Zobrazeno 1 - 10
of 25
pro vyhledávání: '"Niall Gaffney"'
Autor:
Breschine Cummins, Justin Vrana, Robert C Moseley, Hamed Eramian, Anastasia Deckard, Pedro Fontanarrosa, Daniel Bryce, Mark Weston, George Zheng, Joshua Nowak, Francis C Motta, Mohammed Eslami, Kara Layne Johnson, Robert P Goldman, Chris J Myers, Tessa Johnson, Matthew W Vaughn, Niall Gaffney, Joshua Urrutia, Shweta Gopaulakrishnan, Vanessa Biggers, Trissha R Higa, Lorraine A Mosqueda, Marcio Gameiro, Tomáš Gedeon, Konstantin Mischaikow, Jacob Beal, Bryan Bartley, Tom Mitchell, Tramy T Nguyen, Nicholas Roehner, Steven B Haase
Computational tools addressing various components of design–build–test–learn (DBTL) loops for the construction of synthetic genetic networks exist but do not generally cover the entire DBTL loop. This manuscript introduces an end-to-end sequenc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d2c9b817f1b0a8d922071cda533d340
https://doi.org/10.1101/2022.06.10.495560
https://doi.org/10.1101/2022.06.10.495560
Autor:
Daniel Bryce, Robert P. Goldman, Matthew DeHaven, Jacob Beal, Bryan Bartley, Tramy T. Nguyen, Nicholas Walczak, Mark Weston, George Zheng, Josh Nowak, Peter Lee, Joe Stubbs, Niall Gaffney, Matthew W. Vaughn, Chris John Myers, Robert C. Moseley, Steven Haase, Anastasia Deckard, Bree Cummins, Nick Leiby
Publikováno v:
ACS synthetic biology. 11(2)
Synthetic biology is a complex discipline that involves creating detailed, purpose-built designs from genetic parts. This process is often phrased as a Design-Build-Test-Learn loop, where iterative design improvements can be made, implemented, measur
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1b8df779cbc10b9868c780c9fcf63be5
https://pubmed.ncbi.nlm.nih.gov/35099189
https://pubmed.ncbi.nlm.nih.gov/35099189
Autor:
Benjamin J Garcia, Joshua Urrutia, George Zheng, Diveena Becker, Carolyn Corbet, Paul Maschhoff, Alexander Cristofaro, Niall Gaffney, Matthew Vaughn, Uma Saxena, Yi-Pei Chen, D Benjamin Gordon, Mohammed Eslami
Publikováno v:
Synthetic biology (Oxford, England). 7(1)
Sequencing technologies, in particular RNASeq, have become critical tools in the design, build, test and learn cycle of synthetic biology. They provide a better understanding of synthetic designs, and they help identify ways to improve and select des
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::68c01bbd0da69f7f528367c3f8a98afa
https://pubmed.ncbi.nlm.nih.gov/36035514
https://pubmed.ncbi.nlm.nih.gov/36035514
Autor:
Hamed Eramian, Carolyn Corbet, Diveena Becker, Christopher A. Voigt, Mohammed Eslami, Amin Espah-Borujeni, John M. Fonner, Mark Weston, Matthew Vaugh, Hamid Doost Hosseini, Alexander Cristafaro, Niall Gaffney, Joshua Urrutia, D. Benjamin Gordon, Katie J. Clowers, Jedidiah Singer, Enoch Yeung, Joe Stubbs, Paul Maschhoff, Yuval Dorfan, George Zheng
Motivation Applications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments to cover all possible combinations of perturbations is infeasible. In this paper, we presen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::81b7a8d0cf8f7027d7aa9ea63c6fb12f
https://doi.org/10.1101/2021.04.30.442142
https://doi.org/10.1101/2021.04.30.442142
Autor:
Mihael Hategan, Jarek Nabrzyski, Kyle Chard, Victoria Stodden, Niall Gaffney, Timothy M. McPhillips, Bertram Ludäscher, Thomas Thelen, Ian Taylor, Matthew J. Turk, Craig Willis, Kacper Kowalik
Publikováno v:
PARCO
Whole Tale http://wholetale.org is a web-based, open-source platform for reproducible research supporting the creation, sharing, execution, and verification of “Tales” for the scientific research community. Tales are executable research objects t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f8708e5515154953195bc34b21278307
https://doi.org/10.3233/apc200107
https://doi.org/10.3233/apc200107
Autor:
Bertram Ludäscher, Timothy M. McPhillips, Ian Taylor, Craig Willis, Kacper Kowalik, Jarek Nabrzyski, Thomas Thelen, Niall Gaffney, Victoria Stodden, Kyle Chard, Matthew J. Turk, Matthew B. Jones
Publikováno v:
eScience
In this paper we describe our experience adopting the Research Object Bundle (RO-Bundle) format with BagIt serialization (BagIt-RO) for the design and implementation of "tales" in the Whole Tale platform. A tale is an executable research object inten
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ed611d390dce01c77861dc69c2aa3c99
https://doi.org/10.1109/escience.2019.00068
https://doi.org/10.1109/escience.2019.00068
Autor:
Matthew B. Jones, Bertram Ludäscher, Kacper Kowalik, Ian Taylor, Kyle Chard, Mihael Hategan, Jarek Nabrzyski, Bryce Mecum, Niall Gaffney, Kandace Turner, Sivakumar Kulasekaran, Victoria Stodden, Matthew J. Turk, Adam Brinckman
The act of sharing scientific knowledge is rapidly evolving away from traditional articles and presentations to the delivery of executable objects that integrate the data and computational details (e.g., scripts and workflows) upon which the findings
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::191993a7cdc3e90a020597f1ed7cabcb
https://orca.cardiff.ac.uk/id/eprint/109724/1/1-s2.0-S0167739X17310695-main.pdf
https://orca.cardiff.ac.uk/id/eprint/109724/1/1-s2.0-S0167739X17310695-main.pdf
Autor:
Niall Gaffney, Marcos André Gonçalves
Publikováno v:
JCDL
With the advancements in data driven research ushered in with the "Big Data" era, many research fields from astrophysics to genomics have discovered previously impossible outcomes including exoplanet detection and precision medicine. As with many oth
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e46fc2e6f5cf081fb1d8b36be3f9b83e
https://doi.org/10.1145/3197026.3202665
https://doi.org/10.1145/3197026.3202665
Autor:
P. Teller, Niall Gaffney, Kelly Gaither, Chris Hempel, Henry M. Tufo, Dan Stanzione, S. Mehringer, Eric Wernert, Bill Barth, Tommy Minyard, Dhabaleswar K. Panda
Publikováno v:
PEARC
The Stampede 1 supercomputer was a tremendous success as an XSEDE resource, providing more than eight million successful computational simulations and data analysis jobs to more than ten thousand users. In addition, Stampede 1 introduced new technolo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6ef78b197df67be7f2185c7d46eeeec6
https://doi.org/10.1145/3093338.3093385
https://doi.org/10.1145/3093338.3093385
Publikováno v:
PyHPC@SC
When the identity of a next generation sequencing sample is lost, reads or assembled contigs are aligned to a database of known genomes and classified as the match with the most hits. However, any alignment based methods are very expensive when deali
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f9e74eb7b7e0cb274feb4d7ac99dd6de
https://doi.org/10.1145/2835857.2835862
https://doi.org/10.1145/2835857.2835862