scholarly journals BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts

2015 ◽  
Vol 32 (6) ◽  
pp. 937-939 ◽  
Author(s):  
Kun Yang ◽  
Giovanni Stracquadanio ◽  
Jingchuan Luo ◽  
Jef D. Boeke ◽  
Joel S. Bader
Keyword(s):  
Large Scale ◽  
Supplementary Information ◽  
Market Place ◽  
Design Standards ◽  
Reusable Components ◽  
Assembly Design ◽  
Amazon Web Services ◽  
Dna Elements ◽  
Combinatorial Assembly ◽  
The Cost

Abstract Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

OPTIMAL ENERGY DESIGN AND RETROFIT RECOMMENDATIONS FOR THE TURKISH BUILDING SECTOR

2021 ◽  
Vol 16 (1) ◽  
pp. 61-90
Author(s):  
Selçuk Sayin ◽  
Godfried Augenbroe
Keyword(s):  
Energy Saving ◽  
Large Scale ◽  
Optimal Strategies ◽  
Energy Performance ◽  
Optimization Approach ◽  
Investment Strategies ◽  
Single Family ◽  
Building Sector ◽  
Design Standards ◽  
The Cost

ABSTRACT This paper introduces methodologies and optimal strategies to reduce the energy consumption of the building sector with the aim to reduce global energy usage of a given .region or country. Many efforts are underway to develop investment strategies for large-scale energy retrofits and stricter energy design standards for existing and future buildings. This paper presents a study that informs these strategies in a novel way. It introduces support for the cost-optimized retrofits of existing, and design improvements of new buildings in Turkey with the aim to offer recommendations to individual building owners as well as guidance to the market. Three building types, apartment, single-family house and office are analyzed with a novel optimization approach. The energy performance of each type is simulated in five different climate regions of Turkey and four different vintages. For each vintage, the building is modelled corresponding to local Turkish regulations that applied at the time of construction. Optimum results are produced for different goals in terms of energy saving targets. The optimization results reveal that a 50% energy saving target is attainable for the retrofit and a 40% energy saving target is attainable for new design improvements for each building type in all climate regions.

scholarly journals Falco: A quick and flexible single-cell RNA-seq processing framework on the cloud

2016 ◽  
Author(s):  
Andrian Yang ◽  
Michael Troup ◽  
Peijie Lin ◽  
Joshua W. K. Ho
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Low Cost ◽  
Supplementary Information ◽  
Data Sets ◽  
Rna Seq ◽  
Single Node ◽  
Big Data Technologies ◽  
Amazon Web Services ◽  
Supplementary Material

AbstractSummarySingle-cell RNA-seq (scRNA-seq) is increasingly used in a range of biomedical studies. Nonetheless, current RNA-seq analysis tools are not specifically designed to efficiently process scRNA-seq data due to their limited scalability. Here we introduce Falco, a cloud-based framework to enable paralellisation of existing RNA-seq processing pipelines using big data technologies of Apache Hadoop and Apache Spark for performing massively parallel analysis of large scale transcriptomic data. Using two public scRNA-seq data sets and two popular RNA-seq alignment/feature quantification pipelines, we show that the same processing pipeline runs 2.6 – 145.4 times faster using Falco than running on a highly optimised single node analysis. Falco also allows user to the utilise low-cost spot instances of Amazon Web Services (AWS), providing a 65% reduction in cost of analysis.AvailabilityFalco is available via a GNU General Public License at https://github.com/VCCRI/Falco/[email protected] informationSupplementary data are available at BioRXiv online.

Cost- und Monitoring-Projekt: Zwei neue forstliche Meinungsumfragen im Vergleich | The Cost- and Monitoring-Projects: A Comparison of Two New Forestry Opinion Polls

2000 ◽  
Vol 151 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Stephan Wild-Eck ◽  
Willi Zimmermann
Keyword(s):  
Large Scale ◽  
Forest Policy ◽  
Forest Economics ◽  
Positive Attitudes ◽  
Federal Institute ◽  
Swiss Confederation ◽  
Institute Of Technology ◽  
The Cost ◽  
Near Future ◽  
Opinion Polls

