Saturday 24 May 2014

Arduino for Biologists (I'm writing a book)

Here's a description:

Technology has become crucial to biological science, from sensor networks to satellite imagery. These technologies are often expensive and difficult to modify, even if they do suit your specific needs. In contrast, multi-purpose platforms, coupled with open-source software, increasingly offer the biologist a way to set-up and use off-the-shelf components and code to create a customised, but affordable biological recording systems. The Arduino is a hugely popular, low-cost platform, that allows you to create your own technological solutions to problems quickly and easily with little prior electronics or programming knowledge.
The Arduino system comprises a development board containing a small micro-controller that can be reprogrammed via the Arduino desktop software and a USB cable. The system is easily expanded to add Internet connectivity, data recording tools and your own custom electronics.
This book explains everything you need to know about Arduino and how to use it. It starts with an introduction to practical electronics and the Arduino platform, and moves on through a series of projects solving specific biological problems. Each of these projects can be used as described, or modified for your specific needs. In addition, information is provided on how to share and publish your own designs and integrate them with the global infrastructures that support biodiversity informatics.
This book is for anybody who wants to design and build their own technology-based research equipment, whether it is for use in the laboratory or the field. It is of particular relevance to those who wish to develop their own sensor networks, whether they are professional ecologists or citizen scientists.
Ed Baker's work focusses on acoustic sensor networks for monitoring singing insects, remotely monitoring environments and how digital tools can help the process of science from data collection to publication.
There's a page here where I'll be putting links to relevant things: Arduino for Biologists.

Any suggestions/ideas/comments/requests welcomed!

Saturday 17 May 2014

Living ammonites: recreating a Jurassic sea

Last year Paddy from Lyme Regis Museum (well worth a visit) took over the window of Alice's Bear Shop (well worth a visit) for Lyme Regis Fossil Festival. Paddy also runs the Fossil Workshop below the bear shop (you guessed it - well worth a visit).

Seeing this re-ignited a much talked about idea among the Buckland Club of doing something to recreate a Jurassic Sea. The opportunity provided itself with Adrian, Maggie and Helena from the NHM bringing the underwater rover REX to this year's Fossil Festival (along with a replica ammonite and belemnite).

Maggie and I preparing the replicas for the sea

After attaching the creatures to some large weights Adrian ventured out to return them to the sea.

After waiting for the next day's morning high tide we launched REX and went to see if we could find the 'living' animals.

REX the remotely operated vehicle

Launching REX off of the Cobb at Lyme Regis

REX finds the 'living' ammonite. Now that's a Nature paper, surely?

Wednesday 14 May 2014

BDJ Paper on Encyclopedia of Life

A new paper where I acted as editor in the Biodiversity Data Journal: The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth.

The Encyclopedia of Life (EOL, aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.5 million distinct pages for taxa and provides content for 1.3 million of those pages. The content is primarily contributed by EOL content partners (providers) that have a more limited geographic, taxonomic or topical scope. EOL aggregates these data and automatically integrates them based on associated scientific names and other classification information. EOL also provides interfaces for curation and direct content addition. All materials in EOL are either in the public domain or licensed under a Creative Commons license. In addition to the web interface, EOL is also accessible through an Application Programming Interface.
In this paper, we review recent developments added for Version 2 of the web site and subsequent releases through Version 2.2, which have made EOL more engaging, personal, accessible and internationalizable. We outline the core features and technical architecture of the system. We summarize milestones achieved so far by EOL to present results of the current system implementation and establish benchmarks upon which to judge future improvements.
We have shown that it is possible to successfully integrate large amounts of descriptive biodiversity data from diverse sources into a robust, standards-based, dynamic, and scalable infrastructure. Increasing global participation and the emergence of EOL-powered applications demonstrate that EOL is becoming a significant resource for anyone interested in biological diversity

PDF can be downloaded here: The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth.