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Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs

Uriel Urquiza-García, Tomasz Zieliński, Andrew J Millar
2019 Synthetic Biology  
Here, we define the minimal requirements for a repository in this context and develop three usage scenarios, where we then examine the two platforms: (i) supporting the synthetic biology design-build-test-learn  ...  This approach demands new resources for cataloging and sharing biological components and designs, in order to accelerate the design-build-test-learn cycle.  ...  Acknowledgments We would like to thank Hector Plahar from ICE and Chris Myers from SynBioHub for checking the accuracy of our evaluation. Conflict of interest statement. None declared. Funding  ... 
doi:10.1093/synbio/ysz016 pmid:31423466 pmcid:PMC6690502 fatcat:eufcu6bt4bgblkoaya52ajlnt4

Generation of synthetic data sets for evaluating the accuracy of knowledge discovery systems

Daniel R. Jeske, Ryan Rich, Behrokh Samadi, Pengyue J. Lin, Lan Ye, Sean Cox, Rui Xiao, Ted Younglove, Minh Ly, Douglas Holt
2005 Proceeding of the eleventh ACM SIGKDD international conference on Knowledge discovery in data mining - KDD '05  
Information Discovery and Analysis Systems (IDAS) are designed to correlate multiple sources of data and use data mining techniques to identify potential events that could occur in the future.  ...  In this paper, we give an overview of the design and architecture of an IDAS Data Set Generator (IDSG) that will enable a fast and comprehensive test of an IDAS.  ...  An important part of testing of IDAS's is the generation of synthetic data sets for use in test cases.  ... 
doi:10.1145/1081870.1081969 dblp:conf/kdd/JeskeSLYCXYLHR05 fatcat:bcjx7hsay5g25cnopw3v3crxii

Computing for human experience: Semantics-empowered sensors, services, and social computing on the ubiquitous Web

A. Sheth
2010 IEEE Internet Computing  
The proposed system approach helps overcome the problem of having insufficient information on the structure of the ontology and data used for benchmarking and allows us to develop benchmarks for a variety  ...  At the core, we have a synthetic data generation approach for RDF that is scalable and models the real world data.  ...  A successful test is one that uncovers an as yet Synthetic Data Generation and Access Authorization: undiscovered error.Software testing is an important In this module the process of synthetic data generation  ... 
doi:10.1109/mic.2010.4 fatcat:vwf5qmh2u5fh3bgjyb46dw3spq

Idea2Data: Towards a New Paradigm for Drug Discovery

Christos A Nicolaou, Christine Humblet, Hong Hu, Eva-Marie Martín de la Nava, Frank C. Dorsey, Thomas M. Castle, Keith Ian Burton, Haitao Hu, Jorg Hendle, Michael J. Hickey, Joel Duerksen, Jibo Wang (+1 others)
2019 ACS Medicinal Chemistry Letters  
This new paradigm enables researchers to process billions of virtual molecules and select structures that can be prepared on automated systems and made available for biological testing, allowing for timely  ...  Hit identification can be carried out through large compound collection screening and often involves the generation and testing of many hypotheses based on available knowledge.  ...  Ten-fold cross validation studies using a random 25% of the set for training and the remainder as a test set yielded an average cross-validated r 2 and q 2 of ca. 0.5.  ... 
doi:10.1021/acsmedchemlett.8b00488 pmid:30891127 pmcid:PMC6421544 fatcat:k5tax75o5jds5ifymiblgf3u3m

Generating synthetic photogrammetric data for training deep learning based 3D point cloud segmentation models [article]

Meida Chen, Andrew Feng, Kyle McCullough, Pratusha Bhuvana Prasad, Ryan McAlinden, Lucio Soibelman
2020 arXiv   pre-print
Furthermore, it is generally difficult for segmentation models to differentiate objects, such as buildings and tree masses, and these types of scenarios do not always exist in the collected data set.  ...  We have investigated methods for generating synthetic UAV-based photogrammetric data to provide a sufficiently sized database for training a deep-learning algorithm with the ability to enlarge the data  ...  ACKNOWLEDGMENTS The authors would like to thank the two primary sponsors of this research: Army Futures Command (AFC) Synthetic Training Environment (STE), and the Office of Naval Research (ONR).  ... 
arXiv:2008.09647v1 fatcat:kek2yubyuzag7luguf5pjksnpi

