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Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale

Alex V. Kotlar, Cristina E. Trevino, Michael E. Zwick, David J. Cutler, Thomas S. Wingo
2018 Genome Biology  
Manipulating data at this scale is difficult. To find the alleles that 42 contribute to traits of interest, two steps must occur.  ...  Bystro (https://bystro.io/) is the first online, cloud-based application that 23 makes variant annotation and filtering accessible to all researchers for terabyte-sized whole-24 genome experiments containing  ...  We thank 551 Viren Patel and the Emory Integrated Genomics Core (EIGC) for technical support.  ... 
doi:10.1186/s13059-018-1387-3 pmid:29409527 pmcid:PMC5801807 fatcat:qv2f4sassrfknohlavfp5g4tyi

Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale [article]

Alex V. Kotlar, Cristina E. Trevino, Michael E. Zwick, David J. Cutler, Thomas S. Wingo
2017 bioRxiv   pre-print
Bystro (https://bystro.io/) is the first online, cloud-based application that makes variant annotation and filtering accessible to all researchers for terabyte-sized whole-genome experiments containing  ...  Its key innovation is a general-purpose, natural-language search engine that enables users to identify and export alleles and samples of interest in milliseconds.  ...  We thank Viren Patel and the Emory Integrated Genomics Core (EIGC) for technical support.  ... 
doi:10.1101/146514 fatcat:p7buiiogtzexlefkjpbstxfqya

BioExcel Webinar #8 - Large-scale analytical workflows on the cloud using Galaxy and Globus

Ravi Madduri
2016 Zenodo  
In this BioExcel webinar, Ravi will present Globus Genomics and the technologies used to achieve large-scale analytical Galaxy workflows on the cloud.  ...  of next-generation sequencing (NGS) genomic data, combining Galaxy workflows with cloud technologies like Amazon EC2 and Globus File Transfer.  ...  Analytical Workflows on the Cloud using Galaxy and Globus Ravi K.  ... 
doi:10.5281/zenodo.3822342 fatcat:22ytw7zkxjfaro2r5bejeaggci

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud

Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor Makunin, Derek Benson, Mark Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie, Christophe Antoniewski
2015 PLoS ONE  
A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference  ...  Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.  ...  Acknowledgments The Genomics Virtual Laboratory has been developed by the Genomics Virtual Laboratory project team (https://genome.edu.au/wiki/About) with funding, in part, supported by the Genomics Virtual  ... 
doi:10.1371/journal.pone.0140829 pmid:26501966 pmcid:PMC4621043 fatcat:6s4gje7sr5eotjs6yfju7ae5hu

Harnessing cloud computing with Galaxy Cloud

Enis Afgan, Dannon Baker, Nate Coraor, Hiroki Goto, Ian M Paul, Kateryna D Makova, Anton Nekrutenko, James Taylor
2011 Nature Biotechnology  
Importantly, cloud resources can provide storage and computation at far less cost than dedicated resources for certain use cases.  ...  Sequencing has moved out of the genome centers into core facilities and individual labs where any investigator can access them for modest and progressively declining cost.  ...  Efforts of the Galaxy Team (Enis Afgan, Dannon Baker, Dan Blankenberg, Nate Coraor, Jeremy Goecks, Greg Von Kuster, Ross Lazarus, Kanwei Li, Kelly Vincent) were instrumental for making this work happen  ... 
doi:10.1038/nbt.2028 pmid:22068528 pmcid:PMC3868438 fatcat:bi254ehyubhzxgdat6sbuztt2e

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses

Bo Liu, Ravi K Madduri, Borja Sotomayor, Kyle Chard, Lukasz Lacinski, Utpal J Dave, Jianqiang Li, Chunchen Liu, Ian T Foster
2014 Journal of Biomedical Informatics  
Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented  ...  Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools).  ...  We are grateful to Amazon, Inc., for an award of Amazon Web Services time that facilitated early experiments. We thank Globus Genomics users for their invaluable contributions.  ... 
doi:10.1016/j.jbi.2014.01.005 pmid:24462600 pmcid:PMC4203338 fatcat:kxtrxip53zhipi2ii63krmqyp4

Experiences building Globus Genomics: a next-generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services

Ravi K. Madduri, Dinanath Sulakhe, Lukasz Lacinski, Bo Liu, Alex Rodriguez, Kyle Chard, Utpal J. Dave, Ian T. Foster
2014 Concurrency and Computation  
We describe Globus Genomics, a system that we have developed for rapid analysis of large quantities of next-generation sequencing (NGS) genomic data.  ...  transfer system); specification, configuration, and reuse of multi-step processing pipelines (via the Galaxy workflow system); creation of custom Amazon Machine Images and on-demand resource acquisition  ...  We are grateful to Amazon, Inc., for an award of Amazon Web Services time that facilitated early experiments. We thank Globus Genomics users for their invaluable contributions.  ... 
doi:10.1002/cpe.3274 pmid:25342933 pmcid:PMC4203657 fatcat:glcie6spdzdllakjibkyniqo5y

Selected Approaches and Frameworks to Carry out Genomic Data Analysis on the Cloud

Philip Church, Andrzej Goscinski
2015 Scalable Computing : Practice and Experience  
While High Performance Computing clouds allow researchers to process large amounts of genomic data, complex resource and software configuration tasks must be carried out beforehand.  ...  This paper examines commonly used cloud-based genomic analysis services, introduces the approach of exposing data as services and proposes two new solutions (HPCaaS and Uncinus) which aim to automate service  ...  Future work will allow end-users to easily provision Hadoop clusters on any cloud. This will facilitate 2.2. Galaxy. Galaxy [13] is an web-based framework for genomic research.  ... 
doi:10.12694/scpe.v16i1.1058 fatcat:7snkmbj24ra27m5mhpgrbs4mzq

