More Like this

1. Terrestrial Parasite Tracker indexed biotic interactions and review summary

   https://doi.org/10.5281/zenodo.6761707  

   Poelen, Jorrit H.; Seltmann, Katja C.; Campbell, Mariel; Orlofske, Sarah A.; Light, Jessica E.; Tucker, Erika M.; Demboski, John R; McElrath, Tommy; Grinter, Christopher C; Diaz-Bastin, Rachel; et al (January 2022, Zenodo)

   {"Abstract":["PLEASE CONTACT AUTHORS IF YOU CONTRIBUTE AND WOULD LIKE TO BE LISTED AS A CO-AUTHOR. (this message will be removed some time weeks/months after the first publication)<\/p>\n\nTerrestrial Parasite Tracker indexed biotic interactions and review summary.<\/p>\n\nThe Terrestrial Parasite Tracker (TPT) project began in 2019 and is funded by the National Science foundation to mobilize data from vector and ectoparasite collections to data aggregators (e.g., iDigBio, GBIF) to help build a comprehensive picture of arthropod host-association evolution, distributions, and the ecological interactions of disease vectors which will assist scientists, educators, land managers, and policy makers. Arthropod parasites often are important to human and wildlife health and safety as vectors of pathogens, and it is critical to digitize these specimens so that they, and their biotic interaction data, will be available to help understand and predict the spread of human and wildlife disease.<\/p>\n\nThis data publication contains versioned TPT associated datasets and related data products that were tracked, reviewed and indexed by Global Biotic Interactions (GloBI) and associated tools. GloBI provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, pathogen-host, parasite-host) by combining existing open datasets using open source software.<\/p>\n\nIf you have questions or comments about this publication, please open an issue at https://github.com/ParasiteTracker/tpt-reporting or contact the authors by email.<\/p>\n\nFunding:\nThe creation of this archive was made possible by the National Science Foundation award "Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease," Award numbers DBI:1901932 and DBI:1901926<\/p>\n\nReferences:\nJorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.<\/p>\n\nGloBI Data Review Report<\/p>\n\nDatasets under review:\n - University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. accessed via https://github.com/EMTuckerLabUMMZ/ummzi/archive/6731357a377e9c2748fc931faa2ff3dc0ce3ea7a.zip on 2022-06-24T14:02:48.801Z\n - Academy of Natural Sciences Entomology Collection for the Parasite Tracker Project accessed via https://github.com/globalbioticinteractions/ansp-para/archive/5e6592ad09ec89ba7958266ad71ec9d5d21d1a44.zip on 2022-06-24T14:04:22.091Z\n - Bernice Pauahi Bishop Museum, J. Linsley Gressitt Center for Research in Entomology accessed via https://github.com/globalbioticinteractions/bpbm-ent/archive/c085398dddd36f8a1169b9cf57de2a572229341b.zip on 2022-06-24T14:04:37.692Z\n - Texas A&M University, Biodiversity Teaching and Research Collections accessed via https://github.com/globalbioticinteractions/brtc-para/archive/f0a718145b05ed484c4d88947ff712d5f6395446.zip on 2022-06-24T14:06:40.154Z\n - Brigham Young University Arthropod Museum accessed via https://github.com/globalbioticinteractions/byu-byuc/archive/4a609ac6a9a03425e2720b6cdebca6438488f029.zip on 2022-06-24T14:06:51.420Z\n - California Academy of Sciences Entomology accessed via