Ed's Blog

Create Drupal 7 biblio nodes programatically

noreply@blogger.com (Edward Baker) — Wed, 30 May 2012 17:47:00 +0000

The biblio module for Drupal is almost certainly essential for anyone trying to use Drupal as a platform for doing science. It is a large module with lots of functionality but parts of it are pretty badly documented (that is: you can read through the code but just Googling might not throw up what you need).

The first issue - how to create a biblio node programatically (that is: in code).

Some things to note:

1) You must set the type of the biblio you wish to make (Journal Article, Book chapter, etc) before the call to node_object_prepare().

2) To set the authors you must set $node->contributors as an array (like that above) and also call biblio_insert_contributors($node).

The above example sets only a fairly minimal number of the biblio fields, but any of the biblio fields may be set using this method.

The field 'start page' in biblio entries is for some reason stored in the field biblio_section (that's not an error in the code above)l.

noreply@blogger.com (Edward Baker) — Sat, 26 May 2012 13:06:00 +0000

Originally posted on the eMonocot blog: Using IPNI to autocomple publication names

One of the advantages of making a custom Scratchpads profile for a particular group of users is that this allows us to tailor the functionality of a site to the specific needs of a particular community or project.

Scratchpads have been developed to be neutral to the nomenclatural codes (unlike SpeciesFile for example, which is developed to precisely follow the International Code of Zoological Nomenclature). While we want to keep as much as we can of what we do within eMonocot useful to zoologists, there are a few cases where the restriction to a subset of botany has allowed us to develop some useful botanically focused extensions. The inclusion of images from the World Orchid Iconography database is an example of this as I blogged about recently.

Another example that we have released today is a link to the International Plant Names Index (IPNI). IPNI has a databse of botanical publications and we now use their webservice to autocomplete various fields on the 'add bibliography' form on the eMonocot Scratchpads.

The IPNI publication autocomplete function in use. Click to enlarge.

Of course this integration with IPNI has applications for many non-eMonocot botanical Scratchpads - a good example of how the eMonocot project can contribute to the wider Scratchpads community.

eMonocot and Swiss Orchid Foundation collaboration

noreply@blogger.com (Edward Baker) — Fri, 18 May 2012 17:46:00 +0000

Originally posted on the eMonocot Blog

Back in April Ruth Bone, Paul Wilkin and I visited the Swiss Orchid Foundation in Basel, Switzerland to discuss ways in which we could work together. As part of this collaboration it was decided that the eMonocot project could display images and digitised specimens from the Swiss Orchid Foundation's database of World Orchid Iconography on the eMonocot Scratchpads and portal.

Paul Wilkin talking to volunteers at the Swiss Orchid Foundation

The images will be automatically harvested at most once per week for each taxon using a custom webservice implemented by Dominique at the Swiss Orchid Foundation. We are currently testing the service on the Cypripedioideae Scratchpad (e.g. Phragmipedium besseae) where the World Orchid Iconography images are now shown alongside images uploaded to the site directly and those harvested from the Encyclopaedia of Life.

Swiss Orchid Foundation images alongside those uploaded to the site and those harvested from EOL

City technology art

noreply@blogger.com (Edward Baker) — Wed, 16 May 2012 19:51:00 +0000

When I went to Barcelona recently to meet the guifi.net and Quick Mesh Project teams I stayed with Efrain from guifi.net. This video shows Efrain and his friend experimenting with using wifi technologies to create art as part of the AirCity project.

Using Maprika for Geology

noreply@blogger.com (Edward Baker) — Mon, 14 May 2012 19:05:00 +0000

In the last post I shared a video of Jeremy Young using the iPad (plus iPhone and Android) app Maprika on the Jurassic Coast as part of the Lyme Regis Fossil Festival.

Maprika is an app originally intended to allow you to find you friends on ski slopes, by taking an image of a ski map and allowing you to georeference it in-app by adding the same points on your map and on Google Maps. The app provides an easy to use interface that can switch between these views while you georeference the map.

