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A Generalized Notion of Non-interference for Flow Security of Sequential and Concurrent Programs 27

A Generalized Notion of Non-interference for Flow Security o...

引用

27th Asia-Pacific Software Engineering Conference (APSEC)

作者： Ghosal, Sandip Shyamasundar, R. K. Indian Inst Technol Dept Comp Sci & Engn Mumbai Maharashtra India

ISBN: (纸本)9781728195537

For the last two decades, a wide spectrum of interpretations of non-interference 1 have been used in the security analysis of programs, starting with the notion proposed by Goguen & Meseguer along with arguments of its impact on security practice. While the majority of works deal with sequential programs, several researchers have extended the notion of non-interference to enforce information flow-security in non-deterministic and concurrent programs. Major efforts of generalizations are based on (i) considering input sequences as a basic unit for input/output with semantic interpretation on a two-point information flow lattice, or (ii) typing of expressions as values for reading and writing, or (iii) typing of expressions along with its limited effects. Such approaches have limited compositionality and, thus, pose issues while extending these notions for concurrent programs. Further, in a general multi-point lattice, the notion of a public observer (or attacker) is not unique as it depends on the level of the attacker and the one attacked. In this paper, we first propose a compositional variant of non-interference for sequential systems that follow a general information flow lattice and place it in the context of earlier definitions of non-interference. We show that such an extension leads to the capturing of violations of information flow security in a concrete setting of a sequential language. Finally, we generalize non-interference for concurrent programs and illustrate its use for security analysis, particularly in the cases where information is transmitted through shared variables.

关键词： information flow control non-interference generalization sequential concurrent programming language

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Design of an IDE for Teaching programming using Graphic Elements 9

Design of an IDE for Teaching Programming using Graphic Elem...

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9th International Conference on Software Process Improvement (CIMPS)

作者： Picie-Alcaraz, Ivan Alejandra Olivares-Zepahua, Beatriz Lopez-Martinez, Ignacio Romero-Torres, Celia Angel Reyes-Hernandez, Luis Tecnol Nacl Mexico Inst Tecnol Orizaba Orizaba Veracruz Mexico

ISBN: (纸本)9781665403764

In recent years, the promotion of the teaching of Science, Technology, Engineering and Mathematics (STEM for its acronym in English) has increased in Mexico and around the world, with the aim that people develop a series of skills related to the use and development of technologies. In Mexico there are associations focused specifically on computer science, with the aim of teaching children and young people to program, but the tools that are available are few in the Spanish language since approximately 80% of the applications are in English. The present work proposes a development environment that allows the generation of geometric patterns in the Spanish language as a support to the teaching of STEM in Mexico.

关键词： development environment programming language geometric patterns

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Multi-purpose Syntax Definition with SDF3 1

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18th International Conference on Software Engineering and Formal Methods (SEFM)

作者： Amorim, Luis Eduardo de Souza Visser, Eelco Australian Natl Univ Canberra ACT Australia Delft Univ Technol Delft Netherlands

ISBN: (数字)9783030587680

ISBN: (纸本)9783030587680;9783030587673

SDF3 is a syntax definition formalism that extends plain context-free grammars with features such as constructor declarations, declarative disambiguation rules, character-level grammars, permissive syntax, layout constraints, formatting templates, placeholder syntax, and modular composition. These features support the multi-purpose interpretation of syntax definitions, including derivation of type schemas for abstract syntax tree representations, scannerless generalized parsing of the full class of context-free grammars, error recovery, layout-sensitive parsing, parenthesization and formatting, and syntactic completion. This paper gives a high level overview of SDF3 by means of examples and provides a guide to the literature for further details.

