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.
________________________________
Tesseract
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___________________________________
GOCR
___________________________________
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.


Technorati Tags: , , , , , ,

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.

Thursday, November 30, 2006

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.

Wednesday, November 29, 2006

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.

Thursday, November 02, 2006

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.

Tuesday, October 17, 2006

Thursday, October 12, 2006

Reduce, re-use, recycle

As anybody seen the TV program "It's mot easy being green". They should have used this as the sound track.

New mouse species on our doorstep.

It is not often that a new mammal species is discoverd in Europe. After careful comparisons of the different mice species on the island of Cyprus, Bonhomme et al. (2004) considered the Cyprus mouse to be sufficiently different to the other known mice in the region to name it as a new species: Mus cypriacus. Sorry, but can't find a photo.

Wednesday, October 11, 2006

Punk finch


A multicolored punk finch (Atlapetes latinuchus yariguierum) has been named as a new bird species in Columbia. It is not often that scientists discover a new species of bird.

Friday, October 06, 2006

Best pears to juice

I have recently bought a juicer and have been testing which pears are best for juicing.

2 Conference pears weighing 480g provided 300mL of juice: 0.62mL/g at a price of £2.40/L
The juice was sweet, creamy but not powdery and gave an olive green colour.


2 Comice pears weighing 510g provided 375mL of juice: 0.73mL/g at a price of £2.36/L
The juice was thick with small bits, pulpy, sweet and a muddy brown colour.


2 Williams pears weighing 285g provided 125mL of juice: 0.43mL/g at a price of £3.47/L
Very thick juice almost like a smoothy, strong pear flavor with a creamy brown colour.

I would suggest using Comice pears for juice as they provided the most juuice per gram although Conference pears are probably just as good as they are usually a bit cheaper so the price per mL is very similar.

Friday, September 22, 2006

Skype on your mobile=> EQO

O.K. I have now used EQO to phone a landline in Mexico city, these are the details.
Virgin mobile, my mobile carrier charged me the following:
21:52:29 Accessing other sites £0.03
21:52:29 Accessing other sites £0.04

I think these two separate charges are for the initial connection to EQO and then the actual call.
The call didn't last but here are the Skype details:
21:55 SkypeOut to my mobile for 00:00:45
21:55 Skypeout to Mexico city landline 00:00:36
With a cost of £0.1548
The total cost to phone a Mexico city landline from my mobile using EQO and Skype for 36 seconds was 22p, calling using my Virgin carrier would have cost 80p.

Thursday, September 21, 2006

EQO revisited

Well, I managed to install EQO on my motorola L6. I use virgin mobile but as this was not an option as a carrier, I selected T-mobile as Virgin piggybacks on T-mobile. Installation was straight forward although I had to install Opera mini onto my mobile as the virgin browser wasn't letting me download EQO.
Installation was not to bad but the pricing system is far more complex. I phone France for 1 min and these are the pricing details:
Virgin charged me twice for data transfer
21-Sep-06 10:41:28 Accessing other sites £0.03
21-Sep-06 10:41:28 Accessing other sites £0.07
And Skype charged me twice:
21/09/2006 10:42 My mobile 00:01:02 duration
21/09/2006 10:42 France, Landline 00:00:47 duration
This cost me €0.22=£0.14
TOTAL COST of £0.24
This is mainly the cost of the SkypeOut from my computer to my mobile for the initial connection (£0.166 including VAT). I've actually been charged a bit less.
Calling France would normally cost me £0.40 per minute with Virgin.
EQO seems a bit cheaper. Next time I call, I will spend a bit more time on the line and I will report back to you. I think that if Skype and EQO got together to give more appropriate information about pricing, they might get a few more people interested.

Wednesday, September 20, 2006

EQO pricing

With virgin mobile the cost of data transfer is 0.5p/kb and apparently with EQO it wuld be possible to make over 100 calls with 1Mb of data transfer. This would mean approx 10kb for 1 call, i.e. with my mobile provider this would cost me 5p. Then, we need to add the cost of the SkypeOut call to your mobile to make the initial connection, this will cost an additional 15p.
The rest is priced as follows:
- For an incoming call to your EQO wireless Skype phone from a Skype buddy there will be no additional charges.
- For an outgoing call to your Skype buddies there will be no additional charges.
- For an outgoing call to a landline or cell phone you will be charged the appropriate Skypeout rates on top of the Skype out rates for the incoming call.
So it would cost me a bit more than 26p to make a 1 min phone call to a landline in Mexico and an extra 6p per additional minute. Whereas phoning Mexico without using EQO and SkypeOut would c ost me 80p per min. I think it could be worth it. I will see whether I can install EQO on my Motorola L6.

Monday, September 18, 2006

New species in Indonesian water

Amid all the recent tragic news about disappearing species, scientist have managed to find approx. 20 new marine species in Indonesia.
Lets hope that Conservation International manages to protect the area before these very localised species disappear.

Technorati Tags: diversity "new species" discovery wildlife

Tuesday, August 15, 2006

More obese in the world than starving people.


I find this BBC news article particularly worrying but unlike the scientists who carried out this research, I don't think that subsidies for fruit and veg are going to change anything. Rather, the companies which produce foods that cause obesity or have any known effects on human health should be heavily taxed and the money directed towards the hospitals and sport centers.

Tuesday, August 08, 2006

EQO and EpyxMobile


Image CC Thomas Favre-Bulle

In an effort to find out whether it was possible to use a bluetooth enabled mobile as a headset for Skype, I have come across some interesting software.
The clever EQO software which you need to install on your PC and your phone enables you to phone from anywhere to anywhere for SkypeOut prices. If I understand correctly, when you make a call to a Mexican landline for example, EQO software on your mobile contacts your computer via some EQO server, for this you will be charged by your mobile carrier for data transfer, then EQO on your PC uses Skype to SkypeOut to the Mexican landline and then SkypeOut to your mobile so essentially it will cost you 2p + carrier data transfer cost to phone Mexico from your mobile.
But really what I am looking for is a way to have something similar to BT fusion, i.e. a set up that would enable me to call for Skype prices when I am at home using my mobile so that I don't need to use a headset and don't need to be in front of the PC.
Now EpyxMobile is close enough to what I wanted as you can see from this Skype article for mobiles. Unfortunately, I have been unable to download the free software for the time being so have been unable to test it. Sorry!

Wednesday, August 02, 2006

Disqus for Evo-Karma