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 A.nnotate.com whilst reading the comments here. In A.nnotate.com 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.

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