By using this technology to georeference the old W. D. Lang maps of the Lyme Regis we were able to study the effects of coastal erosion on the limestone ledges of Monmouth Beach (including the world famous ammonite pavement). As the video in the previous post showed the change has been considerable - both in terms of the amount of cliff that has eroded and the erosion of the limestone pavement.

The photo below (thanks to Aodhan Butler) shows Sam and I standing on a line of stones that we placed along the cliff edge of the Lang maps - showing the extent of the cliff erosion.

Digitising Old Geological Maps with Maprika

noreply@blogger.com (Edward Baker) — Sun, 13 May 2012 11:45:00 +0000

Jeremy Young talks to Marc De'ath about using Maprika with the W. D. Lang geological maps of Lyme Regis as part of the Collaborative Curiosity Digitial Live Science Experiment.

Augmented reality for Geology part 2

noreply@blogger.com (Edward Baker) — Sat, 12 May 2012 16:34:00 +0000

A while ago a wrote about augmented reality for geology. The aim was to use the open source Drupal content management system to provide an easy to use graphical interface for the augmented reality app Layar (which is both iOS and Android compatible).

At the 2012 Lyme Regis Fossil Festival we (The Buckland Club in collaboration with the Lyme Regis Development Trust) finally managed to try out the app with the public, where it was received with enthusiasm (for some of the background to this project as well as some of the technical specifications see Writing a specification for our first Digital Asset).

One of the major issues with deploying a functional app in this environment is the lack of both wireless and 3G access. Even throughout the town there are many black spots where it is impossible to get signal of any kind on a wireless device.

The solution to this was to install a number of long range WiFi links between places in the town that had and were willing to share their internet connection and the places that we wished to test our apps with the public. Working with Victor and Pau from the Quick Mesh Project we managed to create a network of four WiFi nodes, including a battery powered portable node that could be used on the beach between tides.

Pau, Victor and I installing a WiFi node on the roof of the Marine Theatre, Lyme Regis.

I will write more about what we have been up to in Lyme Regis soon.

Worst biodiversity project logos

noreply@blogger.com (Edward Baker) — Sun, 25 Mar 2012 10:21:00 +0000

Two of the worst project logos from the biodiversity world.

Consortium of European Taxonomic Facilities (CETAF):

Drawn by a child?

Consortium for the Barcode of Life (CBOL):

Drawn on by a child?

Buy one get one free socks...

noreply@blogger.com (Edward Baker) — Tue, 10 Jan 2012 12:03:00 +0000

... I would hope so too Berghaus!

Lyme Regis Landslip Video

noreply@blogger.com (Edward Baker) — Sat, 07 Jan 2012 17:20:00 +0000

Just stitched together from a handful of photographs, while stepping back, so the stability leaves a lot to be desired!

(click image below for slideshow)

ICZN Website Redesign

noreply@blogger.com (Edward Baker) — Sat, 05 Nov 2011 14:23:00 +0000

Old:

New:

Quite a change, even on the surface. Now to unify the thematics of iczn.org, ZooBank and the ICZN PodCast blog (more about this shortly)....

Family Planning Advice

noreply@blogger.com (Edward Baker) — Fri, 30 Sep 2011 18:58:00 +0000

Cheesy Royale Yum Yum Good Times Burger

noreply@blogger.com (Edward Baker) — Thu, 29 Sep 2011 20:01:00 +0000

Cheesy Royale Yum Yum Good Times Burger, a photo by edwbaker on Flickr.

Only in America!

LifeDesks SQL -> Scratchpad Import

noreply@blogger.com (Edward Baker) — Mon, 19 Sep 2011 15:21:00 +0000

Parent/child spreadsheet from Drupal taxonomy

noreply@blogger.com (Edward Baker) — Thu, 15 Sep 2011 09:04:00 +0000

So I don't forget:

[EDIT] This doesn't get the root term of a classification (one with no parent) - see comments for a way that does.

