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

PAGES News report on the updated Latin American Pollen Database

A report by Suzette Flantua et al. on the status of and updates to the Latin American Pollen Database (LAPD) appears in the August 2013 issue of PAGES News. LAPD is a Neotoma constituent database.

Posted by Eric Grimm on 08/27

Age Models, Chronologies, and Databases Workshop

Date: January 13-16, 2014 in Belfast, Northern Ireland
Contact: Dr. Eric Grimm

This workshop aims to develop strategies for updating chronologies in a semi-automated manner for paleo databases given new criteria, for example a new radiocarbon calibration curve or revised ages for stratigraphic/biostratigraphic markers (e.g. tephras).  Applications for attendance now being accepted.  Click here for more information.

Posted by Blake Ketchum on 06/20

Neotoma R package now available!

Simon Goring has developed an R package to use the new API tools to interface with the Neotoma Paleoecology Database directly from R.  Great job by Simon!  Check the package out here.

Posted by Jessica Blois on 04/11

New Quick-start for TaxaMapper

The TaxaMapper application has been updated with a new quick-start user guide. Go to TaxaMapper and click the "?" button to view illustrated step-by-step instructions for common tasks.

Posted by Brian Bills on 03/13

GDM paper featuring Neotoma data now available online at Ecography

GDM paper featuring Neotoma data now available online at Ecography

A paper by Jessica Blois, Jack Williams, and co-authors is now available online early at Ecography (link).  This paper paired fossil pollen assemblages across eastern North America from the Neotoma database with paleoclimatic simulations to model the climatic drivers of fossil pollen dissimilarity across space over the past 21,000 years.  We found that the set of climate variables associated with dissimilarity between fossil pollen assemblages across eastern North America changed over the past 21,000 years. Higher magnitudes of climate change between time periods meant lower prediction strength when projecting spatial models of community dissimilarity to different time periods.

Posted by Jessica Blois on 10/29

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