Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: docker
https://packages.ecosyste.ms/registries/pypi.org/packages/docker
A Python library for the Docker Engine API.
61 versions
Latest release: over 1 year ago
818 dependent packages
35,287,016 downloads last month
Papers Mentioning docker 39
10.1186/s12859-021-04142-3
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analysesCited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: over 3 years ago
10.1371/journal.pcbi.1008316
Ten simple rules for writing Dockerfiles for reproducible data scienceCited by: 36
Author(s): Daniel Nüst, Vanessa Sochat, Ben Marwick, Stephen J. Eglen, T. Head, Tony Hirst, Benjamin D. Evans
Software Mentions: 11
Published: about 4 years ago
10.1186/s12859-018-2296-x
Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelinesCited by: 47
Author(s): Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele Calogero
Software Mentions: 10
Published: about 6 years ago
10.1093/gigascience/giz149
Refgenie: a reference genome resource managerCited by: 28
Author(s): Michał Stolarczyk, Vincent Reuter, Jason P. Smith, Neal E. Magee, Nathan C. Sheffield
Software Mentions: 9
Published: almost 5 years ago
10.3389/fmicb.2021.649517
Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLSTCited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: over 3 years ago
10.1093/gigascience/giz147
Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapaCited by: 16
Author(s): Miriam Payá‐Milans, Laura Poza‐Viejo, Patxi San Martín-Úriz, David Lara‐Astiaso, Mark D. Wilkinson, Pedro Crevillén
Software Mentions: 8
Published: almost 5 years ago
10.3390/ijms21010293
Docker4Circ: A Framework for the Reproducible Characterization of circRNAs from RNA-Seq DataCited by: 8
Author(s): Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Calogero, Francesca Cordero, Michele De Bortoli, Marco Beccuti
Software Mentions: 8
Published: almost 5 years ago
10.7554/eLife.14334
TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamicsCited by: 104
Author(s): Raphaël Etournay, Matthias Merkel, Marko Popović, Holger Brandl, Natalie A. Dye, Benoît Aigouy, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
Software Mentions: 7
Published: over 8 years ago
10.7717/peerj.5853
BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platformCited by: 3
Author(s): Jianfeng Li, Bowen Cui, Yuting Dai, Lijun Bai, Huang Jy
Software Mentions: 7
Published: about 6 years ago
10.1186/s12859-020-03648-6
A computational framework for modeling and studying pertussis epidemiology and vaccinationCited by: 4
Author(s): Paolo Castagno, Simone Pernice, Gianni Ghetti, Massimiliano Povero, Lorenzo Pradelli, Daniela Paolotti, Gianfranco Balbo, Matteo Sereno, Marco Beccuti
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pcbi.1005209
BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methodsCited by: 203
Author(s): Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capotă, M. Mallar Chakravarty, Nathan W. Churchill, Alexander L. Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Estéban, Guillaume Flandin, Samik Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Franziskus Liem, Pradeep Reddy Raamana, David Raffelt, Christopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith, Stephen C. Strother, Gaël Varoquaux, Yida Wang, Tal Yarkoni, Russell A. Poldrack
Software Mentions: 5
Published: over 7 years ago
10.3389/fdata.2020.00022
The ADC API: A Web API for the Programmatic Query of the AIRR Data CommonsCited by: 22
Author(s): Scott Christley, Ademar Aguiar, George Blanck, Felix Breden, Syed Ahmad Chan Bukhari, Christian E. Busse, Jerome Jaglale, Srilakshmy L. Harikrishnan, Uri Laserson, Bjoern Peters, Artur Rocha, Chaim A. Schramm, Sarah E. Taylor, Jason A. Vander Heiden, Bojan Zimonja, Corey T. Watson, Brian Corrie, Lindsay G. Cowell
