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Yabi specifications

Information


Unique identifier OMICS_01148
Name Yabi
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Parallelization MapReduce
License GNU General Public License version 2.0
Computer skills Advanced
Version 9.9.7
Stability Stable
Requirements
memcached, sqlite
High performance computing Yes
Maintained No

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Documentation


Maintainers


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Additional information


http://yabi.readthedocs.io/en/latest/

Publication for Yabi

Yabi citations

 (16)
library_books

Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice

2017
Front Plant Sci
PMCID: 5662881
PMID: 29123534
DOI: 10.3389/fpls.2017.01770

[…] es not have to be uploaded to a remote site, but requires expertise in software installation and the Linux environment.The use of web based analytical environments such as Galaxy (Afgan et al., ) and Yabi (Hunter et al., ) appear to offer a solution, but their real advantage only comes if they are installed locally. Local installation of such environments allows them to be customized with the addi […]

library_books

An internet based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids

2017
BMC Bioinformatics
PMCID: 5225587
PMID: 28077064
DOI: 10.1186/s12859-016-1428-4

[…] We have implemented an automated viral surveillance and diagnosis toolkit using the Yabi web-based analytical environment that enables improved detection of viruses and viroids pathogens. We found that all single stranded RNA (+) viruses found in this study were assembled using exclu […]

library_books

Towards agile large scale predictive modelling in drug discovery with flow based programming design principles

2016
J Cheminform
PMCID: 5123367
PMID: 27942268
DOI: 10.1186/s13321-016-0179-6

[…] for new workflows. In many WMS tools, complex workflows cannot be created without combining the workflow tool with shell scripts [], pointing to their limitations for complex use cases.Galaxy [–] and Yabi [] are GUI-centric tools or frameworks with a client/server architecture that require the installation of a server daemon and meta data to support automatic GUI generation. By their GUI-centric n […]

library_books

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

2016
PMCID: 5034103
PMID: 27530749
DOI: 10.1038/emi.2016.90

[…] rated using USEARCH (v6.2). Each sample file was then checked for chimeras in USEARCH using the UCHIME de novo method, which were removed along with singleton reads. The files were then imported into YABI, where a BLASTn search was carried out against the NCBI GenBank nucleotide database., BLAST files were downloaded and imported into the program MEtaGenome ANalyzer (MEGAN v4.70.4) for taxonomic […]

library_books

Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases

2016
PMCID: 4932659
PMID: 27441714
DOI: 10.1089/big.2015.0057

[…] works, Leipzig groups existing technologies according to their interaction mode into command-line/application programming interface (API) and workbench approaches. The first group includes Snakemake, Yabi, Chipster, or Mobyle and relies on textual workflow construction in a script-like format. Certain tools in this group, such as Chipster, enable Web-based collaborative development of workflows.Th […]

library_books

Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM)

2015
Sci Rep
PMCID: 4675079
PMID: 26658160
DOI: 10.1038/srep17475

[…] exact matches) for each sample was generated using USEARCH. These files were then analysed for chimeras in USEARH using the UCHIME de novo method and removed, along with singletons and imported into YABI where a BLASTn search was conducted against the National Centre for Biotechnology Information (NCBI) GenBank NR database. The resultant BLAST files were then imported into the program MEtaGenome […]

Citations

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Yabi institution(s)
Centre for Comparative Genomics, Murdoch, WA, Australia
Yabi funding source(s)
Supported by the Australian Research Collaboration Service, the Australian National Data Service and Bioplatforms Australia through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund Super Science Initiative, as well as by iVEC.

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