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IBM Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale [article]

Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mary Roth, Vandana Mukherjee, James H. Kaufman
2020 arXiv   pre-print
life at scale.  ...  In this paper, we describe IBM Functional Genomics Platform (formerly known as OMXWare), a comprehensive database relating genotype to phenotype for bacterial life.  ...  Parida of IBM Research for helpful discussion and insights into new applications of IBM Functional Genomics Platform.  ... 
arXiv:1911.02095v3 fatcat:bn6kssh2ezbqnashkxqzga3faq

An overview of biomedical platforms for managing research data

Vivek Navale, Denis von Kaeppler, Matthew McAuliffe
2021 Journal of Data, Information and Management  
Many large-scale biomedical platforms use secure cloud computing technology for analyzing, integrating, and storing phenotypic, clinical, and genomic data.  ...  Several web-based platforms are available for researchers to access services and tools for biomedical research.  ...  out) costs from a vendor cloud can be significant, especially if large scale data migrations are necessary at any time.  ... 
doi:10.1007/s42488-020-00040-0 fatcat:itiji5ifu5hjhhcjvtzwz6jq6e

The information science of microbial ecology

Aria S Hahn, Kishori M Konwar, Stilianos Louca, Niels W Hanson, Steven J Hallam
2016 Current Opinion in Microbiology  
Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation.  ...  A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms.  ...  KMK was supported by the Tula Foundation funded Centre for Microbial Diversity and Evolution (CMDE) at UBC.  ... 
doi:10.1016/j.mib.2016.04.014 pmid:27183115 fatcat:bhlgmvfmk5gsflhb6dzkg7jg2i

Big Genomic Data in Bioinformatics Cloud

Prachi Singh
2016 Applied Microbiology open access  
The achievement of Human Genome project has led to the proliferation of genomic sequencing data.  ...  Because, these technologies provide distributed and parallelized data processing and are efficient to analyse even petabyte (PB) scale data sets.  ...  One is cloud-based Easy Genomics for high speed genomic data transfer.  ... 
doi:10.4172/2471-9315.1000113 fatcat:agii5j77zjhjbcuhodv3lqvrha

Perspectives of using Cloud computing in integrative analysis of multi-omics data

Dariusz R Augustyn, Łukasz Wyciślik, Dariusz Mrozek
2021 Briefings in Functional Genomics  
Fortunately, with new technological paradigms, including Cloud computing, virtualization and containerization, these functionalities could be orchestrated for easy scaling and building independent analysis  ...  Moreover, they are implemented for general-purpose scientific computational platforms that most often do not easily scale the calculations natively.  ...  Acknowledgments This work was supported by the professorship grant (02/020/RGPL9/0184) of the Rector of the Silesian University of Technology, Gliwice, Poland, pro-quality grant for highly scored publications  ... 
doi:10.1093/bfgp/elab007 pmid:33676373 fatcat:ykypxevpzfftvnuhqj3gtqj544

Analyzing large scale genomic data on the cloud with Sparkhit

Liren Huang, Jan Krüger, Alexander Sczyrba, Inanc Birol
2017 Bioinformatics  
Motivation: The increasing amount of next-generation sequencing data poses a fundamental challenge on large scale genomic analytics.  ...  We analyzed 100 terabytes of data across four genomic projects in the cloud in 21 h, which includes the run times of cluster deployment and data downloading.  ...  Funding This project has been supported by the German-Canadian DFG international research training group 'Computational Methods for the Analysis of the Diversity and Dynamics of Genomes' (DiDy) GRK 1906  ... 
doi:10.1093/bioinformatics/btx808 pmid:29253074 pmcid:PMC5925781 fatcat:avbzcngwmzdjxib67thpdirc2u

Marine genomics: at the interface of marine microbial ecology and biodiscovery

Karla B. Heidelberg, Jack A. Gilbert, Ian Joint
2010 Microbial Biotechnology  
This review explores the brief history of genomic and metagenomic approaches to study environmental microbial assemblages and describes some of the future challenges involved in broadening our approachesleading  ...  In addition, there is considerable potential to use information about uncultured microbes in biodiscovery research as microbes provide a rich source of discovery for novel genes, enzymes and metabolic  ...  K.B.H. and I.J. also acknowledge funding from the European Commission and NSF to attend the Joint EC-US CIESM Workshop on Marine Genomics: At the Interface of Marine Microbial Ecology and Biotechnological  ... 
doi:10.1111/j.1751-7915.2010.00193.x pmid:20953417 pmcid:PMC2948669 fatcat:yheysknebfhrnp5wg5w4k2zz7m