关键词： Syntax definition programming language Parsing

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Theoretical Basis of language System with State Constraints 5

Theoretical Basis of Language System with State Constraints

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5th International Conference on Complexity, Future Information Systems and Risk (COMPLEXIS)

作者： Yamasaki, Susumu Okayama Univ HCI Grp Dept Comp Sci Tsushima Okayama Japan

ISBN: (纸本)9789897584275

This paper presents theoretical basis of a language system whose program is described as algebraic expressions and implemented as abstract state machine. The behaviors of the described expressions may be captured (with their models) as causing sequences for state transitions, where composition and alternation for state transitions are mechanized in algebraic structure. Monitoring facilities to the language system may be described with state concepts, as well. With respect to intuitionistic logic and logical program containing negatives, Heyting algebra expressions are taken rather than already established nonmonotonic reasoning programs with negations, where 3-valued domain may be of use for the undefined to be allowable such that positives and negatives may be consistently evaluated, instead of rigid 2-valued settlements. We may have a standard form of Heyting algebra expressions in accordance to logical and AI programming, where the expressions are constrained with states. The states may be regarded as environmental conditions or objects as in object-oriented programming. As regards 3-valued models of given expressions, monotonic mapping cannot be in general associated with, but some ways are presented to approximate fixed points of a mapping for the given expression. Then the formal description of programs may be given with reference to state transitions, which is thought of as proposing a language system structure.

关键词： programming language Algebraic Expression State Constraint System

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Teaching programming through Problem Solving: The Role of the programming language

Teaching Programming through Problem Solving: The Role of th...

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Federated Conference on Computer Science and Information Systems

作者： Nikolaos S. Papaspyrou Stathis Zachos School of Electrical and Computer Engineering National Technical University of Athens Polytechnioupoli 15780 Zografou Athens Greece

ISBN: (纸本)9781467344715

In this short paper, we advocate the importance of problem solving for teaching "Introduction to programming", instead of merely teaching the syntax and semantics of a programming language. We focus on the role of the programming language used for an introductory course. For this purpose we propose CAL, a C-like algorithmic language, which is essentially a well-defined and behaved subset of C with a small number of modest, "educational" extensions. We present the design rationale for CAL, its main features, syntax and illustrative examples.

关键词： Teaching programming Problem Solving programming language

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Summarizing RNA-Seq Data or Differentially Expressed Genes Using Gene Set, Network, or Pathway Analysis

Summarizing RNA-Seq Data or Differentially Expressed Genes U...

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作者： Enrica Calura Paolo Martini

The main purpose of pathway or gene set analysis methods is to provide mechanistic insight into the large amount of data produced in high-throughput studies. These tools were developed for gene expression analyses, but they have been rapidly adopted by other high-throughput techniques, becoming one of the foremost tools of omics research. Currently, according to different biological questions and data, we can choose among a vast plethora of methods and databases. Here we use two published examples of RNAseq datasets to approach multiple analyses of gene sets, networks and pathways using freely available and frequently updated software. Finally, we conclude this chapter by presenting a survival pathway analysis of a multiomics dataset. During this overview of different methods, we focus on visualization, which is a fundamental but challenging step in this computational field. less

关键词： RNA-seq Cross-linking Differential Expression Analysis Cytoscape Statistical Calculation Microarray EnrichmentMap programming language Homo sapiens Mus musculus Saccharomyces cerevisiae Rattus norvegicus Networks Pathway Gene set analysis Topological pathway analysis Multiomics data integration

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A Computational Protocol to Analyze PDZ/PBM Affinity Data Obtained by High-Throughput Holdup Assay

A Computational Protocol to Analyze PDZ/PBM Affinity Data Ob...

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作者： Pau Jané Lionel Chiron Goran Bich Gilles Travé Yves Nominé

The holdup assay is an automated high-throughput comparative chromatographic retention approach that allows to measure quantitative binding intensities (BI) for a large number of domain–motif pairs and deduce equilibrium binding affinity constants. We routinely apply this approach to obtain quantitative binding specificity profiles of particular PDZ-binding motifs (PBMs) toward the full library of known human PDZ domains (the PDZome). The quality of the electropherograms extracted from the capillary electrophoresis instrument at the final step of the holdup assay may vary, influencing the accuracy and reproducibility of the measurement. By using bioinformatic tools, we can solve these issues to extract more reliable BIs by means of a better superimposition of the electropherograms. The protocol presented in this chapter describes the main principles and strategies of our curated method to process holdup data and new ways to plot and compare the BIs for the PBM–PDZ interactions. For this particular protocol, all the necessary computing commands are freely available in open Python packages. less

