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1. Elucidating the Magma Plumbing System of Ol Doinyo Lengai (Natron Rift, Tanzania) Using Satellite Geodesy and Numerical Modeling: Supplementary Model Files

   https://doi.org/10.5281/zenodo.7897255  

   Daud, Ntambila; Stamps, D. Sarah; Battaglia, Maurizio; Huang, Mong-Han; Saria, Elifuraha; Ji, Kang-Hyeun (January 2023, Zenodo)

   {"Abstract":["Supplementary code and model files for the manuscript entitled "Elucidating the Magma Plumbing System of Ol Doinyo Lengai (Natron Rift, Tanzania) Using Satellite Geodesy and Numerical Modeling". OlDoinyoLengai_code_and_models.zip contains all necessary Matlab code, functions, input and output files for the GNSS, InSAR, and joint inversions presented in our manuscript necessary to reproduce the results. dMODELS is an open source code developed by the United States Geological Survey. The originally published program is available here: https://pubs.usgs.gov/tm/13/b1/ and the revised software archived here will also be available through the USGS website code.usgs.gov/vsc/publications/OlDoinyoLengai or by contacting Maurizio Battaglia. With this manuscript we are providing an update to dMODELS that includes improved graphics and joint inversion capabilities for both InSAR and GNSS data. <\/p>"],"Other":["This work was funded by the National Science Foundation (NSF) grant number EAR-1943681, Virginia Tech, Korean Institute of Geosciences and Minerals (KIGAM), and Ardhi University. Funding for this work also came from USAID via the Volcano Disaster Assistance Program and from the U.S. Geological Survey (USGS) Volcano Hazards Program.This material is based on services provided by the GAGE Facility, operated by UNAVCO, Inc., with support from the National Science Foundation, the National Aeronautics and Space Administration, and the U.S. Geological Survey under NSF Cooperative Agreement EAR-1724794. We acknowledge and thank Alaska Satellite Facility for making InSAR data freely available and TZVOLCANO GNSS data sets available through the UNAVCO data archive."]} 

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2. Simulation Files for Organic Contaminants and Atmospheric Nitrogen at the Graphene–Water Interface

   https://doi.org/10.5281/zenodo.6050816  

   Thakkar, Ravindra; Sandun, Gajaweera; Comer, Jeffrey (January 2022, Zenodo)

   {"Abstract":["This data set provides files needed to run the simulations described in the manuscript entitled "Organic contaminants and atmospheric nitrogen at the graphene\u2013water interface: A simulation study" using the molecular dynamics software NAMD and LAMMPS. The output of the simulations, as well as scripts used to analyze this output, are also included. The files are organized into directories corresponding to the figures of the main text and supplementary information. They include molecular model structure files (NAMD psf), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and some trajectories in dcd format (downsampled). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts. A modified LAMMPS C++ source file is also included.<\/p>"],"Other":["This material is based upon work supported by the National Science Foundation under Grant No. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE) and Stampede2 at the Texas Advanced Computing Center through allocation BIO200030, which is supported by National Science Foundation grant number ACI-1548562."]} 

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3. Metagenome-assembled genomes from Stordalen Mire, Sweden (MAGs v2)

   https://doi.org/10.5281/zenodo.13984630  

   Aroney, Samuel; Cronin, Dylan; Bagby, Sarah; Hodgkins, Suzanne (October 2024, Zenodo)

