bibliography
You can find out about popular topics really quickly
You can add other peoples references to your bibliography
What's bad:
It doesn't enable you to use your references in your manuscript, you first need to download them to your reference manager

What's good about GoogleScholar:
You can easily get access to references and the associated pdf
Easy search for words, sentences
Books and books sections are available as well as reports etc..
Duplicated articles on the web are removed through clustering
What'bad:
You can't make your own library of interesting articles
You can''t use the references to add into your manuscript
You can't download the references

What do we need?
We need to find some way of sharing our bibliographies on the web (like connotea) so that people can avoid having to type in references manually (which is often necessary for book references in Endnote) and at the same time avoid having duplications of the same reference (like GoogleScholar clusters) and crucially be able to insert a reference from the web directly into our manuscript whilst writing without having to worry about downloading it to our reference manager, because there will only be one reference manager for everybody which will be on the web shared with everybody and tagged diffeently by all the different users.
I can't imagine this being to complicated to do, not that I would know how to do it. The most important thing would be to create a tool that can be added to Word or LateX that enables the linking to the web reference manager and formats the reference section of our manuscript according to all the different formats used by the journals.

Eco-friendly shop for radiator insulation panels

I've been looking for eco-friendly shops to buy radiator insulation panels, I have come across quite a few new sites so I thought I would list them here:
CAPcarbon
earthwhile
ecomerchant
shopeco
ecotopia

Most of these site sell the same products and even use the same pictures, but prices do vary. It seems that CAPcarbon does not have a delivery charge which is good, but the cheapest price per insulation panel I could find (including delivery) was form earthwhile.

Good bye EQO, welcome TerraNet

The future of mobile phone calls is peer-to-peer. Lets hope it works! I'm not sure how EQO is doing these days as I got fed-up with using it. It just didn't seem to work that well on my mobile and I couldn't convince enough friends to use it so it wasn't really worth it financially (see my previous post). I think the peer-to-peer system could work well but it ultimately depends on how many people use it. When you think of how many people share their wireless connection say in New York compared to here in the UK, you might in fact think that it will never work in the UK because we are too selfish. We will just have to wait and see.

Plastic Bag Petition

People in Britain use an average of 300 plastic bags every year. Each bag lasts up to 400 years, spending the vast majority of that time in a landfill site or strewn across the British countryside. Have a look at dumped on channel 4 to see more scary statistics about how much we dump instead of recycling/reusing.

I have 5 cotton bags that I used when I go shopping and have been using for the past 2 years. It is great not to have a cupboard full of plastic bags and I feel much better walking home with my shopping in my cotton bags than in the orange Sainsbury's bags.

"In Ireland, a tax of 15cents per bag resulted in a 90% drop in plastic bag usage, and raised 3.5 million Euros which was spent on environmental projects." Now that sounds brilliant and if only the same could happen in Britain. I think it is important to show people where the tax-money is going, i.e. showing us that it is not just going into the government coffers and not being spent on environmental issues. It has to be visible improvements to make it easier for people to swallow more tax.

Please take a moment to sign the petition to introduce a similar tax (to be spent on environmental projects) of 10p per bag in Britain.

Carpenter/cabinet maker in Normandy

This is a friend's site, he has made some really nice wooden libraries and beds. He works mainly in Normandy but travels around quite a bit for big renovation jobs. Great website!

EQO mobile: the way I see it

Well it has markedly improved. It is easier to install and it doesn't use Skype anymore so you do not need to leave your computer running Skype.
But now you have an additional company to buy credit from instead of Skype credit. The other down side is that now you cannot IM for free Skype users sitting in front of their computers. You can only communicate for free with people who have installed EQO mobile on their phones and this is not entirely free as you have to pay your network provider for data transfer (unless you have an all inclusive deal). I think that EQO mobile has now lost interesting functionality. O.K. it was a pain to have your computer on all the time but at least you could communicate with the millions of Skype users. Additionally, the costs of EQO calls to Mexico for example are higher than they use to be with the Skype set-up.

Travel map

Installing tesseract command line OCR on MacOS X

Installing libpng from source:
http://kenno.wordpress.com/2006/04/20/compiling-libpng-for-mac-os-x/

fink install libjpeg, aspell, aspell-en

I will want to create my own aspell dictionary using taxonomic names:
http://www.mail-archive.com/code4lib@listserv.nd.edu/msg01545.html

Download and installing tesseract following install instructions:
http://code.google.com/p/tesseract-ocr/downloads/list

fink xpdf for pdfimages to extract images from a pdf:
>pdfimages -j LandPlants_paper.pdf LandPlantImg

To convert in imagemagick to tif for tesseract :
convert LandPlantImg.jpg -compress None test.tif

Using tesseract:
tesseract test.tif out.txt

I have now got a script to extract the names and check them against a dictionary of taxonomic names from spira.
I am thinking that using information from the article itself might provide even better results. When tesseract 2.0 comes out, there will also be a way of training the program to improve the character recognition. OCRupus also looks like an interesting program for layout detection but it doesn't work on MacOSx yet
The line extraction is proving to be much more difficult than first thought mainly because the lack of consistn format and the labelling at the nodes that get in the way of edge detection. I have tried a number of methods for cleaning up the image and bit by bit I will get there, I hope.

