New NSF FAIROS RCN grant to advance ethical open science

We are thrilled to announce Disciplinary Improvements for Past Global Change Research: Connecting Data Systems and Practitioners, a National Science Foundation Findable, Accessible, Interoperable, Reusable Open Science Research Coordination Networks (FAIROS RCN) grant to advance ethical scientific practices in the use of paleoecological, contemporary ecological, paleoclimatic, and archaeological data. Our overarching aim is to build technical and social capacity among data resources by supporting technical implementation of ethical open science applications and developing communities of practice around FAIR and CARE (Collective benefit, Authority to control, Responsibility, and Ethics) open science principles. Specifically, our project will:

  1. Improve interoperability and reproducibility of data by developing guidance for community-curated data resources across the paleoecology and archaeology disciplines, and promote adoption of broader metadata standards for interconnectivity of data.

  2. Enable data curation and stewardship by promoting FAIR data curation principles among practitioners, especially through engagement with early-career researchers. These practices will help maximize the scientific and educational value of data created and shared across different disciplines and communities.

  3. Support data equity and improve democratization by promoting CARE data curation principles. These principles align scientific data curation with broader culturally inclusive community needs and interests. They help foster partnerships and collaborations with Indigenous and other community stewards of natural and cultural heritage.

This project provides broad participative support and guidance for these goals by bringing together data managers from a variety of specimen and environmental data resources, including the Neotoma Paleoecology Database, Open Context, ZooArchNet, NEON, and iSamples; metadata stewards; disciplinary practitioners; and early-career researchers. We believe that open science requires a foundation of welcoming collaboration, mutual support, and partnerships across communities.

For more information about all the inaugural FAIROS RCN funded projects, please see this announcement published by the Association of Research Libraries.

This project is supported by the National Science Foundation: NSF-2226368 to Jessica Blois (University of California - Merced), NSF-2226369 to Jack Williams and Simon Goring (University of Wisconsin - Madison), NSF-2226370 to Kitty Emery and Michelle LeFebvre (University of Florida) and Suzanne Pilaar Birch (University of Georgia), NSF-2226371 to Andrea Thomer (University of Michigan, now at U. Arizona), NSF-2226372 to Meghan Balk (NEON), and NSF-2226373 to Leigh Anne Lieberman (The Alexandria Archive Institute/Open Context). For more information, consult the linked individual NSF award abstracts.

Posted by Jessica Blois on 08/19

Neotoma R 1.0->2.0 rapid transition

Hi everyone,
As many of you know, a new version of the Neotoma R package, 2.0, was released in February of this year.  V2.0 is a major update, that points to the new PostgreSQL version of the backend database and includes a major redesign of the R data objects so that they now hold the full suite of all data and metadata associated with a dataset at a site.
We had hoped to keep supporting the 1.0 R package for at least the next several months, but unfortunately this package was housed on an older Penn State server that effectively has been shut down.  This shutdown was unexpected to the Neotoma team. There is some chance that we will be able to restore the services supporting the 1.0 R package, but so far this seems unlikely.  In any case, the 1.0 R package was pointing to pointing to an static version of the database that is already at least a year out of date.
We apologize that the full sunsetting of the 1.0 R package has been more abrupt than intended and are sorry for any disruptions that this may have caused to anyone’s analytical workflows.  Fortunately, Simon and Soccoro have been hard at work adding new features to the 2.0 R package and preparing example vignettes to show users how to use the 2.0 features.  Simon just posted the following information to Neotoma’s Slack workspace, in #it_r. 
In preparation for the #db_epd workshop in Prague and the AMQUA workshop,  and I have been working on getting a bunch more changes to the neotoma2 R package finished up, and some more vignette/workflows written up.  You can see the drafts here:
·        https://open.neotomadb.org/EPD_binder/simple_workflow.html (searching, plots across time, space & climate)
·        https://open.neotomadb.org/EPD_binder/complex_workflow.html (building chronologies)
We'd very much appreciate your feedback, either directly or through DMs. The Rmd documents from which these were generated can be found here: https://github.com/neotomadb/EPD_binder If you feel comfortable working with GitHub we welcome your contributions here as well.
Jack Williams

Posted by Jack Williams on 05/27

Beta version of neotoma2 R package released!

We are excited to announce, at long last, the beta release of the Neotoma R package, neotoma2. Many, many thanks to Simon Goring and Socorro Dominguez for this huge effort, and all of the folks who have contributed suggestions, code, vignette examples, etc. along the way.

The new R package works with the latest Neotoma web services, and is designed to work more closely with the R tidyverse, making data access and analysis more streamlined.

Some features:

  • Nested sites, datasets and samples to more closely mirror the data model of the database.

  • Filter functions to allow you remove sites and datasets easily

  • New set_*() functions, allowing you to add new records directly into your analysis seamlessly

The neotoma2 package is currently hosted on GitHub (https://github.com/NeotomaDB/neotoma2) while we iron out the kinks and see how people use the package.

If you’d like to use the package we’ve provided some RMarkdown vignettes to get you started.  Installation is as easy as:



We’ll be running a live coding day on Wednesday Feb 16 from 9:00am - 12:00pm (Pacific) on Zoom (https://uwmadison.zoom.us/j/97083802266?pwd=OEd3a2hyUlJwLzJyc3Q1dUFtMlVjUT09).  Folks are invited to join and talk with us about their needs, and see the package in action as we work to improve our online resources.