Software Mentions: 4
Published: over 4 years ago
10.1186/s12859-017-1663-3
“gnparser”: a powerful parser for scientific names based on Parsing Expression GrammarCited by: 10
Author(s): Dmitry Mozzherin, Alexander A. Myltsev, David J. Patterson
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pone.0177459
Singularity: Scientific containers for mobility of computeCited by: 895
Author(s): Gregory M. Kurtzer, Vanessa Sochat, Michael Bauer
Software Mentions: 4
Published: over 7 years ago
10.1093/database/bax039
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any speciesCited by: 14
Author(s): Richard Challis, Sujai Kumar, Lewis Stevens, Mark Blaxter
Software Mentions: 4
Published: almost 8 years ago
10.3389/fendo.2021.714561
Biased Coupling to β-Arrestin of Two Common Variants of the CB2 Cannabinoid ReceptorCited by: 9
Author(s): Gábor Turu, Eszter Soltész‐Katona, András Tóth, C.C. Juhasz, Miklós Cserző, Ádám Misák, András Balla, Marc G. Caron, László Hunyady
Software Mentions: 4
Published: over 3 years ago
10.3390/s21030772
Multi-Layer Blockchain-Based Security Architecture for Internet of ThingsCited by: 58
Author(s): Houshyar Honar Pajooh, M. A. Rashid, Fakhrul Alam, Serge Demidenko
Software Mentions: 4
Published: almost 4 years ago
10.3390/s18124226
Design Methodology of Microservices to Support Predictive Analytics for IoT ApplicationsCited by: 25
Author(s): Sajjad Ali, Muhammad Aslam Jarwar, Ilyoung Chong
Software Mentions: 3
Published: almost 6 years ago
10.3389/fchem.2020.00046
ChEMBL-Likeness Score and Database GDBChEMBLCited by: 29
Author(s): Sven Bühlmann, Jean‐Louis Reymond
Software Mentions: 3
Published: almost 5 years ago
10.1016/j.xpro.2021.100505
Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolverCited by: 6
Author(s): Alexey Strokach, David Becerra, Carles Corbi‐Verge, Albert Perez-Riba, Philip M. Kim
Software Mentions: 3
Published: over 3 years ago
10.1093/gigascience/giab001
metaXplor: an interactive viral and microbial metagenomic data managerCited by: 2
Author(s): Guilhem Sempéré, Adrien Pétel, Magsen Abbé, Pierre Lefeuvre, Philippe Roumagnac, Frédéric Mahé, Gaël Baurens
Software Mentions: 3
Published: almost 4 years ago
10.1007/s43926-021-00008-5
End-to-end experimentation of a 5G vertical within the scope of blended learningCited by: 12
Author(s): Ngombo Armando, Rui M. Almeida, José Marcelo Fernandes, Jorge Sá Silva, Fernando Boavida
Software Mentions: 3
Published: over 3 years ago
10.3390/s20164393
A Model for the Remote Deployment, Update, and Safe Recovery for Commercial Sensor-Based IoT SystemsCited by: 1
Author(s): Alexandru Radovici, Ioana Culic, Daniel E. Rosner, Flavia Oprea
Software Mentions: 3
Published: over 4 years ago
10.3390/s19214798
MicroServices Suite for Smart City ApplicationsCited by: 23
Author(s): Claudio Badii, Pierfrancesco Bellini, Angelo Difino, Paolo Nesi, Gianni Pantaleo, Michela Paolucci
Software Mentions: 3
Published: about 5 years ago
10.1186/s12864-020-6568-2
GenomeQC: a quality assessment tool for genome assemblies and gene structure annotationsCited by: 48
Author(s): Nancy Manchanda, John L. Portwood, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence‐Dill, Carson M. Andorf, Matthew B. Hufford
Software Mentions: 3
Published: over 4 years ago
10.3390/e23070914
Leadership Hijacking in Docker Swarm and Its ConsequencesCited by: 4
Author(s): Adi Farshteindiker, Rami Puzis
Software Mentions: 2
Published: over 3 years ago
10.1186/s12859-018-2295-y
BITS 2017: the annual meeting of the Italian Society of BioinformaticsCited by: 0
