Wednesday, December 09, 2009

Motion Chart of NCBI data

The last decade has seen a huge increase in sequence data in public databases with an impressive increase in species coverage. Here, I have used Google's Motion Chart API and Google spreadsheet do illustrate the changes in numbers of sequences and numbers of species for different taxonomic groups. Whilst the nucleotide sequence increase against the number of species sequenced has been exponential for all taxonomic groups, the rate of increase in nucleotide sequences per species appears to have accelerated since 2007 for Fungi and Bacteria. The gap also seems to be widening between the number of nucleotides per species in the Metazoa compared the Viridiplantae. There appears to be no signs of a plateau and with the next-generation sequencers, we are likely to soon see an even sharper increase in the number of nucleotides per species. However, I suspect the rate at which additional species are added to NCBI might begin to slow as we find it harder to collect and sample novel species.

Tuesday, November 10, 2009

Berlin's eco-damaging styrofoam wall of dominoes

It is rather disappointing that the Germans decided to celebrate 20 years since the fall of the wall by generating 1000 styrofoam dominoes. Styrofoam is one of the most ecologically damaging materials we create. Where are all the blocks going to go now? Probably into a land fill and take hundreds of years to degrade. It is surprising that a normally environmentally conscious country like Germany would not think of such issues.
They could have gone for something more environmentally friendly.

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Tuesday, November 03, 2009

Which digital photo printing is best?

Following a previous blog and EditGrid spreadsheet, I got a comment about not including a quality comparison. Well Jon on the Gadget show has now done the job on 13 different companies. Colorama was a definite no no because the photos were all very faded.
Jessops got excluded but I missed the justification for it. OneView was the best but the most expensive at 73p per photo. So Jon chose Snapfish as the favorite because of quality and price.

Friday, October 23, 2009

Why I think a Phylogenetic Standard might not work

Currently we have many different formats for phylogenies (e.g., nexus, newick, extend newick, phylip, xml) and there is no doubt that putting in place a Phylogenetic Standard would be a good thing but just because a group of researchers get together and decide that a Phylogenetic Standard would be good doesn't make it happen. Unless the phylogenetic community is behind the decisions being made which is unlikely to happen any time soon as phylogeneticist already have a poor record of submitting their phylogenies to databases like TreeBase.
These are obviously points that you are aware of as you mention them in your statement. I only remark that unless publishers enforce a particular format and submission of the phylogenetic data into repositories (like GenBank/EMBL), then however noble the idea of a Phylogenetic Standard is, it is unlikely to be put into practice by phylogeneticists.

Installing DBD::mysql on MacosX 10.5

I was having real trouble installing DBD::mysql on my iMac (version 10.5.8) until I found this. So I updated my version of Mysql to Mac OS X 10.5 (PowerPC, 32-bit) from here following the instructions for updating from Marc Liyanage. And finally, it all worked. Thank you Marc Liyanage.

Wednesday, October 21, 2009

Pulling up text sections across multiple documents using searches and filters

Came across whilst reading the comments here. In you can
search and browse the text, tags and notes
any part of the text can be annotated or even regions of an image
In the tools section, you can get an index of all the tags and you can also get a text file with the notes taken.
Unfortunately it is not free so I have only played with the example files and I am not sure my links will work but I thought it could be really good tool to integrate into BHL, GoogleBooks and Mendeley for example as it has the ability to pull up text sections across multiple documents using searches and tags so collaborators can mark-up pdfs and share their tags and notes.

Tuesday, October 13, 2009

Wordle of keywords

I have been monitoring my blog with google analytics for a couple of weeks and wanted to see what the main keywords were that had resulted in a hit on the blog.
Wordle: keyword search
It seems like a number of people have been looking for a iphone app that identifies bird songs. I wrote a while back a blog suggesting that a version of Shazam that had bird songs included would be really useful but as it turns out Shazaam doesn't really work that well when you have a lot of background noise which is likely to be the case when trying to identify birds from their songs in the wild. I will keep my eyes open for such an app as it seems a lot of you are interested. Likewise, if you here about anything, please leave a comment here.