https://github.com/globalbioticinteractions/cas-ent/archive/562aea232ec74ab615f771239451e57b057dc7c0.zip on 2022-06-24T14:07:16.371Z\n - Clemson University Arthropod Collection accessed via https://github.com/globalbioticinteractions/cu-cuac/archive/6cdcbbaa4f7cec8e1eac705be3a999bc5259e00f.zip on 2022-06-24T14:07:40.925Z\n - Denver Museum of Nature and Science (DMNS) Parasite specimens (DMNS:Para) accessed via https://github.com/globalbioticinteractions/dmns-para/archive/a037beb816226eb8196533489ee5f98a6dfda452.zip on 2022-06-24T14:08:00.730Z\n - Field Museum of Natural History IPT accessed via https://github.com/globalbioticinteractions/fmnh/archive/6bfc1b7e46140e93f5561c4e837826204adb3c2f.zip on 2022-06-24T14:18:51.995Z\n - Illinois Natural History Survey Insect Collection accessed via https://github.com/globalbioticinteractions/inhs-insects/archive/38692496f590577074c7cecf8ea37f85d0594ae1.zip on 2022-06-24T14:19:37.563Z\n - UMSP / University of Minnesota / University of Minnesota Insect Collection accessed via https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip on 2022-06-24T14:20:27.232Z\n - Milwaukee Public Museum Biological Collections Data Portal accessed via https://github.com/globalbioticinteractions/mpm/archive/9f44e99c49ec5aba3f8592cfced07c38d3223dcd.zip on 2022-06-24T14:20:46.185Z\n - Museum for Southern Biology (MSB) Parasite Collection accessed via https://github.com/globalbioticinteractions/msb-para/archive/178a0b7aa0a8e14b3fe953e770703fe331eadacc.zip on 2022-06-24T15:16:07.223Z\n - The Albert J. Cook Arthropod Research Collection accessed via https://github.com/globalbioticinteractions/msu-msuc/archive/38960906380443bd8108c9e44aeff4590d8d0b50.zip on 2022-06-24T16:09:40.702Z\n - Ohio State University Acarology Laboratory accessed via https://github.com/globalbioticinteractions/osal-ar/archive/876269d66a6a94175dbb6b9a604897f8032b93dd.zip on 2022-06-24T16:10:00.281Z\n - Frost Entomological Museum, Pennsylvania State University accessed via https://github.com/globalbioticinteractions/psuc-ento/archive/30b1f96619a6e9f10da18b42fb93ff22cc4f72e2.zip on 2022-06-24T16:10:07.741Z\n - Purdue Entomological Research Collection accessed via https://github.com/globalbioticinteractions/pu-perc/archive/e0909a7ca0a8df5effccb288ba64b28141e388ba.zip on 2022-06-24T16:10:26.654Z\n - Texas A&M University Insect Collection accessed via https://github.com/globalbioticinteractions/tamuic-ent/archive/f261a8c192021408da67c39626a4aac56e3bac41.zip on 2022-06-24T16:10:58.496Z\n - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/825678ad02df93f6d4469f9d8b7cc30151b9aa45.zip on 2022-06-24T16:12:29.854Z\n - University of Hawaii Insect Museum accessed via https://github.com/globalbioticinteractions/uhim/archive/53fa790309e48f25685e41ded78ce6a51bafde76.zip on 2022-06-24T16:12:41.408Z\n - University of New Hampshire Collection of Insects and other Arthropods UNHC-UNHC accessed via https://github.com/globalbioticinteractions/unhc/archive/f72575a72edda8a4e6126de79b4681b25593d434.zip on 2022-06-24T16:12:59.500Z\n - Scott L. Gardner and Gabor R. Racz (2021). University of Nebraska State Museum - Parasitology. Harold W. Manter Laboratory of Parasitology. University of Nebraska State Museum. accessed via https://github.com/globalbioticinteractions/unl-nsm/archive/6bcd8aec22e4309b7f4e8be1afe8191d391e73c6.zip on 2022-06-24T16:13:06.914Z\n - Data were obtained from specimens