cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.1479668
title: Bioinformatic Pipeline: Genomic Diversity Landscape Of The Honey Bee Gut Microbiota

description: This data-set describes the full bioinformatic pipeline used to analyze 54 metagenomic samples of the honey bee gut microbiota. Each sample was isolated from an individual honey bee, and all samples originate from two colonies of the Engel laboratory at the University of Lausanne, Switzerland. The full raw data-set is available from the sequence-read archive: SRP150166.

A publication based on this analysis is currently under review, with the title: "Genomic diversity landscape of the honey bee gut microbiota", and an upload to Biorxiv is also underway.

The data-set contains tar-balls for the different main workflows of the analysis. Dowload and unpack to view the contents (tar -zxvf filename.tar.gz). For each workflow, all directories contain README.txt files, describing the contents of the directory. Due to size constraints, some intermediate files have been omitted, and some workflows are demonstrated for a subset of the data. However, the full analysis can be reproduced from the raw data, using the provided scripts.

Scripts are included within workflow directories, and are also provided as a separate tar-ball for convenience. All perl-scripts come with documentation, which can be viewed by typing: "perl script_name.pl -h". For R scripts, the usage is indicated as a comment in the top lines of each script. Note that many of the scripts require specific input-files to be present in the run-directory. Their usage is demonstrated within the workflow directories in bash-scripts (*.sh). Commands used for generating plots and some statistics are given within workflow directories in text-files "R.commands" when applicable.

Aside from custom code, the pipeline also utilizes various open-source Software packages, which are detailed in the file "software_dependencies.txt". Note, while many of the scripts will run fast on any computer, some steps of the pipeline are computationally demanding, and will require significant computing time, as well as storage space. When scripts are known to be time-consuming, this is indicated in the script help message.
DOI: 10.5445/ir/1000087278
title: Deutsches Mobilitätspanel (MOP) - Statistiken zur Alltagsmobilität sowie zu Fahrleistung und Kraftstoffverbrauch 2007 - 2016
DOI: 10.5517/ccdc.csd.cc1zp651
title: CCDC 1837623: Experimental Crystal Structure Determination

description: Related Article: Lizhu Chen, Hunter A. Dulaney, Branford O. Wilkins, Sarah Farmer, Yanbing Zhang, Frank R. Fronczek, Jonah W. Jurss|2018|New J.Chem.|42|18667|doi:10.1039/C8NJ02072H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zp662
title: CCDC 1837624: Experimental Crystal Structure Determination

description: Related Article: Lizhu Chen, Hunter A. Dulaney, Branford O. Wilkins, Sarah Farmer, Yanbing Zhang, Frank R. Fronczek, Jonah W. Jurss|2018|New J.Chem.|42|18667|doi:10.1039/C8NJ02072H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zp785
title: CCDC 1837657: Experimental Crystal Structure Determination

description: Related Article: Xiang Zhao,  Huajun Yang,  Edward T. Nguyen,  Joshua Padilla,  Xitong Chen,  Pingyun Feng,  Xianhui Bu|2018|J.Am.Chem.Soc.|140|13566|doi:10.1021/jacs.8b08316
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zp796
title: CCDC 1837658: Experimental Crystal Structure Determination

description: Related Article: Xiang Zhao,  Huajun Yang,  Edward T. Nguyen,  Joshua Padilla,  Xitong Chen,  Pingyun Feng,  Xianhui Bu|2018|J.Am.Chem.Soc.|140|13566|doi:10.1021/jacs.8b08316
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpgdj
title: CCDC 1837878: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2052t3
title: CCDC 1851934: Experimental Crystal Structure Determination

description: Related Article: Kunchala Dhanunjayarao, Shreenibasa Sa, Basava Punna Rao Aradhyula, Krishnan Venkatasubbaiah|2018|Tetrahedron|74|5819|doi:10.1016/j.tet.2018.08.019
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.ccvkrw0
title: CCDC 791643: Experimental Crystal Structure Determination

description: Related Article: Antonis Messinis, William R. H. Wright, Andrei S. Batsanov, Judith A. K. Howard, Martin J. Hanton, and Philip W. Dyer|2018|ACS Catalysis|8|11235|doi:10.1021/acscatal.8b02201
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.1479667
title: Bioinformatic Pipeline: Genomic Diversity Landscape Of The Honey Bee Gut Microbiota

description: This data-set describes the full bioinformatic pipeline used to analyze 54 metagenomic samples of the honey bee gut microbiota. Each sample was isolated from an individual honey bee, and all samples originate from two colonies of the Engel laboratory at the University of Lausanne, Switzerland. The full raw data-set is available from the sequence-read archive: SRP150166.

A publication based on this analysis is currently under review, with the title: "Genomic diversity landscape of the honey bee gut microbiota", and an upload to Biorxiv is also underway.

The data-set contains tar-balls for the different main workflows of the analysis. Dowload and unpack to view the contents (tar -zxvf filename.tar.gz). For each workflow, all directories contain README.txt files, describing the contents of the directory. Due to size constraints, some intermediate files have been omitted, and some workflows are demonstrated for a subset of the data. However, the full analysis can be reproduced from the raw data, using the provided scripts.

Scripts are included within workflow directories, and are also provided as a separate tar-ball for convenience. All perl-scripts come with documentation, which can be viewed by typing: "perl script_name.pl -h". For R scripts, the usage is indicated as a comment in the top lines of each script. Note that many of the scripts require specific input-files to be present in the run-directory. Their usage is demonstrated within the workflow directories in bash-scripts (*.sh). Commands used for generating plots and some statistics are given within workflow directories in text-files "R.commands" when applicable.

