13 papers · ranked by Valyu relevance
Jacob M. Luber, Braden T. Tierney, Evan M. Cofer, Chirag J. Patel + 1 more
Across biology we are seeing rapid developments in scale of data production without a corresponding increase in data analysis capabilities. Here, we present Aether (http://aether.kosticlab.org), an intuitive, easy-to-use, cost-effective, and scalable framework that uses linear programming (LP) to optimally bid on and…
Li Chen, Bai Zhang, Michael Schnaubelt, Punit Shah + 4 more
Rapid development and wide adoption of mass spectrometry-based proteomics technologies have empowered scientists to study proteins and their modifications in complex samples on a large scale. This progress has also created unprecedented challenges for individual labs to store, manage and analyze proteomics data, both…
Seyhan Yazar, George E C Gooden, David A Mackey, Alex W Hewitt
A major bottleneck in biological discovery is now emerging at the computational level. Cloud computing offers a dynamic means whereby small and medium-sized laboratories can rapidly adjust their computational capacity. We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR)…
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…
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…
Chet Birger, Megan Hanna, Edward Salinas, Jason Neff + 11 more
FireCloud, one of three NCI Cloud Pilots, is a collaborative genome analysis platform built on a cloud computing infrastructure. FireCloud aims to solve the many challenges presented by the increasingly large data sets and computing requirements employed in cancer research. However, cost uncertainty associated with…
Qianqian Fang, Shijie Yan
Despite the ample progress made towards faster and more accurate Monte Carlo (MC) simulation tools over the past decade, the limited usability and accessibility of these advanced modeling tools remain key barriers towards widespread use among the broad user community. An open-source, high-performance, web-based MC…
PJ Tatlow, Stephen R. Piccolo
Public compendia of raw sequencing data are now measured in petabytes. Accordingly, it is becoming infeasible for individual researchers to transfer these data to local computers. Recently, the National Cancer Institute funded an initiative to explore opportunities and challenges of working with molecular data in…
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…
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…
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…
Ben C. Shirley, Eliseos J. Mucaki, Joan H.M. Knoll, Peter K. Rogan
Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System…
Tazro Ohta, Tomoya Tanjo, Osamu Ogasawara
Container virtualization technologies such as Docker became popular in the bioinformatics domain as they improve portability and reproducibility of software deployment. Along with software packaged in containers, the workflow description standards Common Workflow Language also enabled to perform data analysis on…