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

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.</jats:p

An Agent Based Market Design Methodology for Combinatorial Auctions

Auction mechanisms have attracted a great deal of interest and have been used in diverse e-marketplaces. In particular, combinatorial auctions have the potential to play an important role in electronic transactions. Therefore, diverse combinatorial auction market types have been proposed to satisfy market needs. These combinatorial auction types have diverse market characteristics, which require an effective market design approach. This study proposes a comprehensive and systematic market design methodology for combinatorial auctions based on three phases: market architecture design, auction rule design, and winner determination design. A market architecture design is for designing market architecture types by Backward Chain Reasoning. Auction rules design is to design transaction rules for auctions. The specific auction process type is identified by the Backward Chain Reasoning process. Winner determination design is about determining the decision model for selecting optimal bids and auctioneers. Optimization models are identified by Forward Chain Reasoning. Also, we propose an agent based combinatorial auction market design system using Backward and Forward Chain Reasoning. Then we illustrate a design process for the general n-bilateral combinatorial auction market. This study serves as a guideline for practical implementation of combinatorial auction markets design.Combinatorial Auction, Market Design Methodology, Market Architecture Design, Auction Rule Design, Winner Determination Design, Agent-Based System

Bayesian Incentive Compatibility via Fractional Assignments

Very recently, Hartline and Lucier studied single-parameter mechanism design problems in the Bayesian setting. They proposed a black-box reduction that converted Bayesian approximation algorithms into Bayesian-Incentive-Compatible (BIC) mechanisms while preserving social welfare. It remains a major open question if one can find similar reduction in the more important multi-parameter setting. In this paper, we give positive answer to this question when the prior distribution has finite and small support. We propose a black-box reduction for designing BIC multi-parameter mechanisms. The reduction converts any algorithm into an eps-BIC mechanism with only marginal loss in social welfare. As a result, for combinatorial auctions with sub-additive agents we get an eps-BIC mechanism that achieves constant approximation.Comment: 22 pages, 1 figur

Environmental analysis for application layer networks

Die zunehmende Vernetzung von Rechnern über das Internet lies die Vision von Application Layer Netzwerken aufkommen. Sie umfassen Overlay Netzwerke wie beispielsweise Peer-to-Peer Netzwerke und Grid Infrastrukturen unter Verwendung des TCP/IP Protokolls. Ihre gemeinsame Eigenschaft ist die redundante, verteilte Bereitstellung und der Zugang zu Daten-, Rechen- und Anwendungsdiensten, während sie die Heterogenität der Infrastruktur vor dem Nutzer verbergen. In dieser Arbeit werden die Anforderungen, die diese Netzwerke an ökonomische Allokationsmechanismen stellen, untersucht. Die Analyse erfolgt anhand eines Marktanalyseprozesses für einen zentralen Auktionsmechanismus und einen katallaktischen Markt. --Grid Computing