Author(s): Giuliano Armano, Giorgio Fotia, Andrea Manconi
Software Mentions: 2
Published: about 6 years ago
10.1186/s13742-015-0073-6
Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plantCited by: 65
Author(s): Andreas Bremges, Irena Maus, Peter Belmann, Felix Gregor Eikmeyer, Anderson M. Winkler, Andreas Albersmeier, Alfred Pühler, Andreas Schlüter, Alexander Sczyrba
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pcbi.1008194
Discovering functional sequences with RELICS, an analysis method for CRISPR screensCited by: 5
Author(s): Patrick C. Fiaux, Hsiuyi V. Chen, Poshen B. Chen, Aaron R Chen, Graham McVicker
Software Mentions: 2
Published: about 4 years ago
10.1186/s12967-020-02675-4
Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variantsCited by: 12
Author(s): Alice Massacci, Eleonora Sperandio, Lorenzo D’Ambrosio, Mariano Maffei, Fabio Palombo, Luigi Aurisicchio, Gennaro Ciliberto, Matteo Pallocca
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41598-017-06453-z
Identification of a Flavonoid Glucosyltransferase Involved in 7-OH Site Glycosylation in Tea plants (Camellia sinensis)Cited by: 34
Author(s): Xinlong Dai, Juhua Zhuang, Ying-Ling Wu, Peiqiang Wang, Guifu Zhao, Yajun Li, Xiaolan Jiang, Liping Gao, Tao Xia
Software Mentions: 1
Published: over 7 years ago
10.1186/s13742-015-0080-7
NCBI BLAST+ integrated into GalaxyCited by: 164
Author(s): Peter J. A. Cock, John Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo
Software Mentions: 1
Published: about 9 years ago
10.3389/fphar.2018.00127
Tricaproin Isolated From Simarouba glauca Inhibits the Growth of Human Colorectal Carcinoma Cell Lines by Targeting Class-1 Histone DeacetylasesCited by: 18
Author(s): Asha Jose, Motamarri Venkata Naga Lalitha Chaitanya, K Elango, SubbaRao V. Madhunapantula
Software Mentions: 1
Published: over 6 years ago
10.3390/s20113268
Implementation of High-Performance Blockchain Network Based on Cross-Chain Technology for IoT ApplicationsCited by: 17
Author(s): Ting‐Hui Lin, Xu Yang, Taoyi Wang, Peng Tu, Feng Xu, Shengxiong Lao, Siyuan Ma, Hanfeng Wang, Hao Wen-jiang
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0221858
Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assembliesCited by: 3
Author(s): Giltae Song, Jongin Lee, Ju‐Yeon Kim, Seok-Woo Kang, Ho-Yong Lee, Daehong Kwon, Daehwan Lee, Gregory I. Lang, J. Michael Cherry, Jaebum Kim
Software Mentions: 1
Published: about 5 years ago
10.12688/f1000research.8935.1
Bringing your tools to CyVerse Discovery Environment using DockerCited by: 25
Author(s): Upendra Kumar Devisetty, Kathleen Kennedy, Paul Sarando, Nirav Merchant, Eric Lyons
Software Mentions: 1
Published: over 8 years ago
10.1093/database/baz077
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databasesCited by: 21
Author(s): Shawna Spoor, Cuixia Cheng, Lacey-Anne Sanderson, Bradford Condon, Abdullah Almsaeed, Ming Chen, Anthony Bretaudeau, Helena Rasche, Sook Jung, Dorrie Main, Kirstin E. Bett, Margaret Staton, Jill L. Wegrzyn, F. Alex Feltus, Stephen P. Ficklin
Software Mentions: 1
Published: almost 6 years ago
10.12688/f1000research.20590.2
Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat mapsCited by: 26
Author(s): Michaël Ryan, Mark Stucky, Chris Wakefield, James Melott, Rehan Akbani, John N. Weinstein, Bradley M. Broom
Software Mentions: 1
Published: over 4 years ago
10.1186/s12864-020-06875-6
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS dataCited by: 4
Author(s): Chi-Ming Leung, Dinghua Li, Xin Yan, Wai-Chun Law, Yifan Zhang, Hing-Fung Ting, Ruibang Luo, Tak-Wah Lam
Software Mentions: 1
Published: almost 4 years ago