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Towards programming languages for genetic engineering of living cells

JOURNAL OF THE ROYAL SOCIETY INTERFACE 2009年第sup4期6卷 S437-S450页

作者： Pedersen, Michael Phillips, Andrew Microsoft Res Cambridge Cambridge CB3 0FB England Univ Edinburgh LFCS Sch Informat Edinburgh EH8 9AB Midlothian Scotland

Synthetic biology aims at producing novel biological systems to carry out some desired and well-defined functions. An ultimate dream is to design these systems at a high level of abstraction using engineering-based tools and programming languages, press a button, and have the design translated to DNA sequences that can be synthesized and put to work in living cells. We introduce such a programming language, which allows logical interactions between potentially undetermined proteins and genes to be expressed in a modular manner. Programs can be translated by a compiler into sequences of standard biological parts, a process that relies on logic programming and prototype databases that contain known biological parts and protein interactions. Programs can also be translated to reactions, allowing simulations to be carried out. While current limitations on available data prevent full use of the language in practical applications, the language can be used to develop formal models of synthetic systems, which are otherwise often presented by informal notations. The language can also serve as a concrete proposal on which future language designs can be discussed, and can help to guide the emerging standard of biological parts which so far has focused on biological, rather than logical, properties of parts.

关键词： synthetic biology programming language formal methods constraints logic programming

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programming languages for synthetic biology

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Systems and Synthetic Biology 2010年第4期4卷 265-269页

作者： Umesh, P. Naveen, F. Rao, Chanchala Uma Maheswara Nair, Achuthsankar S. State Inter University Centre of Excellence in Bioinformatics University of Kerala Thiruvananthapuram India Travancore Analytics Technopark Trivandrum Kerala India Innovation Labs Tata Consultancy Services Madhapur Hyderabad Andhra Pradesh India

In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented. © 2011 Springer Science+Business Media B.V.

关键词： Computational biology Design and construction of organisms programming language Synthetic biology

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Exploration on Educational Reform of C language programming at Vocational Colleges

Exploration on Educational Reform of C Language Programming ...

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2012 2nd International Conference on Education and Education Management(EEM 2012)

作者： Yan Yang Chengdu Polytechnic

C language programming is a specialized basic course of students who major in Computer and others at vocational colleges,which has great impacts on the study of many related follow-up ***,we not only explore but also carry out teaching methods of C language programming at vocational *** various teaching methods and ways mainly represented by the project teaching method have been utilized,favorable teaching effects are obtained in practical teaching.

关键词： Vocational Project driving method programming language

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A Study of Bug Resolution Characteristics in Popular programming languages

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IEEE TRANSACTIONS ON SOFTWARE ENGINEERING 2021年第12期47卷 2684-2697页

作者： Zhang, Jie M. Li, Feng Hao, Dan Wang, Meng Tang, Hao Zhang, Lu Harman, Mark Peking Univ Key Lab High Confidence Software Technol MoE Haidian 100871 Peoples R China UCL London WC1E 6BT England Facebook London London W1T 1FB England Univ Bristol Dept Comp Sci Bristol BS8 1TH Avon England

This paper presents a large-scale study that investigates the bug resolution characteristics among popular Github projects written in different programming languages. We explore correlations but, of course, we cannot infer causation. Specifically, we analyse bug resolution data from approximately 70 million Source Line of Code, drawn from 3 million commits to 600 GitHub projects, primarily written in 10 programming languages. We find notable variations in apparent bug resolution time and patch (fix) size. While interpretation of results from such large-scale empirical studies is inherently difficult, we believe that the differences in medians are sufficiently large to warrant further investigation, replication, re-analysis and follow up research. For example, in our corpus, the median apparent bug resolution time (elapsed time from raise to resolve) for Ruby was 4X that for Go and 2.5X for Java. We also found that patches tend to touch more files for the corpus of strongly typed and for statically typed programs. However, we also found evidence for a lower elapsed resolution time for bug resolution committed to projects constructed from statically typed languages. These findings, if replicated in subsequent follow on studies, may shed further empirical light on the debate about the importance of static typing.