关键词： Capillary Electrophoresis (CE) Rearrangement Python programming language Computational approach Holdup assay PDZ–PBM interaction Processing accuracy Electropherogram superimposition

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3D extrusion bioprinting

3D extrusion bioprinting

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作者： Yu Shrike Zhang Ghazaleh Haghiashtiani Tania Hübscher Daniel J. Kelly Jia Min Lee Matthias Lutolf Michael C. McAlpine Wai Yee Yeong Marcy Zenobi-Wong Jos Malda

Three-dimensional (3D) bioprinting strategies use computer-aided processes to enable automated simultaneous spatial patterning of cells and/or biomaterials. These technologies are suitable for a broad range of biomedical applications owing to their capability to produce structurally sophisticated and functionally relevant tissue constructs. Extrusion-based 3D bioprinting strategies were among the first modalities developed and are now arguably the most widely used for producing 3D tissue constructs. These technologies have rapidly evolved over the past two decades, providing a powerful tool set for the biofabrication of tissues that can facilitate translational efforts in the field. In this Primer, we describe the methodology of 3D extrusion bioprinting, focusing on the selection of hardware, software and bioinks. We expand upon recent advances in 3D extrusion bioprinting by illustrating the key variations that promote its biofabrication abilities. Finally, we provide an outlook on possible future refinements of the technology. less

关键词： Tissue Engineering MRI Medical Imaging MATLAB Machine Learning Cell Proliferation Assay Chemical Cross-linking Cell And Tissue Culture Click Chemistry Wet Spinning Extrusion Bioprinting Bioprinting programming language Synthetic biology Design, synthesis and processing Biomaterials – cells

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Large-Scale Molecular Dynamics Simulations of Cellular Compartments

Large-Scale Molecular Dynamics Simulations of Cellular Compa...

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作者： Eric Wilson John Vant Jacob Layton Ryan Boyd Hyungro Lee Matteo Turilli Benjamín Hernández Sean Wilkinson Shantenu Jha Chitrak Gupta Daipayan Sarkar Abhishek Singharoy

Molecular dynamics or MD simulation is gradually maturing into a tool for constructing in vivo models of living cells in atomistic details. The feasibility of such models is bolstered by integrating the simulations with data from microscopic, tomographic and spectroscopic experiments on exascale supercomputers, facilitated by the use of deep learning technologies. Over time, MD simulation has evolved from tens of thousands of atoms to over 100 million atoms comprising an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium. In this chapter, we present a step-by-step outline for preparing, executing and analyzing such large-scale MD simulations of biological systems that are essential to life processes. All scripts are provided via GitHub. less

关键词： Molecular Dynamics Simulation Deep learning X-ray Crystallography Cryo-EM Mass Spectrometry Tomography Protein Structure Analysis Python programming language High-performance computing NAMD VMD Multiscale simulation Photosynthetic chromatophore Ensemble toolkit

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LIVECell—A large-scale dataset for label-free live cell segmentation

LIVECell—A large-scale dataset for label-free live cell seg...

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作者： Christoffer Edlund Timothy R. Jackson Nabeel Khalid Nicola Bevan Timothy Dale Andreas Dengel Sheraz Ahmed Johan Trygg Rickard Sjögren

Light microscopy combined with well-established protocols of two-dimensional cell culture facilitates high-throughput quantitative imaging to study biological phenomena. Accurate segmentation of individual cells in images enables exploration of complex biological questions, but can require sophisticated imaging processing pipelines in cases of low contrast and high object density. Deep learning-based methods are considered state-of-the-art for image segmentation but typically require vast amounts of annotated data, for which there is no suitable resource available in the field of label-free cellular imaging. Here, we present LIVECell, a large, high-quality, manually annotated and expert-validated dataset of phase-contrast images, consisting of over 1.6 million cells from a diverse set of cell morphologies and culture densities. To further demonstrate its use, we train convolutional neural network-based models using LIVECell and evaluate model segmentation accuracy with a proposed a suite of benchmarks. less

关键词： Light Microscopy Cell And Tissue Culture Cellular Imaging Image Annotation Machine Learning Deep learning Data analysis Python programming language Cell biology Technology Research data

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