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SciApps: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data

Liya Wang, Zhenyuan Lu, Melissa delaBastide, Peter Van Buren, Xiaofei Wang, Cornel Ghiban, Michael Regulski, Jorg Drenkow, Xiaosa Xu, Carlos Ortiz Ramirez, Cristina F. Marco, Jason Williams (+9 others)
2019 biorxiv/medrxiv  
The SciApps portal is a flexible platform that allows integration of new analysis tools, workflows, and genomic data from multiple projects.  ...  Based on the SciApps workflow platform, we generated new components to support the complete cycle of the MaizeCODE data management.  ...  a bioinformatics workflow platform called SciApps (Wang et al., 2018) .  ... 
doi:10.1101/852269 fatcat:kegvnnwljfhctntcnsqdzqghsq

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

Liya Wang, Zhenyuan Lu, Melissa delaBastide, Peter Van Buren, Xiaofei Wang, Cornel Ghiban, Michael Regulski, Jorg Drenkow, Xiaosa Xu, Carlos Ortiz-Ramirez, Cristina F. Marco, Sara Goodwin (+9 others)
2020 Frontiers in Plant Science  
The SciApps portal is a flexible platform that allows the integration of new analysis tools, workflows, and genomic data from multiple projects.  ...  Based on the SciApps workflow platform, we generated new components to support the complete cycle of MaizeCODE data management.  ...  To automate bioinformatics analysis over both the XSEDE/TACC cloud and CyVerse Data Store, we developed a bioinformatics workflow platform called SciApps (Wang et al., 2018) .  ... 
doi:10.3389/fpls.2020.00289 pmid:32296450 pmcid:PMC7136414 fatcat:ntooyljyfvf5lhc3gf7jzqimam

BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations [article]

Liya Wang
2020 bioRxiv   pre-print
The workflow is intuitive and straightforward, facilitating its adoption by users without bioinformatics analysis skills.  ...  In this study, we developed the BSAseq workflow, which includes an automated bioinformatics analysis pipeline with a probabilistic model for estimating the segregation region and an interactive Shiny web  ...  Acknowledgments We thank the CyVerse project, the XSEDE project at TACC, and CSHL for providing computational resources.  ... 
doi:10.1101/2020.04.08.029801 fatcat:bj7phtt2cbghxbqbvjgal7nrcm

The MGX framework for microbial community analysis

Sebastian Jaenicke
2020
Acknowledgements Alexander Goesmann and Jens Stoye are acknowledged for the opportunity and supervision of this PhD thesis.  ...  My colleagues Jochen Blom and Burkhard Linke are thanked for advice, collaboration on many different projects and many fruitful and sometimes heated discussions. Gießen, June 2019 Sebastian Jaenicke  ...  CyVerse CyVerse (Merchant et al., 2016) , formerly known as iPlant Collaborative, is a virtual infrastructure for data management and analysis.  ... 
doi:10.4119/unibi/2940338 fatcat:ef3zg6nqlrhdzm4ysj533576ee