Aside from custom code, the pipeline also utilizes various open-source Software packages, which are detailed in the file "software_dependencies.txt". Note, while many of the scripts will run fast on any computer, some steps of the pipeline are computationally demanding, and will require significant computing time, as well as storage space. When scripts are known to be time-consuming, this is indicated in the script help message.
DOI: 10.5517/ccdc.csd.cc1n7hzc
title: CCDC 1526563: Experimental Crystal Structure Determination

description: Related Article: Qingsong Dai, Xiang Zhang, Kai‐Chuan Yang, Mao‐Hua Li, Jie Yang, Qing‐Zhu Li, Xin Feng, Bo Han, Jun‐Long Li|2018|Adv.Synth.Catal.|360|4435|doi:10.1002/adsc.201800806
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1n7rrd
title: CCDC 1526804: Experimental Crystal Structure Determination

description: Related Article: BC Manjunath, S Madan Kuma, GS Lingaraju, MP Sadashiva, NK Lokanath, K Byrappa|2018|Der Pharma Chemica: J. Med. Chem. Pharm. Chem. Comput. Chem|10|1|
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1nbbw6
title: CCDC 1529288: Experimental Crystal Structure Determination

description: Related Article: Miroslava Puchoňová, Simona Matejová, Jozef Švorec, Milan Mazúr, Vladimír Jorík, Ján Moncoľ, Dušan Valigura|2019|Inorg.Chim.Acta|486|324|doi:10.1016/j.ica.2018.10.059
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1pl8n6
title: CCDC 1566698: Experimental Crystal Structure Determination

description: Related Article: Lucas W. Souza, Richard A. Squitieri, Christine A. Dimirjian, Blanka M. Hodur, Leslie A. Nickerson, Corinne N. Penrod, Jesus Cordova, James C. Fettinger, Jared T. Shaw|2018|Angew.Chem.,Int.Ed.|57|15213|doi:10.1002/anie.201809344
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpgfk
title: CCDC 1837879: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpggl
title: CCDC 1837880: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpghm
title: CCDC 1837881: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpgjn
title: CCDC 1837882: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpgkp
title: CCDC 1837883: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpglq
title: CCDC 1837884: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpgmr
title: CCDC 1837885: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpgns
title: CCDC 1837886: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpgpt
title: CCDC 1837887: Experimental Crystal Structure Determination

description: Related Article: Ross Davidson, Yu-Ting Hsu, Gareth C. Griffiths, Chenfei Li, Dmitry Yufit, Robert Pal, Andrew Beeby|2018|Inorg.Chem.|57|14450|doi:10.1021/acs.inorgchem.8b02818
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpqhw
title: CCDC 1838129: Experimental Crystal Structure Determination

description: Related Article: Zheng Gu, Bo Wu, Guo‐Fang Jiang, Yong‐Gui Zhou|2018|Chin.J.Chem.|36|1130|doi:10.1002/cjoc.201800330
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2057gx
title: CSD 1852078: Experimental Crystal Structure Determination

description: Related Article: Zhizhong Zhang, Ying Wang, Bingbing Zhang, Zhihua Yang, ShiLie Pan|2018|Chem.-Eur.J.|24|11267|doi:10.1002/chem.201802866
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc205c7t
title: CCDC 1852195: Experimental Crystal Structure Determination

description: Related Article: Monika Joharian, Ali Morsali, Alireza Azhdari Tehrani, Lucia Carlucci, Davide M. Proserpio|2018|Green Chemistry|20|5336|doi:10.1039/C8GC02367K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc205dg2
title: CCDC 1852233: Experimental Crystal Structure Determination

description: Related Article: Sören Rösel,  Jonathan Becker,  Wesley D. Allen,  Peter R. Schreiner|2018|J.Am.Chem.Soc.|140|14421|doi:10.1021/jacs.8b09145
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20g1q8
title: CCDC 1860549: Experimental Crystal Structure Determination

description: Related Article: Yu-Ting Hung, Glenn P.A. Yap, Klaus H. Theopold|2019|Polyhedron|157|381|doi:10.1016/j.poly.2018.10.030
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20g1r9
title: CCDC 1860550: Experimental Crystal Structure Determination

description: Related Article: Yu-Ting Hung, Glenn P.A. Yap, Klaus H. Theopold|2019|Polyhedron|157|381|doi:10.1016/j.poly.2018.10.030
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20g1sb
title: CCDC 1860551: Experimental Crystal Structure Determination

description: Related Article: Yu-Ting Hung, Glenn P.A. Yap, Klaus H. Theopold|2019|Polyhedron|157|381|doi:10.1016/j.poly.2018.10.030
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20g1tc
title: CCDC 1860552: Experimental Crystal Structure Determination

description: Related Article: Yu-Ting Hung, Glenn P.A. Yap, Klaus H. Theopold|2019|Polyhedron|157|381|doi:10.1016/j.poly.2018.10.030
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20g1vd
title: CCDC 1860553: Experimental Crystal Structure Determination

description: Related Article: Yu-Ting Hung, Glenn P.A. Yap, Klaus H. Theopold|2019|Polyhedron|157|381|doi:10.1016/j.poly.2018.10.030
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20g2n7
title: CCDC 1860578: Experimental Crystal Structure Determination

description: Related Article: Fengli Li, Weiguang Sun, Jiankun Guan, Yuanyuan Lu, Shuang Lin, Sitian Zhang, Weixi Gao, Junjun Liu, Guang Du, Jianping Wang, Hucheng Zhu, Changxing Qi, Zhengxi Hu, Yonghui Zhang|2018|Org.Biomol.Chem.|16|8751|doi:10.1039/C8OB02353K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.