Wednesday, November 28, 2007

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
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.

Tuesday, November 27, 2007

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:

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.

Tuesday, September 11, 2007

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.

Wednesday, September 05, 2007

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.

Thursday, August 16, 2007

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!

Monday, July 09, 2007

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.

Wednesday, July 04, 2007

Tuesday, July 03, 2007

Installing tesseract command line OCR on MacOS X

Installing libpng from source:

fink install libjpeg, aspell, aspell-en

I will want to create my own aspell dictionary using taxonomic names:

Download and installing tesseract following install instructions:

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.

Tuesday, June 12, 2007

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 and 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 and diverted to another ad.
Freewebsitedirectory allows you to put a link to your website with a description line or two. 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.

Thursday, June 07, 2007

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.

Thursday, April 12, 2007

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

Wednesday, March 14, 2007

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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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

Thursday, March 08, 2007

Juicing apples

Using Braeburns at £1.28/kg, I got 375ml from 0.740kg, so you get 0.5mL per gram. This means that 1L of Braeburn apple juice would cost £2.52 per Liter. That is quite a bit! Actually more than some pear juices. The juice was tasty, clear, tasting slightly like cider (farm-yardy/earthy).
Royal Gala, my personal favorite. Price of £1.18/kg. From 0.48kg, I got 325mL. That £1.75 per Liter. That's half the price of Braeburn and it is a much sweeter juice, it looks slightly pink, but maybe does not have such a strong apple flavour.

Tuesday, February 13, 2007

Syncing motorola L6 mobile with iCal and Google calendar: gcalsync doesn't work on my Motorola L6.

This is how I want to sync it :
Contacts are sourced from my phone + Thunderbird at home
Calendar is sourced from Google Calendar when away + iCal at work + Thunderbird at home via ScheduleWorld
I only want to synchronize my mobile when I'm at home because I have bluetooth at home and don't want to have to carry around USB cables
I don't want to synchronize of WAP because I am cheap and my mobile network provider charges me for data transfer.

First use Spanning Sync to synchronize your Google Calendar with iCal.
Then use ScheduleWorld to sync Google calendar to Schedule World.
At home, install the TSync Thunderbird plugin for syncing the contacts.

gcalsync didn't work on my Motorola L6.

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Monday, February 12, 2007

Juicing carrots

I'm still trying to find the best fruit and veg to juice in terms of mL per pound. Carrots seems like quite a cheap veg to juice. For 463 grams of carrots (0.69/kg) I got 255mL, this means that it is £1.17 per litre. Almost half the price of juicing a pear.
On a related issue, did you know that the government is charging 17.5% on natural juice and smoothies whereas foods (burgers and ready-made pizzas) are not taxed. It doesn't quite seem right that good healthy juice is taxed the same as coca-cola. They are suppose to be encouraging use to eat and drink healthily.

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