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50th Annual Convention of the Computer-Society-of-India (CSI) on Digital Life

作者： Chandra, Tej Bahadur Verma, Pushpak Dwivedi, Anuj Kumar MATS Univ Sch Informat Technol Raipur Chhattisgarh India Govt Vijay Bhushan Singh Deo Girls Degree Coll Jashpur 496331 Chhattisgarh India

ISBN: (纸本)9789811088483;9789811088476

In today's scenario, this world is moving rapidly toward the global warming. Various experiments are performed, to concentrate more on the energy efficiency. One way to achieve this is by implementing the sorting algorithms in such a programming language which consumes least amount of energy which is our current area of research in this paper. In this study, our main goal is to find such a programming language which consumes least amount of energy and contributes to green computing. In our experiment, we implemented different sorting algorithms in different programming languages in order to find the most power-efficient language.

关键词： programming language Sorting algorithms Power consumption Joulemeter

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Online Judgment System for Assessing C Program Structure

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JOURNAL OF INFORMATION SCIENCE AND ENGINEERING 2022年第2期38卷 275-294页

作者： Koong, Chorng-Shiuh Wei, Zih-Yu Chen, Chun-Hsien Guo, Cheng-Yan Natl Taichung Univ Educ Dept Comp Sci Taichung 403 Taiwan

The Online Judge (OJ) system solves many teaching problems of programming course design in traditional teaching modes and enhances teaching quality and learning effectiveness. Most of the OJ systems rate students by compiling and executing their code and then comparing the output with the standard output. However, program code content and students' ability to program structure cannot be accessed with such design. To improve this shortcoming, we have developed an "automatic structure assessment module" and added it to the existing system. The module functions to check the student program structure, enabling the OJ system to measure code quality. Such extended functionalities enable the OJ system to produce more accurate assessments of programming learning performance. Furthermore, how the program structure can be described in the program structure specification is another challenge. Thus, we have also developed a visual program structure description editor. The teacher can handily specify the program structure specification required by the program structure according to the teaching topic so that the OJ system can execute program structure checking. The functionalities of automatic program structure assessment combined with the visual program structure description editor can be used to rapidly generate many examinations and practice questions that require program structure evaluation, and thus truly achieve the efficiency of automatic program structure assessment as well as enhancing students' quality of program structure. Finally, in the six-week teaching experiment, there are a total of 61 valid samples. Using our structure comparison system can effectively improve the learning effectiveness of low-score group students in programming.

关键词： program structure assessment automatic assessment online judge system programming teaching syntax tree programming language

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EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

EzMechanism: an automated tool to propose catalytic mechanis...

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作者： Antonio J. Ribeiro Ioannis G. Riziotis Jonathan D. Tyzack Neera Borkakoti Janet M. Thornton

Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as ‘Easy’ Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literature on both related and unrelated enzymes. We validated EzMechanism on a set of 62 enzymes and have identified paths for further improvement, including the need for additional and more generic catalytic *** the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as ‘Easy’ Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literature on both related and unrelated enzymes. We validated EzMechanism on a set of 62 enzymes and have identified paths for further improvement, including the need for additional and more generic ca

关键词： Python programming language Cytoscape Computational models Software Protein function predictions Enzymes

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Peripheral Nervous System Responses to Food Stimuli:

Peripheral Nervous System Responses to Food Stimuli:

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作者： Maelle Moranges Marc Plantevit Moustafa Bensafi

In the field of food, as in other fields, the measurement of emotional responses to food and their sensory properties is a major challenge. In the present protocol, we propose a step-by-step procedure that allows a physiological description of odors, aromas, and their hedonic properties. The method rooted in subgroup discovery belongs to the field of data science and especially data mining. It is still little used in the field of food and is based on a descriptive modeling of emotions on the basis of human physiological responses.

关键词： Data Mining Python programming language Emotions Pleasantness Odors Aromas Food stimuli Subgroup discovery

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Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS

Inferring cellular and molecular processes in single-cell da...

