Collections digitization relies increasingly upon computational and data management resources that occasionally exceed the capacity of natural history collections and their managers and curators. Digitization of many tens of thousands of micropaleontological specimen slides, as evidenced by the effort presented here by the Indiana University Paleontology Collection, has been a concerted effort in adherence to the recommended practices of multifaceted aspects of collections management for both physical and digital collections resources. This presentation highlights the contributions of distributed cyberinfrastructure from the National Science Foundation-supported Extreme Science and Engineering Discovery Environment (XSEDE) for web-hosting of collections management system resources and distributed processing of millions of digital images and metadata records of specimens from our collections. The Indiana University Center for Biological Research Collections is currently hosting its instance of the Specify collections management system (CMS) on a virtual server hosted on Jetstream, the cloud service for on-demand computational resources as provisioned by XSEDE. This web-service allows the CMS to be flexibly hosted on the cloud with additional services that can be provisioned on an as-needed basis for generating and integrating digitized collections objects in both web-friendly and digital preservation contexts. On-demand computing resources can be used for the manipulation of digital images for automated file I/O, scripted renaming of files for adherence to file naming conventions, derivative generation, and backup to our local tape archive for digital disaster preparedness and long-term storage. Here, we will present our strategies for facilitating reproducible workflows for general collections digitization of the IUPC nomenclatorial types and figured specimens in addition to the gigapixel resolution photographs of our large collection of microfossils using our GIGAmacro system (e.g., this slide of conodonts). We aim to demonstrate the flexibility and nimbleness of cloud computing resources for replicating this, and other, workflows to enhance the findability, accessibility, interoperability, and reproducibility of the data and metadata contained within our collections.
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The GEOTRACES Intermediate Data Products: Rich Resources for Research, Education, and Outreach
By mid-2023, the international GEOTRACES program had released three intermediate data products (IDP2014, IDP2017, and IDP2021), and in July 2023, an update of the latest product, IDP2021v2, was issued. All IDPs consist of two parts: (1) a compilation of digital data for large numbers of trace elements and isotopes (TEIs), and (2) the eGEOTRACES Electronic Atlas containing almost 1,500 pre-created section plots and 269 animated three-dimensional scenes that can be browsed via an interactive web interface. GEOTRACES IDPs are used extensively and have proven to be rich resources for research, education, and outreach. Here, we demonstrate how these resources can be used efficiently and effectively via online services. Data browsing, analysis, and visualization occur in the user’s web browser, with the IDP data remaining on a dedicated server. Users simply visit specific resource URLs to access eGEOTRACES visuals and the GEOTRACES digital data directly. We first demonstrate how to navigate the eGEOTRACES Electronic Atlas to view TEI sections and three-dimensional animations. We then focus on two research use cases and provide detailed hands-on instructions for creating publication-ready figures related to the marine Zn cycle.
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- Award ID(s):
- 2140395
- PAR ID:
- 10534318
- Publisher / Repository:
- The Oceanography Society
- Date Published:
- Journal Name:
- Oceanography
- Volume:
- 37
- Issue:
- 2
- ISSN:
- 1042-8275
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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