Pairwise Genome Comparison Workflow in the Cloud Using Galaxy

Oscar Torreno, Michael T. Krieger, Paul Heinzlreiter, Oswaldo Trelles
2015 Procedia Computer Science  
We have addressed these problems by integrating a tools management platform (Galaxy) and a Cloud infrastructure, which prevents moving the big datasets between different locations and allows the dynamic  ...  scaling of the computing resources depending on the user needs.  ...  Introduction Nowadays, the cost of obtaining genome-scale molecular and biomedical data continues to drop rapidly.  ... 
doi:10.1016/j.procs.2015.05.449 fatcat:gjk22m2lxzh5ro4t5og2f2hdma

Building and provisioning bioinformatics environments on public and private Clouds

Enis Afgan, Konstantinos Krampis, Nuwan Goonasekera, Karolj Skala, James Taylor
2015 2015 38th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO)  
To take advantage of the scalability offered by the cloud, additional frameworks are required to create virtualized compute clusters and emulate the most common infrastructure found on institutional resources  ...  Unlike newly developed web applications that can be designed from the ground up to utilize cloud APIs and run natively within cloud infrastructure, most complex bioinformatics pipelines that are in advanced  ...  Further funding has been provided by the Australian NeCTAR project, under the Genomics Virtual Laboratory.  ... 
doi:10.1109/mipro.2015.7160269 dblp:conf/mipro/AfganKGST15 fatcat:grslkqjyt5glhpbuefpefwdr7u

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy

Saskia Hiltemann, Hailiang Mei, Mattias de Hollander, Ivo Palli, Peter van der Spek, Guido Jenster, Andrew Stubbs
2014 GigaScience  
Furthermore, we have developed a cloud-based public Galaxy instance to host the CGtag toolkit and other associated modules.  ...  have implemented the open-source Complete Genomics tool set, CGATools, in Galaxy.  ...  CLOUD implementation NBIC Galaxy is hosted at a high performance computing (HPC) cloud system operated by SURFsara [19] .  ... 
doi:10.1186/2047-217x-3-1 pmid:24460651 pmcid:PMC3905657 fatcat:xs4u4qnjvneydbni4mrpqf5lui

A case study for cloud based high throughput analysis of NGS data using the globus genomics system

Krithika Bhuvaneshwar, Dinanath Sulakhe, Robinder Gauba, Alex Rodriguez, Ravi Madduri, Utpal Dave, Lukasz Lacinski, Ian Foster, Yuriy Gusev, Subha Madhavan
2015 Computational and Structural Biotechnology Journal  
The Globus Genomics system is built on Amazon 's cloud computing infrastructure.  ...  The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.  ...  Acknowledgments We thank Globus Genomics users for their invaluable feedback and contributions. We thank Dr. Laura Sheahan for editing the manuscript.  ... 
doi:10.1016/j.csbj.2014.11.001 pmid:26925205 pmcid:PMC4720014 fatcat:ca7nkznpnjafjcgxtcghst5flm

Galaxy CloudMan: delivering cloud compute clusters

Enis Afgan, Dannon Baker, Nate Coraor, Brad Chapman, Anton Nekrutenko, James Taylor
2010 BMC Bioinformatics  
Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research.  ...  Results: We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon's EC2 cloud infrastructure  ...  We would also like to thank the participants of BOSC Codefest 2010, and the Bio-Linux community. This work was supported by NIH grant HG005542 (J.T. and A.N.).  ... 
doi:10.1186/1471-2105-11-s12-s4 pmid:21210983 pmcid:PMC3040530 fatcat:edyk2xhac5bv7imvw32arm5fpa

Laniakea: an open solution to provide Galaxy "on-demand" instances over heterogeneous cloud infrastructures

Marco Antonio Tangaro, Giacinto Donvito, Marica Antonacci, Matteo Chiara, Pietro Mandreoli, Graziano Pesole, Federico Zambelli
2020 GigaScience  
A Laniakea-based Galaxy on-demand service, named Laniakea@ReCaS, is currently hosted at the ELIXIR-IT ReCaS cloud facility.  ...  At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance and to the underlying virtual machine (VM  ...  Globus Genomics [22] provides a Galaxy-based bioinformatics workflow platform, built on Amazon cloud services, for large-scale next-generation sequencing analyses.  ... 
doi:10.1093/gigascience/giaa033 pmid:32252069 fatcat:jel5cyph2bbt7k7wogxtmopkum

Cloud Computing for Next-Generation Sequencing Data Analysis [chapter]

Shanrong Zhao, Kirk Watrous, Chi Zhang, Baohong Zhang
2017 Cloud Computing - Architecture and Applications  
share the lessons we learned from the implementation of Rainbow, a cloud-based tool for large-scale genome sequencing data analysis.  ...  Fortunately, cloud computing has recently emerged as a viable option to quickly and easily acquire the computational resources for large-scale NGS data analyses.  ...  Galaxy Cloud [57] , a cloudbased Galaxy platform for the analysis of data at a large scale, is the most used platform for bioinformatics.  ... 
doi:10.5772/66732 fatcat:2ewdbtp2bjhx7j7tj4e3auwqke
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