Two large-scale surveys looking at attitudes towards forests, forestry and forest policy in the second half ofthe nineties have been carried out. This work was done on behalf of the Swiss Confederation by the Chair of Forest Policy and Forest Economics of the Federal Institute of Technology (ETH) in Zurich. Not only did the two studies use very different methods, but the results also varied greatly as far as infrastructure and basic conditions were concerned. One of the main differences between the two studies was the fact that the first dealt only with mountainous areas, whereas the second was carried out on the whole Swiss population. The results of the studies reflect these differences:each produced its own specific findings. Where the same (or similar) questions were asked, the answers highlight not only how the attitudes of those questioned differ, but also views that they hold in common. Both surveys showed positive attitudes towards forests in general, as well as a deep-seated appreciation ofthe forest as a recreational area, and a positive approach to tending. Detailed results of the two surveys will be available in the near future.

Waste minimization program in Shuaiba Industrial Area

1999 ◽  
Vol 39 (10-11) ◽  
pp. 289-295
Author(s):  
Saleh Al-Muzaini
Keyword(s):  
Solid Waste ◽  
Power Plants ◽  
Large Scale ◽  
Industrial Area ◽  
Waste Minimization ◽  
Regulatory Body ◽  
Eastern Sector ◽  
Western Sector ◽  
Petroleum Companies ◽  
The Cost

The Shuaiba Industrial Area (SIA) is located about 50 km south of Kuwait City. It accommodates most of the large-scale industries in Kuwait. The total area of the SIA (both eastern and western sectors) is about 22.98 million m2. Fifteen plants are located in the eastern sector and 23 in the western sector, including two petrochemical companies, three refineries, two power plants, a melamine company, an industrial gas corporation, a paper products company and, two steam electricity generating stations, in addition to several other industries. Therefore, only 30 percent of the land in the SIA's eastern sector and 70 percent of land in the SIA's western sector is available for future expansion. Presently, industries in the SIA generate approximately 204,000 t of solid waste. With future development in the industries in the SIA, the estimated quantities will reach 240,000 t. The Shuaiba Area Authority (SAA), a governmental regulatory body responsible for planning and development in the SIA, has recognized the problem of solid waste and has developed an industrial waste minimization program. This program would help to reduce the quantity of waste generated within the SIA and thereby reduce the cost of waste management. This paper presents a description of the waste minimization program and how it is to be implemented by major petroleum companies. The protocols employed in the waste minimization program are detailed.

An Out-of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers

2012 ◽  
Author(s):  
Zheng Zhou ◽  
Erik Saule ◽  
Hasan Metin Aktulga ◽  
Chao Yang ◽  
Esmond G. Ng ◽  
...  
Keyword(s):  
Large Scale ◽  
Iterative Solvers ◽  
The Cost

scholarly journals Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Young-Dan Cho ◽  
Woo-Jin Kim ◽  
Hyun-Mo Ryoo ◽  
Hong-Gee Kim ◽  
Kyoung-Hwa Kim ◽  
...  
Keyword(s):  
Large Scale ◽  
Periodontal Diseases ◽  
Research Trends ◽  
Main Body ◽  
Research Projects ◽  
Encode Project ◽  
Dna Elements ◽  
Crucial Information ◽  
Future Direction ◽  
Systemic Health

Abstract Background The Encyclopedia of DNA Elements (ENCODE) project has advanced our knowledge of the functional elements in the genome and epigenome. The aim of this article was to provide the comprehension about current research trends from ENCODE project and establish the link between epigenetics and periodontal diseases based on epigenome studies and seek the future direction. Main body Global epigenome research projects have emphasized the importance of epigenetic research for understanding human health and disease, and current international consortia show an improved interest in the importance of oral health with systemic health. The epigenetic studies in dental field have been mainly conducted in periodontology and have focused on DNA methylation analysis. Advances in sequencing technology have broadened the target for epigenetic studies from specific genes to genome-wide analyses. Conclusions In line with global research trends, further extended and advanced epigenetic studies would provide crucial information for the realization of comprehensive dental medicine and expand the scope of ongoing large-scale research projects.

