Information & computer science publications
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The Versatile Synchronous Observer
The paper describes and illustrates these applications of synchronous observers.
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Expanding the Metabolite Mimic Approach to Identify Hits for Mycobacterium Tuberculosis
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Template-Based Circuit Understanding
We propose a template-based approach that extracts a functional description for a low-level combinational circuit by showing it to be equivalent to a reference implementation, while synthesizing an appropriate mapping…
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A Nonlinear Real Arithmetic Fragment
We present a new procedure for testing satisability (over the reals) of a conjunction of polynomial equations.
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Metabolic Pathways for the Whole Community
Here we adopt the MetaPathways annotation and analysis pipeline and Pathway Tools to construct environmental pathway/genome databases that describe microbial community metabolism using MetaCyc.
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A Tale of Two Solvers: Eager and Lazy Approaches to Bit-Vectors
In this paper we describe the architecture and features of our lazy solver (LBV). We provide a comparative analysis of the eager and lazy approaches, and show how they are…
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Yices 2.2
We describe the latest release of Yices, namely, Yices 2.2. We present the tool’s architecture and discuss the algorithms it implements, and we describe recent developments such as support for…
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The CHERI Capability Model: Revisiting RISC in an Age of Risk
Motivated by contemporary security challenges, we reevaluate and refine capability-based addressing for the RISC era. We present CHERI, a hybrid capability model that extends the 64-bit MIPS ISA with byte-granularity…
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A Genome-Scale Metabolic Flux Model of Escherichia coli K-12 Derived from the EcoCyc Database
We present EcoCyc–18.0–GEM, a genome-scale model of the E. coli K–12 MG1655 metabolic network.
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Curation Accuracy of Model Organism Databases
We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in…
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Efficiently Gap-Filling Reaction Networks
We present a computational technique, called FastGapFilling, that efficiently completes a reaction network by using only Linear Programming, not MILP.
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PIDGIN: Privacy-Preserving Interest and Content Sharing in Opportunistic Networks
This paper addresses the research challenges inherent to the exchange of content and interests without compromising the privacy of subscribers, and allowing unauthorised access to untrusted brokers. Specifically, this paper…