10 papers · ranked by Valyu relevance
Andrea Kölzsch, Sarah C. Davidson, Dominik Gauggel, Clemens Hahn + 10 more
Bio-logging and animal tracking datasets continuously grow in volume and complexity, documenting animal behaviour and ecology in unprecedented extent and detail, but greatly increasing the challenge of extracting knowledge from the data obtained. A large variety of analysis methods are being developed, many of which in…
Ling-Hong Hung, Niharika Nasam, Chris Biju, Wes Lloyd + 1 more
Singe cell RNA sequencing (scRNA-seq) has become a routine method for measuring cell activities. Processing large scRNA-seq datasets requires high-performance computing resources. The emergence of cloud computing allows us to leverage its on-demand capabilities without major investment in infrastructure. Serverless…
Ling-Hong Hung, Niharika Nasam, Wes Lloyd, Ka Yee Yeung
Singe cell RNA sequencing (scRNA-seq) has become a routine method for measuring cell activities. Processing large scRNA-seq datasets requires high-performance computing resources. The emergence of cloud computing allows us to leverage its on-demand capabilities without major investment in infrastructure. Serverless…
Jody Clements, Cristian Goina, Philip M. Hubbard, Takashi Kawase + 4 more
Neuroscience research in Drosophila is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons in a brain and their connections. In order to exploit this knowledge base, researchers target individual neurons and study their function. Therefore, vast libraries of fly…
Jacob Bradford, Divya Joy, Mattias Winsen, Nicholas Meurant + 4 more
Gene editing has been revolutionised by the CRISPR-Cas9 technology. The versatility and ease-of-use of the technology far exceeds its predecessors, however, the selection of a high-quality guide RNA (gRNA) is critical to directing it to a target site. Selecting gRNA calls upon high-performance algorithms that evaluate…
Daniel P. Ramirez-Echemendia, Luís Borges-Araújo, Chelsea M. Brown, Riccardo Alessandri + 3 more
The Martini coarse-grained force field is widely used for biomolecular simulations by a large and rapidly expanding community worldwide. Over time, the development of Martini parameters, tools, and documentation has become increasingly dispersed across numerous research groups, leading to fragmentation and making it…
Christiam Camacho, Grzegorz M. Boratyn, Victor Joukov, Roberto Vera Alvarez + 1 more
Biomedical researchers use alignments produced by BLAST (Basic Local Alignment Search Tool) to categorize their query sequences. Producing such alignments is an essential bioinformatics task that is well suited for the cloud. The cloud can perform many calculations quickly as well as store and access large volumes of…
Chih Chuan Shih, Jieqi Chen, Ai Shan Lee, Nicolas Bertin + 34 more
Genomic researchers are increasingly utilizing commercial cloud platforms (CCPs) to manage their data and analytics needs. Commercial clouds allow researchers to grow their storage and analytics capacity on demand, keeping pace with expanding project data footprints and enabling researchers to avoid large capital…
Joseph Giustizia, Wilson Hodgson, Cameron Andress, Satpal Bilkhu + 2 more
As sequencing technologies have matured, bioinformatics tasks have become more complex, computationally demanding, and data intensive. Workflow management software has been developed to aid in simplifying the replicable chaining of complex bioinformatics jobs, and cloud computing has emerged as a potential solution to…
Kevin Kang, Jinwen Wo, Jon Jiang, Zhong Wang
We propose Adaptive Container Service (ACS), a new paradigm for deploying bioinformatics workflows in cloud computing environments. By encapsulating the entire workflow within a single virtual container, combined with automatic workflow checkpointing and dynamic migration to appropriately scaled containers, ACS-based…