Beginning Wednesday, July 1, Neotoma will be down for several days during a server upgrade at Penn State University. This downtime will affect the Neotoma database and all software services associated with it (e.g. Neotoma Explorer, APIs, R package, Tilia-to-Neotoma services). We do not yet know the exact duration of this downtime but hope it will be less than a week. All Neotoma services on the new server are being tested during this upgrade, to ensure that everything runs smoothly afterwards. However, there is a possibility that some Neotoma services will need patching after this server upgrade.
We apologize for the short advance notice of this upgrade and for any disruptions caused. We are monitoring this situation closely and will post updates as soon as we have them.If you run into any issues during or after the server upgrade, please contact the Neotoma Executive Committee at Neotomafirstname.lastname@example.org or post a note to the NeotomaDB Slack workspace (neotomadb.slack.com #it-dev).
-Jack Williams, Jessica Blois, Steve Crawford, Simon Goring, Eric Grimm, Doug Miller, Mike Stryker
PS Many of you know that we are also working on a backend migration of the Neotoma database from a SQL Server/Windows server to a PostgreSQL/Linux server. That migration is nearly complete but is separate from this PSU server upgrade. We likely will need to schedule a second downtime window to complete this migration. We will send out updates as soon as we establish the timeline for this database migration.
[Update 6/26/2020 3:13pm US CT: changed contact email to Neotomaemail@example.com]
[Update 8/5/2020 The server upgrade is underway and we are experiencing a few broken links as we repoint services from the old PSU server to the new one. Additionally, services are running slower than normal, which we are working on as well. We are working to get these issues resolved as fast as possible.]
Posted by Jack Williams on 06/26
The Leadership Council approved the new bylaws adding early-career representatives to the council as full voting members! 9 people voted, 9 yes to 0 no. In addition, after internal discussion the LC unanimously voted to elevate the ad hoc ECR reps to full voting reps rather than holding a new election, since they were just voted into their roles in late fall 2019. So welcome to Dana Reuter and Suzette Flantua to the Neotoma Leadership Council! They will both be on the council through the end of their original term, December 2021.
Posted by Jessica Blois on 05/16
The Leadership Council unanimously approved the addition of a new constituent database to the Neotoma Paleoecology Database! The new database is named PaVeLA (PaleoVertebrates of Latin America). Joaquín Arroyo-Cabrales (Instituto Nacional de Antropología e Historia, México) is the lead for the database, and is working with graduate student Deborah V. Espinosa-Martínez and overall vertebrates lead Jessica Blois on integrating the Quaternary Mammals of Mexico Database into PaVeLA. If you are interested in adding sites to the database, or learning more, please contact Joaquín Arroyo-Cabrales (firstname.lastname@example.org) or Jessica Blois (email@example.com).
Posted by Jessica Blois on 04/22
Neotoma and the University of Wisconsin will be hosting a workshop to lay the groundwork for a robust cyberinfrastructure dedicated to supporting the open access for ancient environmental DNA and integrating it with existing cyberinfrastructure in genomics and paleoecology. This workshop will be held May 18-20 in Madison, WI, USA. The workshop is supported by the National Science Foundation and standard travel costs will be covered for all participants.
This ca. 20-person workshop includes several open participant slots specifically dedicated to early career scientists and scientists from underrepresented populations. If you are interested in attending, please email your CV and a short statement of research interests to Jack Williams (firstname.lastname@example.org) by March 6.
Planned activities include: 1) review the current state of the art with respect to ancient DNA data generation, data handling, data archival, and analytical pipelines; 2) review the latest advances and capabilities of existing cyberinfrastructures in genomics and paleoecology; 3) identify paleogenomic-relevant gaps and semantic misalignments among existing resources; 4) establish priorities and initial standards for data and metadata reporting in community paleodata resources. The Steering Committee for this workshop is Inger Alsos, Jessica Blois, Mary Edwards, Eric Grimm, Laura Parducci, Beth Shapiro, and Jack Williams.
If you have any questions please reach out to Jack Williams.
Posted by Jack Williams on 02/17
The Neotoma Data Use Policy has been updated and posted. Neotoma data are provided under a CC-BY 4.0 license and are open for use with citation. The revised Data Use Policy clarifies that proper citation of Neotoma data operates at three levels: Neotoma itself, the Constituent Database(s) that curate these data, and the original data providers. Appendix 1 provides standard citation endpoint and acknowledgment text for Neotoma itself, while Appendix 2 provides preferred citation endpoints and acknowledgments for individual Constituent Databases.
Posted by Jack Williams on 01/15
For an update on recent Neotoma activities, check out the article published in the fall 2019 issue of the Quaternary Times, the newsletter for the American Quaternary Association (AmQua). https://www.amqua.org/public/news/Quaternary Times_Vol. 41 Fall 2019-2.pdf
Posted by Jack Williams on 11/19
All Neotoma datasets are now being assigned DOIs and each DOI/dataset is linked to a unique landing page. (Example: Ballysheen Bog). The automatic generation of DOIs is still in the beta stage and for now we will generate DOIs in batches on an as-needed basis. To find a DOI for a particular dataset, look up the dataset ID in Explorer, then enter the URL: http://data-dev.neotomadb.org/[dataset id] We will be developing new services to find DOIs programmatically.
Posted by Jack Williams on 04/26
Dr. Raleigh Martin, an AAAS Science & Technology Policy fellow, has prepared a report on Neotoma, as part of a broader survey of NSF-supported Data Facilities. His report is based in part on an interview with Dr. Jack Williams. Please note that this report is the opinion of the interviewer and the interviewee alone and does not reflect an official position of the American Association for the Advancement of Science (AAAS), the U.S. National Science Foundation (NSF), or any NSF-funded institution.
Posted by Jack Williams on 04/26