Presentation: Pollen databases: from von Post to Neotoma

The presentation "Pollen Databases: from von Post to Neotoma" is to be presented by Eric Grimm at the symposium Centenary (1916-2016) of Pollen Analysis and the Legacy of Lennart von Post at the Royal Swedish Academy of Sciences in Stockholm, 24-25 November 2016. The symposium celebrates the 100 years since the first pollen diagram was presented by Lennart von Post and to examine his legacy in the science of pollen analysis and vegetation history.

Posted by Eric Grimm on 11/23

Presentation: Community-Curated Data Resources and the Children of COHMAP

Neotoma talk given at the 2016 Annual Meeting of the Geological Society of America, at a special session in honor of Herb Wright.  Talk title:  Community-Curated Data Resources and Large-Scale Data-Model Syntheses: The Children of COHMAP.  Slides have been posted to FigShare, link below

Posted by Jack Williams on 09/30

New Education Modules

Two new educational modules built around the Neotoma Explorer web application are available: Exploring the Neotoma Paleoecology Database and Climate Change and Mammal Dispersal.

Posted by Brian Bills on 11/02

Paper describing the R package neotoma published

A paper by Simon Goring et al. describing the R package neotoma has just been published in the inaugural issue of the new open-access journal Open Quaternary. The paper is here. A direct link to the pdf is here.

Posted by Eric Grimm on 03/09

“Tales” of the Bushy-tailed Woodrat (Neotoma cinerea)

A blog post about the Neotoma Paleoecology Database mascot.

Posted by Eric Grimm on 09/16

Neotoma Explorer 2.0 is here!

Neotoma Explorer has been re-engineered from the ground up to provide more flexible, easier, and full-featured access to the Neotoma Paleoecology Database through modern Web browsers.  Explorer 2.0 uses the publicly available Neotoma Application Programming Interface (API) to search and extract the most current data available via REST-ful web services.  An entirely new JavaScript and HTML application, Explorer is built with free and open source Dojo and OpenLayers libraries making it more easily extended and customized compared to previous versions.

A lot of work has been done to migrate to the new JavaScript/HTML platform and API.  Part of this work is a new modular search architecture which we will be expanding in near-term minor releases planned for this summer.  Our goal for 2.0 has been to deliver the same functionality available in the current Explorer plus many usability enhancements and bug fixes.  With the exception of a few minor open issues, this has been accomplished.  We are adopting a rapid release cycle to deliver new functionality, enhancements, and bug fixes monthly.

With the transition from Adobe Flash, we are now subject to web browser-specific differences in the implementations of JavaScript, HTML, and CSS.  While the differences are not as great as they once were and the Dojo Framework helps to mitigate them, we have found issues during our testing.  Of particular note is the way Internet Explorer and Safari handle file downloads.  Both do not allow access to the local file system.  Whereas both Chrome and Firefox allow us to easily save datasets already processed by the Explorer application, IE and Safari require us to prepare and retrieve downloads directly from the web server.  Thus, we’ll need to do a little extra work to move some client functionality to the server to support multiple file downloads; this feature will be coming soon.

Another difference is the speed of the web browser JavaScript engines.  In our testing, the latest versions of Chrome and Firefox are the top performers, respectively.  These browsers also give the best user experience with the application.   Additionally, we have discovered a performance issue that appears to affect all browsers—extensions/add-ons.  In particular, we have found that the Skype Click-to-Call browser add-on severely degrades the performance of the dataset table (i.e., spreadsheet) component.  We recommend disabling this add-on in your browser settings.  Other add-ons that scan/inspect web page content may cause slowdowns as well.

Please give the new Explorer a try here and send us your feedback.  Thanks.

Posted by Brian Bills on 05/16

Palynological Databases: Hands-on Computer Workshop

Palynological Databases: Hands-on Computer Workshop will be held October 19-20 in conjunction with the 46th Annual Meeting of the American Association of Stratigraphic Palynologists in San Francisco. This workshop will provide training in the use of various software packages with application to palynology, with emphasis on the Neotoma Paleoecology Database, but also including Tilia, RNeotoma, an R package for Neotoma, and the Neotoma Application Programming Interface. For more information please visit the workshop webpage

Posted by Eric Grimm on 09/03

Model Systems for a No-analog Future

The early view version of Model systems for a no-analog future: species associations and climates during the last deglaciation has just been published online (Williams et al, 2013, in a special issue of the Annals of the New York Academy of Sciences). With global climate change, Earth ecosystems may be moving into novel states that have no modern analogs. Thus, predicting and modeling the behavior of these ecosystems present major challenges. This paper explores model systems from the last deglaciation that also have no modern analogs and how these may help understand future ecosystem response. The paper, which utilizes pollen data from Neotoma, emanates from a workshop "Climate Change and Species Interactions: Ways Forward" held at the Cary Institute of Ecosystem Studies in November, 2012.

Posted by Eric Grimm on 08/28

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