SYNBIOCHEM Synthetic Biology Research Centre, Manchester – A UK foundry for fine and speciality chemicals production

Le Feuvre RA, Carbonell P, Currin A, Dunstan M, Fellows D, Jervis AJ, Rattray NJW, Robinson CJ, Swainston N, Vinaixa M, Williams A, Yan C (+12 others)
2016 Synthetic and Systems Biotechnology  
predictable engineering of microbial bio-factories for fine and speciality chemicals production.  ...  The UK Synthetic Biology Research Centre, SYNBIOCHEM, hosted by the Manchester Institute of Biotechnology at the University of Manchester is delivering innovative technology platforms to facilitate the  ...  Acknowledgement This is a contribution from the Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) and acknowledges the Biotechnology and Biological Sciences Research  ... 
doi:10.1016/j.synbio.2016.07.001 pmid:29062953 pmcid:PMC5625740 fatcat:ei3mgd3kqvbsplxeqnucucngti

Exploring Novel Biologically-Relevant Chemical Space Through Artificial Intelligence: The NCATS ASPIRE Program

Katharine K. Duncan, Dobrila D. Rudnicki, Christopher P. Austin, Danilo A. Tagle
2020 Frontiers in Robotics and AI  
A National Center for Advancing Translational Sciences (NCATS) program called A Specialized Platform for Innovative Research Exploration (ASPIRE) leverages advances in AI/ML, automated synthetic chemistry  ...  , and high-throughput biology, and seeks to enable translation and drug development by catalyzing exploration of biologically active chemical space.  ...  ACKNOWLEDGMENTS The authors wish to thank Kyle Brimacombe for the design of the ASPIRE Challenges badge that is part of Figure 1 .  ... 
doi:10.3389/frobt.2019.00143 pmid:33501158 pmcid:PMC7805902 fatcat:bqlltix7z5hjzddrekggt5ro6i


2022 Asian Journal of Pharmaceutical and Clinical Research  
now giving a cornerstone for the establishment of greater automation into detail of this process.  ...  AI has stimulated computer-aided drug discovery. This could likely speed up time duration for compound discovery and enhancement and authorize more productive hunts of related chemicals.  ...  ., a set of approaches that can use prior knowledge to obtain better generalization when data is scarce) and meta-learning (i.e., a branch of metacognition that aims to develop a set of learnable frameworks  ... 
doi:10.22159/ajpcr.2022.v15i4.43890 fatcat:ptfmpvfxuvdffijfzztko3hmpu

The role of a reference synthetic data generator within the field of learning analytics

Alan M. Berg, Stefan T. Mol, Gábor Kismihók, Niall Sclater
2016 Journal of Learning Analytics  
), we explore the need for an on-demand tool for generating a wide range of synthetic data.  ...  The role of a reference synthetic data generator within the field of learning analytics Berg, A.M.; Mol, S.T.; Kismihók, G.; Sclater, N.  ...  ACKNOWLEDGEMENTS We would like to acknowledge Professor Robin Boast and thank him for his valuable comments.  ... 
doi:10.18608/jla.2016.31.7 fatcat:3arede3dwbd25jean6y2vvnbbe

Crystallography companion agent for high-throughput materials discovery [article]

Phillip M. Maffettone, Lars Banko, Peng Cui, Yury Lysogorskiy, Marc A. Little, Daniel Olds, Alfred Ludwig, Andrew I. Cooper
2021 arXiv   pre-print
Here, we describe a computer program for the autonomous characterization of XRD data, driven by artificial intelligence (AI), for the discovery of new materials.  ...  It was demonstrated on a diverse set of organic and inorganic materials characterization challenges.  ...  This research utilized the PDF (28-ID-1) Beamline and resources of the National Synchrotron Light Source II, a U.S.  ... 
arXiv:2008.00283v2 fatcat:3x76navyrzga7hosstyhsehcqe