Processing and USB ports /dev/ttyACM0, /dev/ttyACM1, ....

noreply@blogger.com (Edward Baker) — Mon, 12 Sep 2011 21:39:00 +0000

Processing doesn't like reading Linux USB devices like /dev/ttyACM0 or /dev/ttyACM1.

The solution is easy, just symlink the devices like this...

ln -s /dev/ttyACM[x] /dev/ttyS8[x]

You can put any number after the ttyS, although it is possible that ttyS0 and other low numbers are defined, numbers in the eighties are (almost) guaranteed to work.

Pub Quiz Worries

noreply@blogger.com (Edward Baker) — Tue, 30 Aug 2011 20:23:00 +0000

Pub Quiz Worries, a photo by edwbaker on Flickr.

People of Burnham, can you not use English?

If you sleep in at my house, you are "Doom"ed.

noreply@blogger.com (Edward Baker) — Tue, 23 Aug 2011 07:15:00 +0000

"My son decided that he wanted to sleep in till 9:30AM. When I asked him to get out of bed he told me, "no." No one tells me "no" especially when they are four years old."

The Science of Guinness

noreply@blogger.com (Edward Baker) — Tue, 02 Aug 2011 10:23:00 +0000

A Flowchart for Fixers

noreply@blogger.com (Edward Baker) — Fri, 17 Jun 2011 11:45:00 +0000

From thereifixed: A Flowchart for Fixers

Alan Turing Documentary Preview

noreply@blogger.com (Edward Baker) — Sat, 11 Jun 2011 20:37:00 +0000

http://www.turingfilm.com/

NASA video of comet hitting the sun

noreply@blogger.com (Edward Baker) — Wed, 25 May 2011 07:12:00 +0000

Lego Machines

noreply@blogger.com (Edward Baker) — Thu, 12 May 2011 13:59:00 +0000

The Antikythera Mechanism in Lego from Small Mammal on Vimeo.

Read more about the machine: Watch an Apple Engineer Recreate a 2,000-Year-Old Computer Using Legos

Although I'm pretty sure the plural of Lego is Lego. Legos sounds bad to my ear.

Bill Bailey's Bunker

noreply@blogger.com (Edward Baker) — Tue, 10 May 2011 11:31:00 +0000

First of a series - this one features conspiracy theories and the Royal Wedding. Slightly surreal. Very good.

Augmented Reality for Geology (a Drupal approach)

noreply@blogger.com (Edward Baker) — Thu, 10 Mar 2011 21:21:00 +0000

Yesterday in a discussion with Jeremy Young we thought about the concept of having an augmented reality app that would point out a few major points of interest in Lyme Regis (we'll be down for the Fossil Festival again this year). The discussion came from playing with the Layar app, for which it is possible to provide custom data layers.

As there will be a few of us around at the festival this year (many of us living in an iPhone augmented world) I thought the idea was worth investigating a little bit more. The first challenge was to provide some kind of editing environment where we could collaboratively provide the relevant co-ordinates, altitude, text and image. Thanks to the Layar module for Drupal this was achieved pretty easily - adding items to the augmented reality layer becomes just as simple as filling out a form.

I created a handful of Points of Interest (including The Whole Hog - perhaps the world's best sandwich shop) and then submitted the necessary details to the Layar team (the layer is currently still awaiting approval).

The next issue was how we could add points (including photographs) while roaming around the town and seashore. The obvious answer was the ubiquitous iPhone (other smartphones are available), but mobile Safari doesn't allow uploads to websites.

The solution was Flickr (I use it to manage almost all my photographs). The Flickr app is easy to use and can upload photographs complete with titles, descriptions, location data and tags. Importing data from Flickr was achieved using a version of the FlickrSync module I had previously hacked to import geolocation data. The system can be set to only import photographs with specific tags - an easy way to only get the data I want. Individual users of the site will be able to associate their Flickr account and specify what tags they want to use to label items for inclusion in the layer.

I have also made an overview map that shows the points of geological interest around Lyme Regis that have been collected so far.

All in an evening (and a half)'s work.....