belonging to the United States National Museum of Natural History (USNM), Smithsonian Institution, Washington DC and digitized by the Walter Reed Biosystematics Unit (WRBU). accessed via https://github.com/globalbioticinteractions/usnmentflea/archive/ce5cb1ed2bbc13ee10062b6f75a158fd465ce9bb.zip on 2022-06-24T16:13:38.013Z\n - US National Museum of Natural History Ixodes Records accessed via https://github.com/globalbioticinteractions/usnm-ixodes/archive/c5fcd5f34ce412002783544afb628a33db7f47a6.zip on 2022-06-24T16:13:45.666Z\n - Price Institute of Parasite Research, School of Biological Sciences, University of Utah accessed via https://github.com/globalbioticinteractions/utah-piper/archive/43da8db550b5776c1e3d17803831c696fe9b8285.zip on 2022-06-24T16:13:54.724Z\n - University of Wisconsin Stevens Point, Stephen J. Taft Parasitological Collection accessed via https://github.com/globalbioticinteractions/uwsp-para/archive/f9d0d52cd671731c7f002325e84187979bca4a5b.zip on 2022-06-24T16:14:04.745Z\n - Giraldo-Calderón, G. I., Emrich, S. J., MacCallum, R. M., Maslen, G., Dialynas, E., Topalis, P., \u2026 Lawson, D. (2015). VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic acids research, 43(Database issue), D707\u2013D713. doi:10.1093/nar/gku1117. accessed via https://github.com/globalbioticinteractions/vectorbase/archive/00d6285cd4e9f4edd18cb2778624ab31b34b23b8.zip on 2022-06-24T16:14:11.965Z\n - WIRC / University of Wisconsin Madison WIS-IH / Wisconsin Insect Research Collection accessed via https://github.com/globalbioticinteractions/wis-ih-wirc/archive/34162b86c0ade4b493471543231ae017cc84816e.zip on 2022-06-24T16:14:29.743Z\n - Yale University Peabody Museum Collections Data Portal accessed via https://github.com/globalbioticinteractions/yale-peabody/archive/43be869f17749d71d26fc820c8bd931d6149fe8e.zip on 2022-06-24T16:23:29.289Z<\/p>\n\nGenerated on:\n2022-06-24<\/p>\n\nby:\nGloBI's Elton 0.12.4 \n(see https://github.com/globalbioticinteractions/elton).<\/p>\n\nNote that all files ending with .tsv are files formatted \nas UTF8 encoded tab-separated values files.<\/p>\n\nhttps://www.iana.org/assignments/media-types/text/tab-separated-values<\/p>\n\n\nIncluded in this review archive are:<\/p>\n\nREADME:\n  This file.<\/p>\n\nreview_summary.tsv:\n  Summary across all reviewed collections of total number of distinct review comments.<\/p>\n\nreview_summary_by_collection.tsv:\n  Summary by reviewed collection of total number of distinct review comments.<\/p>\n\nindexed_interactions_by_collection.tsv: \n  Summary of number of indexed interaction records by institutionCode and collectionCode.<\/p>\n\nreview_comments.tsv.gz:\n  All review comments by collection.<\/p>\n\nindexed_interactions_full.tsv.gz:\n  All indexed interactions for all reviewed collections.<\/p>\n\nindexed_interactions_simple.tsv.gz:\n  All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.<\/p>\n\ndatasets_under_review.tsv:\n  Details on the datasets under review.<\/p>\n\nelton.jar: \n  Program used to update datasets and generate the review reports and associated indexed interactions.<\/p>\n\ndatasets.zip:\n  Source datasets used by elton.jar in process of executing the generate_report.sh script.<\/p>\n\ngenerate_report.sh:\n  Program used to generate the report<\/p>\n\ngenerate_report.log:\n  Log file generated as part of running the generate_report.sh script\n <\/p>"]} 