Bug reports can be made to Simon Goring (goring@wisc.edu), online at https://github.com/NeotomaDB/neotoma2/issues or in the #it_r channel of our Slack workspace (https://join.slack.com/t/neotomadb/shared_invite/zt-cvsv53ep-wjGeCTkq7IhP6eUNA9NxYQ).

Folks are more than welcome to contribute to the project.  Please let us know if you’d like to help out with documentation, examples, code, or helping us craft useful case studies for using the R package!

Posted by Jessica Blois on 02/11

NSF Facilities/Resources/Equipment standard text available

For PIs writing proposals to NSF, standard text about Neotoma resources is available here: https://www.neotomadb.org/documents

Posted by Jack Williams on 09/20

Eric24 Event, Good overview talks about Neotoma

On April 28, 2020, Neotoma leaders organized and convened an all-day (17hour) online zoom webinar in remembrance of Eric’s life and work, across four sessions organized by continent and timezone: Asia and IndoPacific, Europe, Africa, and the Americas. All talks were recorded and posted to YouTube.

The event includes a nice series of short (15 min) introductory overviews about Neotoma, that are excellent starting points for students or other newcomers to Neotoma.  They include talks about the history of Neotoma (Russ Graham), its current directions (Jack Williams), what makes Neotoma unique as a long-lasting data resource (Andrea Thomer), and lessons learned by the next generation of Neotoma stewards and leaders (Jessica Blois and Simon Goring).

Posted by Jack Williams on 05/14

Strat Diagrammer 2.0 released

I'm delighted to report that a new version of Stratigraphic Diagrammer is now released for Neotoma!  Stratigraphic Diagrammer is available in Neotoma Explorer and provides a stratigraphic view of a site-level dataset.  It can be accessed by first finding a site, then clicking on it to get a small popup box, then clicking on the 'view dataset' icon (looks like an eyeball) next to a dataset. 

The original version only supported pollen data, whereas this new version supports pollen, diatom, ostracodes, testate amoebae, and vertebrates.  This new version can be extended to other variables as well, with some case-by-case decisions needed about how to handle expected range values, missing values, units, etc. 
And the new version is quite beautiful as well and allows popups of values for individual points. Thanks to all on the Neotoma IT team and particularly Mike Stryker and Jonathan Nelson for their great work on designing and launching this.  

Posted by Jack Williams on 02/02

Migration update Nov 20, 2020

Dear Colleagues,

I'm pleased to report several additional milestones in the porting of Neotoma services over from Windows/SQLServer to Linux/Postgres:

1) An updated version of Tilia (v3.0.1) was released today to Data Stewards, and is ready and enabled for Stewards to resume uploading data to Neotoma.  Eric had been working on this new version for several months, with roughly 70 new datasets uploaded, to ensure it was fully connected with the new postgres version of Neotoma.  This version of Tilia can download sites, upload new sites, and add new datasets to existing sites.  There are a few minor known issues that we are working on fixing.

2) Neotoma Explorer has now been fully repointed to the new version of Neotoma, so as new sites are added, you will be able to find them in Explorer.  Jonathan Nelson at Penn State soon will start to work on next-stage improvements to Explorer, in response to Neotoma user and steward requests.  [11/25/20 Update: Several bugs have been reported, in some search windows and in Stratigraphic Diagrammer and its display of chronologies.  We're working on them now and discussing in Slack: https://neotomadb.slack.com.]

3) Landing pages for individual Neotoma datasets are now re-enabled.  For example, https://data.neotomadb.org/14194   Simon Goring is also about to turn on the minting of DOIs for all Neotoma records.  This capability has been available for a while, but has been put on hold while bugs were ironed out of the uploading process; we wanted to avoid minting DOIs for datasets that might need to be removed if errors were found.

See the updated summary table for details about individual components, their current status, and their locations. 



Posted by Jack Williams on 11/20

In memoriam: Eric Grimm

Hi all,

It is with great sorrow that we pass along the news that Eric Grimm, one of the co-founders of the Neotoma Paleoecology Database, passed away unexpectedly over the weekend. Eric was a giant in the fields of palynology and paleoecology, whose work was marked both by great breadth of vision and deep meticulousness.  Eric’s vision and hard work was instrumental in creating a culture of open data and transparent science so that as individuals, we could all contribute to a greater good of answering globally relevant questions about the influence of climate on Earth’s vegetation and the interactions among species. His contributions to the fields of paleoecology and open biological and geological databases cannot be overemphasized.  He will be sorely missed by all of us, as a leader, and as our friend.

Eric’s vision of an open and shared data architecture for paleoecology, first realized as the continental pollen databases, and now as the multi-proxy Neotoma Paleoecology Database, lives on.  We have known that for an institution to be sustainable, it cannot be solely dependent on any single person.  Hence, several years ago, we embarked on a process of expanding and solidifying the governance and day-to-day work of maintaining the Neotoma database and its software ecosystem, following Eric’s example of open, collaborative work. So the Neotoma Executive Team and Leadership Council is in the process of planning our next steps forward.  We have many ideas here, but they will take some days to solidify into plans and can also can wait until we process the news and our grief.

In the meantime, if you have any questions about this news, or anything related to Tilia or Neotoma, you can contact the Neotoma Executive Team (neotoma-contact@googlegroups.com), or Jack Williams (Exec Chair, jwwilliams1@wisc.edu) or Jessica Blois (Assoc Exec Chair, jblois@ucmerced.edu) directly, and we can figure out how best to address them.


Jack and Jessica, on behalf of the Neotoma Executive Committee

Posted by Jack Williams on 11/16

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