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作者： Jeanette A. Johnson Ashley P. Tsang Jacob T. Mitchell David L. Zhou Julia Bowden Emily Davis-Marcisak Thomas Sherman Ted Liefeld Melanie Loth Loyal A. Goff Jacquelyn W. Zimmerman Ben Kinny-Köster Elizabeth M. Jaffee Pablo Tamayo Jill P. Mesirov Michael Reich Elana J. Fertig Genevieve L. Stein-O’Brien

Non-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional post hoc statistics and annotation for interpretation of learned features. Here, we introduce a suite of computational tools that implement NMF and provide methods for accurate and clear biological interpretation and analysis. A generalized discussion of NMF covering its benefits, limitations and open questions is followed by four procedures for the Bayesian NMF algorithm Coordinated Gene Activity across Pattern Subsets (CoGAPS). Each procedure will demonstrate NMF analysis to quantify cell state transitions in a public domain single-cell RNA-sequencing dataset. The first demonstrates PyCoGAPS, our new Python implementation that enhances runtime for large datasets, and the second allows its deployment in Docker. The third procedure steps through the same single-cell NMF analysis using our R CoGAPS interface. The fourth introduces a beginner-friendly CoGAPS platform using GenePattern Notebook, aimed at users with a working conceptual knowledge of data analysis but without a basic proficiency in the R or Python programming language. We also constructed a user-facing website to serve as a central repository for information and instructional materials about CoGAPS and its application programming interfaces. The expected timing to setup the packages and conduct a test run is around 15 min, and an additional 30 min to conduct analyses on a precomputed result. The expected runtime on the user’s desired dataset can vary from hours to days depending on factors such as dataset size or input ***-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional post hoc statistics and annotation for interpretation of learned features. Here, we

关键词： Machine Learning Python Statistical Calculation Single-cell RNA-seq Data analysis programming language Seurat Apis Software Computational platforms and environments Bayesian inference

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CD4+ T Cell Epitope Identification from Complex Parasite Antigen Mixtures

CD4+ T Cell Epitope Identification from Complex Parasite Ant...

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作者： Miguel Álvaro-Benito Friederike Ebner Miriam Bertazzon Eliot Morrison

Antigen complexity represents a major challenge for scoring CD4+ T cell immunogenicity, a key hallmark of immunity and with great potential to improve vaccine development. In this chapter, we provide a comprehensive picture of a pipeline that can be applied to virtually any complex antigen to overcome different limitations. Antigens are characterized by Mass Spectrometry to determine the available protein sources and their abundances. A reconstituted in vitro antigen processing system is applied along with bioinformatics tools to prioritize the list of candidates. Finally, the immunogenicity of candidate peptides is validated ex vivo using PBMCs from HLA-typed individuals. This protocol compiles the essential information for executing the whole pipeline while focusing on the candidate epitope prioritizing scheme. less

关键词： Spectroscopy Mass Spectrometry Cell And Tissue Culture Isotope Labeling SDS-PAGE Proteomics Peptide Identification programming language Flow Cytometry DNA Ligation Long-term Culture Co-culture Chromatography FPLC FACS Homo sapiens Antigen presentation MHC II CD4+ T cell reactivity Ascaris spp. parasites Excretory-secretory products (ES) Reconstitution in vitro antigen processing Complex antigen mixtures Anti-human CD40 Anti-human CD28 Anti-biotin Anti-CD3 Anti-HLA-DR

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Manipulating and Basic Analysis of Tabular Metagenomics Datasets Using R

Manipulating and Basic Analysis of Tabular Metagenomics Data...