   more » « less
2. Einsums/Einsums: v1.0.0 release

   https://doi.org/10.5281/zenodo.14968301  

   Turney, Justin; Briggs, Connor; Burns, Lori A; Jiang, Andy; Mitchell, Erica (January 2025, Zenodo)

   What's Changed Optimize some vector operations by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/90 Add a way to create a tensor view of a pointer by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/92 Add python bindings by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/87 Update IndexUtils.hpp by @jturney in https://github.com/Einsums/Einsums/pull/95 Einsums Restructuring by @jturney in https://github.com/Einsums/Einsums/pull/97 Fix print. by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/102 Docs: Docs were not deploying by @jturney in https://github.com/Einsums/Einsums/pull/104 Fix performance issues by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/107 Fix parsing bug by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/110 Fix performance again by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/111 Fixing docs by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/101 Docs: Tweaks for consistency. by @jturney in https://github.com/Einsums/Einsums/pull/120 Move Design Patterns by @cgbriggs99 in https://github.com/Einsums/Einsums/pull/121 Full Changelog: https://github.com/Einsums/Einsums/compare/v0.6.1...v1.0.0 

   more » « less
3. QMCSoftware/QMCSoftware: QMCPy v2.0

   https://doi.org/10.5281/zenodo.16822646  

   Sorokin, Aleksei G; Hickernell, Fred J; Jain, Adit; Choi, Sou-Cheng; Rathinavel, Jagadeeswaran; Zhang, David; Lin, Lijia; Robbe, Pieterjan; Pascual_Kwan, Ally; Haji-Ali, Abdul-Lateef; et al (August 2025, Zenodo)

   What's Changed Hpc stabilize by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/382 Update README.md by @zitterbewegung in https://github.com/QMCSoftware/QMCSoftware/pull/385 Geometric brownian motion by @larissensium in https://github.com/QMCSoftware/QMCSoftware/pull/392 QMCPy Overhaul by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/391 v2.0 by @alegresor in https://github.com/QMCSoftware/QMCSoftware/pull/394 New Contributors @larissensium made their first contribution in https://github.com/QMCSoftware/QMCSoftware/pull/392 Full Changelog: https://github.com/QMCSoftware/QMCSoftware/compare/v1.6.1...v2.0 

   more » « less
4. A Biodiversity Dataset Graph: Gbif, Idigbio, Biocase

   https://doi.org/10.5281/zenodo.1472394  

   Poelen, Jorrit H. (January 2018, Zenodo)

   Biodiversity datasets, or descriptions of biodiversity datasets, are increasingly available through open digital data infrastructures such as Global Biodiversity Information Facility (GBIF, https://gbif.org), Integrated Digitized Biocollections (iDigBio, https://www.idigbio.org) and the Biological Collection Access Service (BioCASE, http://www.biocase.org). </p> However, little is known about how these networks, and the data accessed through them, change over time. This dataset provide snapshots of the biodiversity dataset graphs as tracked by Preston (https://github.com/bio-guoda/preston , https://doi.org/10.5281/zenodo.1410543 ).</p> The rdf/nquad and tsv snapshots were generated using the respective commands:</p> preston ls | bzip2 > preston-ls.nq.bz2</p> and</p> preston ls --log tsv | bzip2 > preston-ls.tsv.bz2</p> For convenience, the first 100 uncompressed entries of both files are included, as well as the sha256 hashes of the content of the files.</p> 

   more » « less
5. Cloud-Drift/clouddrift: v0.40.0

   https://doi.org/10.5281/zenodo.11081647  

   Elipot, Shane; Miron, Philippe; Curcic, Milan; Santana, Kevin; Lumpkin, Rick (January 2024, Zenodo)

   What's Changed 🔎 type comparison with isinstance by @philippemiron in https://github.com/Cloud-Drift/clouddrift/pull/491 🧹 Update type comparison in ragged.py by @selipot in https://github.com/Cloud-Drift/clouddrift/pull/497 🧹 Update random number generator in gdp1h and gdp6h adapters by @selipot in https://github.com/Cloud-Drift/clouddrift/pull/496 🐛 fix locationtype bug in dataset by @kevinsantana11 in https://github.com/Cloud-Drift/clouddrift/pull/494 Update .zenodo.json by @selipot in https://github.com/Cloud-Drift/clouddrift/pull/498 ++ increment version (v0.40.0) by @kevinsantana11 in https://github.com/Cloud-Drift/clouddrift/pull/499 Full Changelog: https://github.com/Cloud-Drift/clouddrift/compare/v0.39.0...v0.40.0 

   more » « less