scholarly journals A Survey on Contrastive Self-Supervised Learning

Technologies ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 2
Author(s):  
Ashish Jaiswal ◽  
Ashwin Ramesh Babu ◽  
Mohammad Zaki Zadeh ◽  
Debapriya Banerjee ◽  
Fillia Makedon
Keyword(s):  
Computer Vision ◽  
Supervised Learning ◽  
Language Processing ◽  
Large Scale ◽  
Performance Comparison ◽  
Extensive Review ◽  
Future Directions ◽  
Dominant Component ◽  
Supervised Methods ◽  
The Cost

Self-supervised learning has gained popularity because of its ability to avoid the cost of annotating large-scale datasets. It is capable of adopting self-defined pseudolabels as supervision and use the learned representations for several downstream tasks. Specifically, contrastive learning has recently become a dominant component in self-supervised learning for computer vision, natural language processing (NLP), and other domains. It aims at embedding augmented versions of the same sample close to each other while trying to push away embeddings from different samples. This paper provides an extensive review of self-supervised methods that follow the contrastive approach. The work explains commonly used pretext tasks in a contrastive learning setup, followed by different architectures that have been proposed so far. Next, we present a performance comparison of different methods for multiple downstream tasks such as image classification, object detection, and action recognition. Finally, we conclude with the limitations of the current methods and the need for further techniques and future directions to make meaningful progress.

scholarly journals A Review on Terahertz Technologies Accelerated by Silicon Photonics

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1646
Author(s):  
Jingya Xie ◽  
Wangcheng Ye ◽  
Linjie Zhou ◽  
Xuguang Guo ◽  
Xiaofei Zang ◽  
...  
Keyword(s):  
Integrated Circuit ◽  
Silicon Photonics ◽  
Large Scale ◽  
Cost Effective ◽  
Single Chip ◽  
Photonic Integrated Circuit ◽  
Hybrid Silicon ◽  
The Cost ◽  
Silicon Based ◽  
Thz Applications

In the last couple of decades, terahertz (THz) technologies, which lie in the frequency gap between the infrared and microwaves, have been greatly enhanced and investigated due to possible opportunities in a plethora of THz applications, such as imaging, security, and wireless communications. Photonics has led the way to the generation, modulation, and detection of THz waves such as the photomixing technique. In tandem with these investigations, researchers have been exploring ways to use silicon photonics technologies for THz applications to leverage the cost-effective large-scale fabrication and integration opportunities that it would enable. Although silicon photonics has enabled the implementation of a large number of optical components for practical use, for THz integrated systems, we still face several challenges associated with high-quality hybrid silicon lasers, conversion efficiency, device integration, and fabrication. This paper provides an overview of recent progress in THz technologies based on silicon photonics or hybrid silicon photonics, including THz generation, detection, phase modulation, intensity modulation, and passive components. As silicon-based electronic and photonic circuits are further approaching THz frequencies, one single chip with electronics, photonics, and THz functions seems inevitable, resulting in the ultimate dream of a THz electronic–photonic integrated circuit.

Network effect in shared supply chain platform value co-creation behavior in evolutionary game1

2021 ◽  
pp. 1-12
Author(s):  
Zou Xiaohong ◽  
Chen Jinlong ◽  
Gao Shuanping
Keyword(s):  
Boundary Condition ◽  
Supply Chain ◽  
Large Scale ◽  
Simulation Analysis ◽  
Supply And Demand ◽  
Evolutionary Game ◽  
Dynamic Game ◽  
Network Effect ◽  
Chain Model ◽  
The Cost

The shared supply chain model has provided new ideas for solving contradictions between supply and demand for large-scale standardized production by manufacturers and personalized demands of consumers. On the basis of a platform network effect perspective, this study constructs an evolutionary game model of value co-creation behavior for a shared supply chain platform and manufacturers, analyzes their evolutionary stable strategies, and uses numerical simulation analysis to further verify the model. The results revealed that the boundary condition for manufacturers to participate in value co-creation on a shared supply chain platform is that the net production cost of the manufacturers’ participation in the platform value co-creation must be less than that of nonparticipation. In addition, the boundary condition for the shared supply chain platform to actively participate in value co-creation is that the cost of the shared supply chain platform for active participation in value co-creation must be less than that of passive participation. Moreover, value co-creation behavior on the shared supply chain platform is a dynamic game interaction process between players with different benefit perceptions. Finally, the costs and benefits generated by the network effect can affect value co-creation on shared supply chain platforms.

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