关键词： Computer bugs Software engineering Java Correlation programming languages Data mining programming language bug resolution empirical study

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Wordplay: Accessible, Multilingual, Interactive Typography 25

Wordplay: Accessible, Multilingual, Interactive Typography

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Proceedings of the 2025 CHI Conference on Human Factors in Computing Systems

作者： Amy J Ko Carlos Aldana Lira Isabel Amaya The Information School University of Washington Seattle Washington USA Middle Tennessee State University Murfreesboro Tennessee USA University of Washington Seattle Washington USA

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DENOTATIONAL SEMANTICS OF programming languageS

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COMMUNICATIONS OF THE ACM 1976年第8期19卷 437-453页

作者： TENNENT, RD QUEENS UNIV DEPT COMP & INFORMATION SCIKINGSTONONTARIOCANADA

This paper is a tutorial introduction to the theory of programming language semantics developed by D. Scott and C. Strachey. The application of the theory to formal language specification is demonstrated and other applications are surveyed. The first language considered, LOOP, is very elementary and its definition merely introduces the notation and methodology of the approach. Then the semantic concepts of environments, stores, and continuations are introduced to model classes of programming language features and the underlying mathematical theory of computation due to Scott is motivated and outlined. Finally, the paper presents a formal definition of the language GEDANKEN.

关键词： GEDANKEN LOOP applicative continuation environment higher-order function imperative programming language recursive definition semantics store theory of computation

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PROBLEMATIC FEATURES OF programming-languageS - A SITUATIONAL-CALCULUS APPROACH

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ACTA INFORMATICA 1981年第4期16卷 371-426页

作者： MANNA, Z WALDINGER, R SRI INT ARTIFICIAL INTELLIGENCE CTRMENLO PKCA 94025

Certain features of programming languages, such as data structure operations and procedure call mechanisms, have been found to resist formalization by conventional program verification techniques. An alternate approach is presented, based on a “situational calculus,” which makes explicit reference to the states of a computation. For each state, a distinction is drawn between an expression, its value, and the location of the *** this conceptual framework, the features of a programming language can be described axiomatically. Programs in the language can then be synthesized, executed, verified, or transformed by performing deductions in this axiomatic system. Properties of entire classes of programs, and of programming languages, can also be expressed and proved in this way. The approach is amenable to machine *** a situational-calculus formalism it is possible to model precisely many “problematic” features of programming languages, including operations on such data structures as arrays, pointers, lists, and records, and such procedure call mechanisms as call by reference, call by value, and call by name. No particular obstacle is presented by aliasing between variables, by declarations, or by recursive *** this paper, we introduce our conceptual framework and present an axiomatic definition of the assignment statement. If suitable restrictions on the programming language are imposed, the well-known Hoare assignment axiom can then be proved as a theorem. However, our definition can also describe the assignment statement of unrestricted programming languages, for which the Hoare axiom does not hold. In forthcoming papers, we apply the situational-calculus framework to the description of data structure operations and procedure call mechanisms.

关键词： Conceptual Framework programming language Assignment Statement Axiomatic System Explicit Reference

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EMBEDDING UNIVERSAL COMPUTER ARITHMETIC IN HIGHER programming-languageS

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COMPUTING 1980年第2-3期24卷 149-160页

作者： BOHLENDER, G Institut für Angewandte Mathematik Universität Karlsruhe Kaiserstrasse 12 D-7500 Karlsruhe Federal Republic of Germany

In numerical computations mainly real and complex numbers, intervals as well as matrices and vectors with such components occur. It is well known that the arithmetic operations with real numbers, complex numbers etc. can be carried over to real floating-point numbers, complex floating-point numbers etc. using roundings. This proceeding results in agreeable arithmetic-, order- and compatibility-properties for an abundance of numerical data types and the accompanying arithmetic operations. Most programming languages however only provide real floating-point numbers; all the other data types and operations have to be simulated, e. g. in the form of arrays and procedure calls, which often causes loss of accuracy and arithmetic properties. Furthermore the complicate notation makes programs difficult to read. Therefore in this article an extension of PASCAL is presented which serves as an example for the way these numerical data types can be embedded into the syntax of a programming language.