Complex Adaptive Systems Drive Innovations in Synthetic Biology

Melvin Greer, Manuel Rodriguez-Martinez, Jamie Seguel
2013 Procedia Computer Science  
The resultant outcome of synthetic biology research offers the promise of changing the way that we create energy, produce food, optimize industrial processing, and detect, prevent, and cure diseases.  ...  Researchers can now realize the significant benefits of the cloud computing model to reduce IT cost and complexity, enhance R&D collaboration, and improve bioinformatics to allow lifesciences organizations  ...  Big Data is a general term used to describe the velocity, variety and volumes of unstructured and semi-structured king at Big Data is to discovery of data patterns.  ... 
doi:10.1016/j.procs.2013.09.291 fatcat:ncdgoz62jvb6xmeaj2ojmyykrm

OpenMolGRID, a GRID Based System for Solving Large-Scale Drug Design Problems [chapter]

Ferenc Darvas, Ákos Papp, István Bágyi, Géza Ambrus, László Ürge
2004 Lecture Notes in Computer Science  
These "high-throughput" informatics systems provide the facility to develop QSAR models on a vast number of model compounds in a short time and also the fast application of the novel method on an unprecedently  ...  Using these experimental data, linear and non-linear forward-QSAR models is being developed and the predictive capability of these models is going to be validated.  ...  Thanks for colleagues from the following partners involved in the project: • -University of Tartu, Tartu, Estonia  ... 
doi:10.1007/978-3-540-28642-4_8 fatcat:3owq6wz6yzcmzjkrtlj6ta7anq

Smart camera system for aircraft and spacecraft

Francisco J. Delgado, Janis White, Michael F. Abernathy, Jacques G. Verly
2003 Enhanced and Synthetic Vision 2003  
This paper details its development and flight test results. Figure i : A SlIIart Call1era System in action during Vehicle J3iR /ligltHesling.  ...  This paper describes a new approach to situation awareness that combines video sensor technology and synthetic vision technology in a unique fashion to create a hybrid vision system.  ...  The hybrid system developed augments a live sensor data stream (video in this case) with information from a synthetically created scene.  ... 
doi:10.1117/12.484801 fatcat:5us5z7ojl5ebdjkz55zvzbqnkq

Linguistic unit discovery from multi-modal inputs in unwritten languages: Summary of the "Speaking Rosetta" JSALT 2017 Workshop [article]

Odette Scharenborg, Laurent Besacier, Alan Black, Mark Hasegawa-Johnson, Florian Metze, Graham Neubig, Sebastian Stueker, Pierre Godard, Markus Mueller, Lucas Ondel, Shruti Palaskar, Philip Arthur, Francesco Ciannella (+5 others)
2018 arXiv   pre-print
We summarize the accomplishments of a multi-disciplinary workshop exploring the computational and scientific issues surrounding the discovery of linguistic units (subwords and words) in a language without  ...  We study the replacement of orthographic transcriptions by images and/or translated text in a well-resourced language to help unsupervised discovery from raw speech.  ...  These phone sequences were then sent to the TTS system. On a development set of 514 utterances BLEU4 scores at the character level were of 31.95% with true phones and 8.32% with pseudo-phones 3 .  ... 
arXiv:1802.05092v1 fatcat:xzelus33z5hapcddpppqqnhyq4

Synthetic biology UK: progress, paradigms and prospects

Lionel J. Clarke
2017 Engineering Biology  
The UK Synthetic Biology Roadmap 2012 and subsequent 2016 Strategy set out to develop a mechanism to respond nationally to this wider perspective, and examples, both UK and global, are drawn upon to help  ...  Drawing comparisons with the study of scientific revolutions by Thomas Kuhn over 50 years ago it is possible to frame synthetic biology as a new paradigm, approaching biology and its potential for redesign  ...  A further engineering constructthe design-build-test (DBT) cyclemust invariably be applied to discover, refine and optimise the target system.  ... 
doi:10.1049/enb.2017.0022 fatcat:w5fsbj7oi5dhfbefxx2wzylgsm
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