Wednesday, 30 May 2012

Create Drupal 7 biblio nodes programatically

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.

Saturday, 26 May 2012

Using IPNI to autocomplete publication names

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.

Friday, 18 May 2012

eMonocot and Swiss Orchid Foundation collaboration

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.

Swiss Orchid Foundation and eMonocot
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

Wednesday, 16 May 2012

City technology art

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

Monday, 14 May 2012

Using Maprika for Geology

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.

Sunday, 13 May 2012

Digitising Old Geological Maps with Maprika

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.

Saturday, 12 May 2012

Augmented reality for Geology part 2

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.