Looking for a needle in a haystack…and finding it!

Bettisfield Moss.  Photo: C Bell

Last Friday I found myself crouched over a plastic sheet in the middle of a National Nature Reserve, squinting at Sphagnum. I’d joined an enthusiastic team of local spider experts, volunteers and Natural England staff at Fenn’s, Whixall and Bettisfield Mosses, a NNR spanning the English and Welsh border. Our mission: to search for the nationally rare spider species Glyphesis cottonae.

Multi-access keys and D3 - what's the link?

D3 is shorthand for 'Data Driven Documents' - an extremely flexible and powerful toolset for visualising data on the web developed by Mike Bostock. Here I outline why D3 is of interest to Tomorrow's Biodiversity.

D3 examples: feel more force

D3 teaser imageFrom Mike Bostock's Force Layout Collision Detection D3 demo. This is another example of how Mike Bostock's D3 javascript library can enable beautifully dynamic and responsive interfaces representing data in very creative ways - limited chiefly by our imaginations.

D3 examples: visualise a hierarchy as a dynamic tree

D3 teaser imageFrom Rob Schmuecker's Collapsible, Zoomable and Drag 'n' Dropable Tree Layout D3 demo. This amazing demonstration from Rob Schmuecker shows how the D3 library can be used to build a fully interactive tree view of hierarchical data. It uses the 'flare' demo dataset, but the actual data is unimportant to us. The interesting thing is how this visualisation puts control into the hands of the person exploring it.

D3 examples: visualise a nested hierarchy

D3 teaser imageFrom Mike Bostock's 'Zoomable Packing' D3 demo. This is a great way of visualising nested hierarchies. You can zoom in to get detail (in this case names relating to some programming paradigm of no importance to us) by clicking over any white object that you want to inspect. Zoom out by clicking again. You can imagine how a taxonomic hierarchy could be represented and explored in this way. We will soon be demonstrating examples that do just that.

D3 examples: feel the force

D3 teaser imageFrom Mike Bostocks Force Layout D3 demo. This example demonstrates the 'force layout' where objects can be attracted or repelled from each other according to properties of the objects. This can be used to demonstrate the relationships between objects. You can interact with the objects, dragging them about and seeing the effect on the others.

TaxonAid demonstration

ThumbnailTaxonAid is an online tool dedicated to the improvement of techniques in taxonomic identification. We think that an approach using high quality interactive movement-based resources and existing identification keys represents the best way to both maximise efficiency of identification and also to provide an engaging learning and teaching environment.

Winter trees: From AIDGAP test version to final book

Winter trees and the River Severn in flood.  Photo: Rich BurkmarThe accurate identification of specimens is an important part of many forms of biological fieldwork. Although popular groups, such as birds and butterflies, are well served with identification guides, other groups are relatively neglected. Back in the 1970s, the Field Studies Council initiated the AIDGAP project, to work towards producing identification materials for these negelected groups. In many cases, the difficulty lay in the absence of a simple and accurate key, and not in any insuperable taxonomic problems.

Invasive aliens and other bad language

Himalayan balsam (Impatiens glandulifera).  Photo: Charlie BellA growing amount of attention is being given to biodiversity loss resulting from the introduction of non-native species. Introduced species that do well, especially if they do so at the expense native flora or fauna, are frequently referred to as ‘invasive aliens’.

Some thoughts on DNA barcoding and biological recording

Wall (Lasiommata megera).  Photo: Rich BurkmarI recently took part in a really interesting email discussion with some other NFBR members (National Forum for Biological Recorders) prompted by the recent publication of a paper on metabarcoding. I think it's fair to say that many biological recorders are very cautious about the use of DNA barcoding as a tool for monitoring biodiversity. There is a perception that the development of DNA barcoding may threaten the traditional morphological identification skills of the biological recorder. I have a more optimistic outlook and the rest of this blog is derived from an email I contributed to the email discussion.


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