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作者： Alex Coleman Martin Callaghan

Handling and manipulating tabular datasets is a critical step in every metagenomics analysis pipeline. The R statistical programming language offers a variety of versatile tools for working with tabular data that allow for the development of computationally efficient and reproducible workflows. Here we outline the basics of the R programming language and showcase a number of tools for data manipulation and basic analysis of metagenomics datasets. less

关键词： programming language Data analysis Metagenomics Data handling Reproducible research Data manipulation

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Evaluate the Understandability of Raku's Syntax

World Scientific Research Journal

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World Scientific Research Journal 2022年第2期8卷 366-379页

作者： Zhiyuan He Xuejing Li

Raku is a 'Practical Extraction And Reporting language', which combines the features of C, sed, awk, shell scripting and many other programming languages, which can simplify simple tasks without losing the ability to deal with difficult problems, but at the same time it is a niche programming language without much People know and use it. This paper aims to evaluate the syntax of Raku in two particular aspects, including manipulating numbers and working with files. The understandability of Raku's syntax by programmers, who have mastered python before, was verified by doing a think‐aloud test and semistructured interview. Comparisons between Raku, Perl5 and Python were added to deepen the study to check that whether Raku is more suitable for programmers who are supporters of previous versions of Perl. Results of the research showed that Raku's syntax in manipulating numbers and working with files is hard and easy respectively for students, who have learned Python, to understand. Also, Perl5 users indeed have some advantages in understanding the syntax of Raku, while the diversity of Raku also made this language is friendly to Python users.

关键词： Raku programming language Python Perl

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Array-Based Multiplex and High-Throughput Serology Assays

Array-Based Multiplex and High-Throughput Serology Assays

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作者： Jennie Olofsson Ceke Hellström Eni Andersson Jamil Yousef Lovisa Skoglund Ronald Sjöberg Anna Månberg Peter Nilsson Elisa Pin

The detection of antibody responses using serological tests provides means to diagnose infections, follow disease transmission, and monitor vaccination responses. The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 virus, highlighted the need for rapid development of robust and reliable serological tests to follow disease spreading. Moreover, the rise of SARS-CoV-2 variants emphasized the need to monitor their transmission and prevalence in the population. For this reason, multiplex and flexible serological assays are needed to allow for rapid inclusion of antigens representing new variants as soon as they appear. In this chapter, we describe the generation and application of a multiplex serological test, based on bead array technology, to detect anti-SARS-CoV-2 antibodies in a high-throughput manner, using only a few microliters of sample. This method is currently expanding to include a multi-disease antigen panel that will allow parallel detection of antibodies towards several infectious agents. less

关键词： Protein Array Data analysis Vaccination Cross-linking PCR programming language SARS-CoV-2 Serology Serum Antibody Multiplex Plasma High-throughput Anti-COVID Anti-human

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Empirical Analysis of the Growth and Challenges of New programming languages 43

Empirical Analysis of the Growth and Challenges of New Progr...

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43rd IEEE-Computer-Society Annual International Computers, Software and Applications Conference (COMPSAC)

作者： Chakraborty, Partha Shahriyar, Rifat Iqbal, Anindya Bangladesh Univ Engn & Technol Dept Comp Sci & Engn Dhaka Bangladesh

ISBN: (纸本)9781728126074

New programming languages (e.g., Swift, Go, Rust, etc.) are being introduced to provide a better opportunity to developers by matching the requirements of new platforms and application contexts. In the beginning, a programming language is likely to have constraints of resources that encourage the developers to seek help from experienced peers active in Question-answering (QA) sites such as Stack Overflow (SO). In this study, we would like to analyze the discussions on three popular new languages that are introduced after the inception of SO (2008). The relevant posts in SO present an interesting representation of the growth/evolution of that language and also expose the demands of the relevant development community. The major findings of the study are: (i) the time when adequate resources are expected to be available vary from language to language, (ii) the unanswered question ratio increases regardless of the age of the language and (iii) a new language is benefited from its predecessor language. The study outcome is likely to help the owner/sponsor of these languages to design better features and documentation and software developers or students to prepare themselves to work on these languages in an informed way.

关键词： Evolution Go Rust programming language Stack Overflow Swift

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