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan (+4 others)
2019 F1000Research  
The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics  ...  The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF).  ...  The BiGi service center offers tools, services and training for microbial genome 11-14 , metagenome 15 , and postgenome research 16 that is complemented by a large-scale hardware infrastructure.  ... 
doi:10.12688/f1000research.20244.1 pmid:33163154 pmcid:PMC7607484 fatcat:g4gztfjahrbkdepxw6rgkjfhjy

The DOE Systems Biology Knowledgebase (KBase) [article]

Adam P. Arkin, Rick L Stevens, Robert W Cottingham, Sergei Maslov, Christopher S Henry, Paramvir Dehal, Doreen Ware, Fernando Perez, Nomi L Harris, Shane Canon, Michael W Sneddon, Matthew L Henderson (+67 others)
2016 bioRxiv   pre-print
KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing  ...  4) a software development kit allowing the community to add functionality to the system.  ...  The physical infrastructure hosting the KBase software platform operates at Argonne National Laboratory and Lawrence Berkeley National Laboratory using an OpenStack managed cloud in combination with large-scale  ... 
doi:10.1101/096354 fatcat:ojeek6qm4nca5c2wtapougjlm4

A Primer on Infectious Disease Bacterial Genomics

Tarah Lynch, Aaron Petkau, Natalie Knox, Morag Graham, Gary Van Domselaar
2016 Clinical Microbiology Reviews  
Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general  ...  SUMMARYThe number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies.  ...  For generation of larger-scale whole-genome alignments, some studies (165) have instead used a reference mapping approach.  ... 
doi:10.1128/cmr.00001-16 pmid:28590251 pmcid:PMC5010755 fatcat:7q5tsfxyzvgtrjfa6buww6pfi4

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan (+4 others)
2020 F1000Research  
The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics  ...  The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF).  ...  The BiGi service center offers tools, services and training for microbial genome 11-14 , metagenome 15 , and postgenome research 16 that is complemented by a large-scale hardware infrastructure.  ... 
doi:10.12688/f1000research.20244.2 fatcat:io4rgsengvddhlhwjgpqv5livu

Genomics tools in microbial food safety

Matthew J Stasiewicz, Henk C den Bakker, Martin Wiedmann
2015 Current Opinion in Food Science  
These platforms provide economies of scale for centralized sequencing of small (< 10 Mb), bacterial genomes.  ...  Other comparative genomics functions that have been scaled to the analysis of multiple microbial genomes include: annotation [25, 26] , mobile element detection [27, 28] and recombination detection  ... 
doi:10.1016/j.cofs.2015.06.002 fatcat:dswic6smqrarfhmrdt7z4h4rhu

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data

Wenyu Shi, Heyuan Qi, Qinglan Sun, Guomei Fan, Shuangjiang Liu, Jun Wang, Baoli Zhu, Hongwei Liu, Fangqing Zhao, Xiaochen Wang, Xiaoxuan Hu, Wei Li (+4 others)
2018 Nucleic Acids Research  
Meta-omics approaches have been increasingly used to study the structure and function of the microbial communities.  ...  This platform is freely accessible at https://gcmeta.wdcm.org/.  ...  ., Beijing, China for Docker container technologies. We would like to thank the technical support staff from BGI Shenzhen for their suggestions on data curation. FUNDING  ... 
doi:10.1093/nar/gky1008 pmid:30365027 pmcid:PMC6324004 fatcat:utuajngwlzagvdoontfbme7gca

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
2021 Zenodo  
genomic surveillance.  ...  and 5 thematic implementation studies.  ...  Development of the GOLD platform from the Inserm Genomic Variability 2018 Cross-Cutting Program to study Human Genome Variability.  ... 
doi:10.5281/zenodo.5324333 fatcat:py5xp6q7ungkdevdqx25zxfwmq

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

H. Teeling, F. O. Glockner
2012 Briefings in Bioinformatics  
This mini review aims to address selected opportunities and challenges of modern metagenomics from a bioinformatics perspective and hopefully will serve as a useful resource for microbial ecologists and  ...  Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable.  ...  for microbial genomics.  ... 
doi:10.1093/bib/bbs039 pmid:22966151 pmcid:PMC3504927 fatcat:xdfujqlljfhzjdr4ljddlznzdm
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