   This release (MAGs v2) is a major new version of this metagenome-assembled genome (MAG) set. All previous releases on this page (which only differ in the metadata) are designated "MAGs v1." The current release (MAGs v2) uses CheckM2 v1.0.2 filtering (≥70% completeness, ≤10% contamination) to expand this dataset to include 36,419 MAGs, with the following subcategories: Cronin_v1:  Manually-curated subset of the "Field" category from MAGs v1. Cronin_v2:  MAGs from raw bin filtering on the same assemblies used to generate Cronin_v1. Woodcroft_v2:  MAGs from raw bin filtering on the same assemblies used to generate the MAGs reported in Woodcroft & Singleton et al. (2018). SIPS:  Updated genomes from samples originating from a stable isotope probing (SIP) incubation experiment by Moira Hough et al. ("SIP" in MAGs v1), re-analyzed due to read truncation and sample linkage issues in MAGs v1. JGI:  Expanded set of genomes from the Joint Genome Institute's metagenome annotation pipeline.   FILES: Emerge_MAGs_v2.tar.gz - Archive containing the MAG files (.fna). metadata_MAGs_v2_EMERGE.tsv - Table containing source sample names and accessions, GTDB taxonomy information, CheckM2 quality reports, NCBI GenomeBatch- and MIMAG(6.0)-formatted sample attributes and other metadata for the MAGs.    FUNDING: This research is a contribution of the EMERGE Biology Integration Institute (https://emerge-bii.github.io/), funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070. This study was also funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research, grant #s DE-SC0004632. DE-SC0010580. and DE-SC0016440. We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164. Data collected at the Joint Genome Institute was generated under the following awards: The majority of sequencing at JGI was supported by BER Support Science Proposal 503530 (DOI: 10.46936/10.25585/60001148), conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Sequencing of SIP samples was performed under the Facilities Integrating Collaborations for User Science (FICUS) initiative (proposal 503547; award DOI: 10.46936/fics.proj.2017.49950/60006215) and used resources at the DOE Joint Genome Institute (https://ror.org/04xm1d337) and the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), which are DOE Office of Science User Facilities. Both facilities are sponsored by the Office of Biological and Environmental Research and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). 

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4. Bathymetric data from T8 Lake, Toolik Field Station, Alaska (2020)

   https://doi.org/10.18739/A2XS5JJ05  

   McPherson, Rowan (January 2021, NSF Arctic Data Center)

   Toolik Field Station is located in the foothills of the Brooks Range on Alaska's North Slope and is administered by the Institute of Arctic Biology at the University of Alaska Fairbanks (UAF). Toolik Field Station was first established to support an aquatic program designed to obtain base-line data on the North Slope and inland coastal ponds in 1975. Research has expanded over the years to include terrestrial, atmospheric, vertebrate and other taxa, making Toolik home to a long running and diversified body of arctic ecology. The station currently supports a long-standing and rapidly expanding community of scientists and research projects representing individual and collaborative efforts from United States and international institutions. Growth of Toolik-based science, the number of researchers, and the facility from a tented camp to a research station prompted the establishment of the Toolik GIS (Geographical Information Systems) and Remote Sensing (RS) Program as part of the 5 year Cooperative Agreement between the National Science Foundation (NSF) and the Institute of Arctic Biology, University of Alaska Fairbanks in 2001 (NSF Award Number 9981914). The mission of this Program is to facilitate and enhance arctic research, and to increase research and management efficiency, effectiveness and capability. This is accomplished: 1) through Information Technology (IT) and GIS-RS support of administrative and management infrastructure and production of planning tools for land management and permitting, and 2) through direct consultation and GIS, RS, and Global Posititioning System (GPS) support services to scientists. ToolikGIS provides a rich spatial geodatabase, project-specific data development, spatial analyses, consultation and documentation. 

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5. Bathymetric data from S4 Lake, Toolik Field Station, Alaska (2019).

   https://doi.org/10.18739/A2W08WH55  

   Stuckey, Jason; Noguera, Jorge; McPherson, Rowan (January 2020, NSF Arctic Data Center)

   Toolik Field Station is located in the foothills of the Brooks Range on Alaska's North Slope and is administered by the Institute of Arctic Biology at the University of Alaska Fairbanks (UAF). Toolik Field Station was first established to support an aquatic program designed to obtain base-line data on the North Slope and inland coastal ponds in 1975. Research has expanded over the years to include terrestrial, atmospheric, vertebrate and other taxa, making Toolik home to a long running and diversified body of arctic ecology. The station currently supports a long-standing and rapidly expanding community of scientists and research projects representing individual and collaborative efforts from United States and international institutions. Growth of Toolik-based science, the number of researchers, and the facility from a tented camp to a research station prompted the establishment of the Toolik GIS (Geographical Information Systems) and Remote Sensing (RS) Program as part of the 5 year Cooperative Agreement between the National Science Foundation (NSF) and the Institute of Arctic Biology, University of Alaska Fairbanks in 2001 (NSF Award Number 9981914). The mission of this Program is to facilitate and enhance arctic research, and to increase research and management efficiency, effectiveness and capability. This is accomplished: 1) through Information Technology (IT) and GIS-RS support of administrative and management infrastructure and production of planning tools for land management and permitting, and 2) through direct consultation and GIS, RS, and Global Posititioning System (GPS) support services to scientists. ToolikGIS provides a rich spatial geodatabase, project-specific data development, spatial analyses, consultation and documentation. 

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