Advertising a holiday home for free on the internet

It's not that easy to find sites that let you advertise your holiday home for free, but I have found a few and I have listed them here. By far the most practical is gumtree as you can actually put photos and links to your website.
Craigslist is almost as good as gumtree. I think it is still very much biased towards the US market.
Google base is quite handy but in most item listings there is an expiry date. I did find one category that did not expire.
Gite-directory is quite good too and the webmaster is very friendly. The submission and modification of info is not that straight forward unfortunately. The site does say it protects your email from spam and sends you any enquiry emails without problem.
I was very impressed with the self-catering-breaks site that makes it very flexible and easy for changing photos and general information. The enquiry email works brilliantly.
I would rate holidaylease second as it puts paid advertisers on the same page as your add, but it does provide a calendar for your bookings which can be quite handy.
Then, there is the whole range of local classified adds like loot.com and exchange.co.uk that let you put a few words on their site. They don't usually let you put a link to your website but they usually let you provide an email address. Unfortunately, I found that the add and email were hijacked on glasgow-times.com and diverted to another ad.
Freewebsitedirectory allows you to put a link to your website with a description line or two.
http://www.frenchentree.com/ is a new one that says you can advertise for free but it is very difficult for users to browser as it is overloaded with info and advertising.
The HomeIsAway website lets you advertise for free for one year. Either you pay for the link to your site or you provide a link from your site to theirs and you get the link for free. That defeats the point though.
rent-holiday-home does not let you put a link to your site but you can upload images and text and locate your property on a map.

Branch thinning and tracking

I think I might have found a way to convert phylogenetic trees from image to nexus format through a process similar to that used in GIS map vectorization. This approach should also enable me to deal with trichotomies. The pattern matching approach that I had used previously turned out to be unsuccessful because of the many inconsistencies in tree drawing making it difficult to find a pattern that would always match a tip or a node. Line tracking offers hope!
All this would be so unnecessary if only researcher submitted their phylogenies to TREEBASE. Still, there are a number of phylogenies published prior to Treebase.

Thatched cottage to let in Normandy

Here is a lovely cottage with 3 bedrooms available to let on a weekly basis during the school holidays or over long week-ends in low-season. It is beautifully situated next to a river in the quiet valley of St Denis le Thiboult in Normandy. The owners are always welcoming and know all the nice places to eat and visit nearby.
Lovely thatched cottage to rent in Normandy | Self Catering Breaks
gite cottage let normandy

OCR taxa names from phylogenies

I have been trying out different open source OCR software, to recognise the taxa used in phylogenies. Tesseract (newly released by Google) did not fair as well as GOCR. If you train GOCR using a database of character images, it does even better.
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GOCR
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c(PICTURE)100 C. _asicus (14)
C. nasicus (_8)
C. jo_e_sjs (30)
C. co_fusoy (32)
C. coMfusoy (12)
C. su_cafu_us (_3)
C. su_cafu_us (68)
C. humey__is(_4)
C. vicoyiensis (_5)
C. p_y__lis (26)
C. vicfoyie_sÌs (54)
C. _ongi_e_s (16)
C. longi_e_s (19)
C. ve_osus (82)
C. veMos_s (166)
C. ve_osus (160)
C. ve_osus (149)
C. s__icivoyus
C.pe_lifus (131)
C. pellifus (151)
C. pellifus (192)
C. eleph_s (_18)
C. eleph_s (_13)
C. eleph_s (_16)
C. c___e (204)
C. cR_Re (205)
C. ca__e (208)
C. pyobosci_eus (58)
C. humey__is (56)
C. p_o_osci_eus (22)
C. scufel1_pjs (5)
C. nucu_ (117)
C. nucum (_43)
C. g____ium (_OO)
C. g__n_ium (gg)
Pakjsfan _p. (_1)
C. c__elli_e (49)
C. c__el_i_e (20)
__iica_ sp. (8)
C. p__yhoce_as (1)
C. p_y_hoceyas (16)
_______________________
GOCR using database option
_______________________
c(PICTURE)100 C. nasicus (14)
C. nasicus (28)
C. iowensis (30)
C. confusor (32)
C. coMfusor (12)
C. sulcatulus (23)
C. sulcatulus (68)
C. humeyalis(24)
C. vicoyiensis (25)
C. paydalis (26)
C. vicforiensÌs (54)
C. longidens (16)
C. longidens (19)
C. venosus (82)
C. veMosus (166)
C. venosus (160)
C. venosus (149)
C. salicivoyus
C.pellifus (131)
C. pellitus (151)
C. pellitus (192)
C. elephas (218)
C. elephas (213)
C. elephas (216)
C. cawae (204)
C. cawae (205)
C. cawae (208)
C. pyoboscideus (58)
C. humeyalis (56)
C. proboscideus (22)
C. scufel1aris (5)
C. nucum (117)
C. nucum (243)
C. glandium (200)
C. glandium (99)
Pakistan sp. (21)
C. camelliae (49)
C. camelliae (20)
Afiican sp. (8)
C. pyrrhoceras (1)
C. pyyrhoceras (16)

Installing GOCR using fink

sudo nano /sw/etc/fink.conf
fink selfupdate
fink index
fink scanpackages
fink install gocr