Monday, October 12, 2009

Zotero linked into Mendeley

Downloaded Mendeley 0.9.4 and now you can import all the references from Zotero. I didn't have too many refs in Zotero (844) so it didn't take too long to import them. After a couple of crashes, it now seems to work fine. I couldn't figure out how to import the pdf links unfortunately. I think this might be quite useful, especially as Zotero is so much better at importing the metadata.

Friday, October 09, 2009

Automating label print out from google lousebase

I have been messing around trying to improve lousebase so that I can have tube labels automatically print out. The idea is that from within the lab, I could use an iPhone or any phone with a browser to add information to lousebase and then the tube identifier and information on which box,row,column I should put the tube in would be automatically generated by google spreadsheet.

So here is the form that you would point your mobile device (wireless laptop, iPhone, web enabled mobile)which should look something like this:

This form is set-up so that when you add a new entry, a label is created on one of the sheets. If changes are made to the label sheet, I receive an email. I was hoping that the email would contain the changes so that I could automatically print out that email with an applescript called Pergamail, I found here.

Unfortunately it only says that changes have occurred on the page so I need to go back to the drawing board. I thought that maybe using the Google Data APIs would be useful but as I am behind a firewall, I think I might be entering a whole world of pain.

Tuesday, September 15, 2009

EndnoteX2, MacOS X and Word 2008 plugin

After half a day figuring out a way to get EndnoteX2 to "cite while you write" I thought I would share my wisdom. There are a load of compatibility issues with word, macs and endnote, have a look here. But the most important thing they don't mention is that you need to update your version of word 2008 with the most recent service packs. You can find these here. Hope this helps.

Friday, September 11, 2009

Using Barcodes in Google Docs

Barcode Software by TEC-IT

Barcode Software

Barcode generated by TEC-IT

Thinking of my future lab where I will have an iphone as a lab book to automatically update collection data in google docs and associate specimen tubes, extraction and PCR with barcodes that I will be able to generate and read with the iphone.

Wednesday, September 02, 2009

Wednesday, August 26, 2009

No citation plugin for Mac in Mendeley => Using Zotero

Mendeley still doesn't have a Word plugin for making citations. I tried for a while to sort out Endnote X2 with word 2008 and gave up. I followed all the suggestions I could find in the Endnote help and the EndnoteX2 submenu in word still didn't appear.
Zotero to the rescue. I installed Zotero version 2.0b6.5 and and the Mac Plugin for word 2008 and hey presto, it works! It works fine so it will do for now and I might be converted.

Thursday, July 30, 2009

What a rigmarole to signup to I had to send them a link to my webpage and then they asked me to put a link to labmeeting on my webpage and finally they let me sign up. It took 4 days!
If Mendeley took had the same strategy they wouldn't have 22,607 users with 2,723,657 articles. Couldn't find any stats for
Pdf data extraction was just as bad in Labmeeting as in Mendeley. In labmeeting you can't provide a doi lookup.

Tuesday, July 28, 2009 versus spotify suggests music that you might not have already heard off. Spotify relies on the fact that you know what you want to listen to.
You can find everything on Spotify, the tracks are a lot less extensive on, especially for classical music.
Spotify has ads in the free version.

Monday, July 13, 2009

Mendeley is getting better day by day.

Unlike some cynics, I think Mendeley is the bees knees! I am currently collaborating on two separate projects and sharing the references thanks to Mendeley couldn't be easier. Now it is even better, with integrated pdf viewer and the ability to highlight and make notes directly on the pdf.
I am sold, I really think it is the best reference manager social networking tool out there.

Thursday, June 04, 2009

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 1-45-4950-99100-149 150-199 200-299 300-499 500+
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
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
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.

Thursday, April 23, 2009

iPhone App to identify a bird song in the field

Bird VocalizationImage 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:
The comment by the user 'nature' is interesting
An education app

UPDATE 05/05/2011
This blog posts explains in a neat way how Shazam works:
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Thursday, March 19, 2009

Thursday, February 26, 2009

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.

Thursday, February 19, 2009


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.

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