关键词： Real Number Numerical Computation Computational Mathematic programming language Complex Number

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Ontology-Based Recommender System for a Learning Sequence in programming languages

INTERNATIONAL JOURNAL OF EMERGING TECHNOLOGIES IN LEARNING

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INTERNATIONAL JOURNAL OF EMERGING TECHNOLOGIES IN LEARNING 2021年第12期16卷 123-141页

作者： Shishehchi, Saman Zin, Nor Azan Mat Seman, Esmadi Abu Abu Imam Khomeini Int Univ Qazvin Iran Univ Kebangsaan Malaysia Fac Informat Sci & Technol Res Ctr Software Technol & Management SOFTAM Interact Comp Bangi Selangor Malaysia Univ Malaysia Sabah Fac Comp & Informat Labuan Int CampusJalan Sungai Pagar WP Labuan 87000 Malaysia

The same learning process in educational systems could be boring and time consuming for some learners. This problem arises from the lack of personalized learning sequence for learners with different knowledge level. Recommender systems play an important role in assisting the learners to find suitable learning materials and personalized learning sequence. Use of ontology for knowledge representation in knowledge-based recommender systems would facilitate sharing, reuse and common terminology. Since programming concepts have logical relationships among together so, traditional education systems are more stressful and very time-consuming. This paper aims to propose an ontology-based recommender system to present a Personalized Learning Sequence in programming (PLSP) domain which is depended to learner's knowledge level. A recommender module and, the knowledge base module are integrated together in the proposed framework. The recommender module as the main module in the framework, has three stages which is working based on semantic rules and ontology representation. Evaluation of the system was carried out by comparing the non-recommender system (web-based search) using 32 ICT respondents. Results demonstrate that the participants who used the proposed system spent 1119 seconds to find the suitable learning path in comparison to those who used a non-recommender system (3480 seconds) in the same learning material. It means that learners who follow learning path with PLSP, are more suitable for them. Furthermore, the average mean value of usability test is 4.47, (5 maximum scale) which indicates that the system proved to be useful, was easy to use, and satisfied the users.

关键词： Learning sequence Ontology programming language Recommender system

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Understanding Conceptual Transfer for Students Learning New programming languages 20

Understanding Conceptual Transfer for Students Learning New ...

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ACM Conference on International Computing Education Research (ICER)

作者： Tshukudu, Ethel Cutts, Quintin Univ Glasgow Glasgow Scotland

ISBN: (纸本)9781450370929

Prior research has shown that students face transition challenges between programming languages (PL) over the course of their education. We could not find research attempting to devise a model that describes the transition process and how students' learning of programming concepts is affected during the shift. In this paper, we propose a model to describe PL transfer for relative novices. In the model, during initial stages of learning a new language, students will engage in learning three categories of concepts, True Carryover Concepts, False Carryover Concepts, or Abstract True Carryover Concepts;during the transition, learners automatically effect a transfer of semantics between languages based on syntax matching. In order to find support for the model, we conducted two empirical studies. Study 1 investigated near-novice undergraduate students transitioning from procedural Python to object-oriented Java while Study 2 investigated near-novice postgraduate students doing a transfer from object-oriented Java to procedural Python. Results for both studies indicate that students had little or no difficulty with transitioning on TCC due to positive semantic transfer based on syntax similarities while they had the most difficulty transitioning on FCC due to negative semantic transfer. Students had little or no semantic transfer on ATCC due to differences in syntax between the languages. We suggest ways in which the model can inform pedagogy on how to ease the transition process.

关键词： programming language transfer code comprehension concepts syntax semantics Java Python

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