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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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

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.

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.


Technorati Tags: motorola, thunderbird, ical, macosx, XP, sync, scheduleworld

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.
carrots VAT tax juice smoothies

EditGrid for scientist

Sharing data and results with EditGrid could be a biologists dream but will they ever want to share data in the same way as other researchers (e.g. economists or computer geeks)? There is no doubt that sharing scientific data would accelerate the pace of research especially in the slow moving fields like taxonomy and systematics. It is also important to put information into the public domain especially as most of the grants we are funded with come from the tax payer. See "Of lice and birds" for further details of my grand plan.

RSPB funds conservation of marshes in Poland

The RSPB have yet a again made history. They are providing several thousand pounds to support the management of marshes in Poland that host 80% of the threatened species in Europe. It is a shame that we are having such an impact on the environment and continuing to inflict such destruction. I recently went to a lecture on the conservation of bumblebees. A little known fact is that 3 bumblebees have become nationally extinct due to man's pressure on the environment. Many more species are under threat. Unfortunately, these poor creatures that are vital to the functioning of our ecosystems (especially for pollination) do no receive the sort of coverage they deserve. A recently set-up Bumblebee Conservation Trust is trying to remedy this. Please be generous with your donations.
biodiversity climate change conservation

The forensic use of bioinformation: ethical issues

My thoughts about the use of DNA samples and the National DNA Database which is the largest in the world.

List of questions


1. The interpretation of bioinformation

a. In your view, is the SGM Plus® system, which uses ten STR markers, sufficiently reliable for use in ascertaining the identity of suspects in criminal investigations and/or criminal trials?
No, Balding (1999) suggests using 11 STR markers and the FBI use 13. We should use as many as possible.

2. Sampling powers

a. From whom should the police be able to take fingerprints and DNA samples? At what stages in criminal investigations and for what purposes? Should the police be able to request further information from DNA analysts, such as physical characteristics or ethnic inferences?
The police should only be able to take DNA samples if someone has been cautioned or they have reason to suspect the person was involved in a crime. DNA samples should only be taken once the police have sufficient evidence to charge the person. The police should be able to request further evidence from the DNA analysts from the crime scene DNA samples if they have no other leads.

b. Should police expenditure on bioinformation collection and analysis be given priority over other budgetary demands?
No, police expenditure should be prioritised towards training more police and increasing wages.

c. Do you consider the current criteria for the collection of bioinformation to be proportionate to the aims of preventing, investigating, detecting and prosecuting criminal offences? In particular: is the retention of bioinformation from those who are not convicted of an offence proportionate to the needs of law enforcement?
No. The recent developments that enable police to take and keep DNA samples from anybody they stop, whether they are charged for an offence or not, is totally disproportionate to the aims of providing justice to society. DNA information should not be retained if the person is not convicted.

d. Is it acceptable for bioinformation to be taken from minors and for their DNA profiles to be put on the NDNAD?
No. Only if the minor is charged with an offence should the police be able to take a DNA profile and only if the minor is convicted should they be able to keep the DNA profile.

3. The management of the NDNAD

a. Is it proportionate for bioinformation from i) suspects and ii) volunteers to be kept on forensic databases indefinitely? Should criminal justice and elimination samples also be kept indefinitely? How should the discretion of Chief Constables to remove profiles and samples from the NDNAD be exercised and overseen?
No, it is not proportionate for either I) suspects or ii) volunteers bioinformation be kept indefinitely, nor should criminal justice and elimination samples be kept indefinitely. Volunteers and unconvicted suspects should be asked whether they want the bioinformation removed from the database after the case has been closed.

b. Is the ethical oversight of the NDNAD adequate? What, if any, research on NDNAD profiles or samples should be permitted? Who should be involved in the oversight of such databases and granting permission to use forensic DNA profiles or samples for research?
No, the ethical oversight does not seem to take into account the human rights of the person. The information is being treated as data without consideration to whom the bioinformation belongs to. A committee that includes representatives from the police, from human right organisations and ethical organisations should determine whether certain research should be permitted on the DNA profiles.

c. Who should have access to information on the NDNAD and IDENT1 databases and how should bioinformation be protected from unauthorised uses and users? Should forensic databases ever be made available for non-criminal investigations, such as parental searches, or the identification of missing or deceased persons?
Police detectives should have access to the information on the NDNAD and this information should be used for the identification of missing or deceased persons but only used for parental searches if it is a criminal investigation. Parental DNA tests in non-criminal investigations could be carried out by companies.


d. What issues are raised by the transfer of bioinformation between agencies and countries? How should such transfers be facilitated and what safeguards should be in place for the storage and use of transferred data?
The British government should be able to ensure that the bioinformation is not being kept by the foreign government, if the person is not convicted for the offence and data should only be shared with foreign governments if the person is a suspect in a criminal case.

4. Ethical issues

a. Is the use of DNA profiles in ‘familial searching’ inquiries proportionate to the needs of criminal investigations? Do you consider the use of familial searching may be an unwarranted invasion of family privacy?
No, ‘familial searching’ is an unnecessary invasion of family privacy.

b. Certain groups, such as ethnic minorities and young males, are disproportionately represented on forensic databases. Is this potential for bias within these databases acceptable?
No, this bias can put certain groups or minorities under greater suspicion.

c. Is it acceptable that volunteers (such as victims, witnesses, mass screen volunteers) also have their profiles retained on the NDNAD? Should consent be irrevocable for individuals who agree initially to the retention of samples voluntarily given to the police? Are the provisions for obtaining consent appropriate? Should volunteers be able to withdraw their consent at a later stage?

No, any volunteer should have an automatic right to withdraw their bioinformation from the database if unconvicted when the case closes. Keeping this type of data, increases the chance of ‘innocent’ matches and automatically increases the risk of suspicion against someone who was in the vicinity of a crime scene even if they were there several days before the crime.

d. Would the collection of DNA from everyone at birth be more equitable than collecting samples from only those who come into contact with the criminal justice system? Would the establishment of such a population-wide forensic database be proportionate to the needs of law enforcement? What are the arguments for and against an extension of the database?
Yes, the collection of DNA of everyone at birth would be more equitable, but it would NOT be proportionate to the needs of law enforcement. There are in my view absolutely no arguments for the extension of the database. Civil liberties and human rights are central to the democratic process.

5. The evidential value of bioinformation

a. What should be done to ensure that police, legal professionals, witnesses and jury members have sufficient understanding of any forensic bioinformation relevant to their participation in the criminal justice system?
Education must be improved so that all strands of society have a better understanding of forensic bioinformation. Courses on DNA forensics and the necessary statistical tests used should be provided to police, legal professionals, witnesses and jury members so that they can make informed decisions in a court of law.

b. How much other evidence should be required before a defendant can be convicted in a case with a declared DNA match? Should a DNA match ever be taken to be sufficient to prove guilt in the absence of other evidence?
A DNA match should never be taken alone as evidence of guilt. Proof that the person was present at the time of the crime and motive for the crime should be prerequisites.

6. Other issues

a. Are there any other issues, within our terms of reference, which we should consider?
Citizens should be able to know at any one time, the bioinformation that is being kept on them and the reason why this bioinformation is being kept.

freedom DNA bioethics forensic liberty ID

Colliding galaxies: beauty!