Python is a powerful high-level open source programming language that is available for multiple platforms. It supports object-oriented programming and has recently become a serious alternative to low-level compiled la...
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Python is a powerful high-level open source programming language that is available for multiple platforms. It supports object-oriented programming and has recently become a serious alternative to low-level compiled languages such as C++. It is easy to learn and use, and is recognized for very fast development times, which makes it suitable for rapid software prototyping as well as teaching purposes. We motivate the use of Python and its free extension modules for high performance stand-alone applications in econometrics and statistics, and as a tool for gluing different applications together. (It is in this sense that Python forms a "unified" environment for statistical research.) We give details on the core language features, which will enable a user to immediately begin work, and then provide practical examples of advanced uses of Python. Finally, we compare the run-time performance of extended Python against a number of commonly-used statistical packages and programming environments.
Parsing in the syntactical analysis of LR(k) grammars has characteristically demanded knowledge of k lookahead symbols, even though this knowledge is rarely needed. This parsing procedure is one reason why the usual ...
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Parsing in the syntactical analysis of LR(k) grammars has characteristically demanded knowledge of k lookahead symbols, even though this knowledge is rarely needed. This parsing procedure is one reason why the usual parsing tables (UTs) frequently have excessive dimensions. An alternative method applies reduced tables (RTs) to any collection of LR(k) sets of time. More auxiliary tables can be developed as needed to be used by the parser as guides for examining the lookahead symbols that follow the actual token. An example is presented of a parse carried out using RTs.
The programming language Pascal is considered as one of the most interesting computer system simulation tools. This paper discusses design facilities required in simulation languages, making use of a model described i...
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The programming language Pascal is considered as one of the most interesting computer system simulation tools. This paper discusses design facilities required in simulation languages, making use of a model described in Pascal. An important area is seen to be that of queues, lists or sets, and the facilities that are powerful yet simple to use are stressed. The problem of parallelism and synchronization in a simulator is solved. The structure of the simulator is considered.
We describe here the Genotype Specification language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language ...
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We describe here the Genotype Specification language (GSL), a language that facilitates the rapid design of large and complex DNA constructs used to engineer genomes. The GSL compiler implements a high-level language based on traditional genetic notation, as well as a set of low-level DNA manipulation primitives. The language allows facile incorporation of parts from a library of cloned DNA constructs and from the "natural" library of parts in fully sequenced and annotated genomes. GSL was designed to engage genetic engineers in their native language while providing a framework for higher level abstract tooling. To this end we define four language levels, Level 0 (literal DNA sequence) through Level 3, with increasing abstraction of part selection and construction paths. GSL targets an intermediate language based on DNA slices that translates efficiently into a wide range of final output formats, such as FASTA and GenBank, and includes formats that specify instructions and materials such as oligonucleotide primers to allow the physical construction of the GSL designs by individual strain engineers or an automated DNA assembly core facility.
Major computational challenges exist in relation to the collection, curation, processing and analysis of large genomic and imaging datasets, as well as the simulation of larger and more realistic models in systems bio...
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Major computational challenges exist in relation to the collection, curation, processing and analysis of large genomic and imaging datasets, as well as the simulation of larger and more realistic models in systems biology. Here we discuss how a relative newcomer among programming languages—Julia—is poised to meet the current and emerging demands in the computational biosciences and beyond. Speed, flexibility, a thriving package ecosystem and readability are major factors that make high-performance computing and data analysis available to an unprecedented degree. We highlight how Julia’s design is already enabling new ways of analyzing biological data and systems, and we provide a list of resources that can facilitate the transition into Julian computing.
This note describes mathematical modeling and programming and determines that they are essentially the same activity. However, differences in the way that the products of the two activities are used force them to be a...
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This note describes mathematical modeling and programming and determines that they are essentially the same activity. However, differences in the way that the products of the two activities are used force them to be applied in very different ways with very different goals. A result of these differences is that programming is harder than mathematical modeling, in that the model that the former produces must be more complete than the model that the latter produces. This note concludes with questions raised to encourage a discussion on the issues.
The Synthetic Biology Open language (SBOL) is an emerging synthetic biology data exchange standard, designed primarily for unambiguous and efficient machine communication. However, manual editing of SBOL is generally ...
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The Synthetic Biology Open language (SBOL) is an emerging synthetic biology data exchange standard, designed primarily for unambiguous and efficient machine communication. However, manual editing of SBOL is generally difficult for nontrivial designs. Here, we describe ShortBOL, a lightweight SBOL scripting language that bridges the gap between manual editing, visual design tools, and direct programming. ShortBOL is a shorthand textual language developed to enable users to create SBOL designs quickly and easily, without requiring strong programming skills or visual design tools.
Software developers seek a standard object-oriented database management system as a substrate on which to build object-oriented products. Convinced of the real value of object-oriented benefits, independent software v...
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Software developers seek a standard object-oriented database management system as a substrate on which to build object-oriented products. Convinced of the real value of object-oriented benefits, independent software vendors seek a platform to minimize development risk. A minimalist position is compared to the object-oriented database programming language position and the latter is shown to be the cleanest but pragmatic considerations may intervene.
Interactive computing, including real-time systems and process control, accounts for at least 50% of all computing. Most interactive systems have been programmed in regular batch programming languages. Provisions fo...
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Interactive computing, including real-time systems and process control, accounts for at least 50% of all computing. Most interactive systems have been programmed in regular batch programming languages. Provisions for handling input and output on an advanced level are lacking. A model is presented, called the input-output tool (IOT). It provides the programmer with facilities to hierarchically construct high-level input-driven tools. The elements of the IOT are the input rule, output rule, internal tool definitions, and a tool body consisting of executable statements. Advantages over traditional interactive programming include: 1. It offers a powerful input specification language. 2. It fosters structured programming. 3. Programmers only have to specify their inputs. 4. It allows interleaving and parallelism in entering inputs. 5. The parser handles input type checking and value checking. 6. Abstracts and simulated devices are easily definable. 7. The high-level IOTs may be considered as input command procedures and entities in a user dialogue language. Use of the IOT model results in ease of programming and efficient execution.
作者：
BEECH, DIBM
UNITED KINGDOM LABSWINCHESTERENGLAND
AbstractAccepting the coexistence of a variety of computer languages as a fact of life, this paper seeks to make a virtue of necessity by proposing a modular framework within which these languages can be used. Example...
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AbstractAccepting the coexistence of a variety of computer languages as a fact of life, this paper seeks to make a virtue of necessity by proposing a modular framework within which these languages can be used. Examples of the types of languages considered are command languages, programming languages, data manipulation and definition languages, data communication languages and text editor *** of syntactic modularity and semantic modularity are distinguished, and some answers to difficult questions are suggested, leading to a proposal for specific RUN and EXECUTE constructs that should be made widely available. Discussion is mainly at the level of the visible and conceptual concerns of the end user and the system architect, but the actual implementation of interconnection mechanisms is not totally ignored.A tutorial outline is offered as an indication of how the underlying ideas might be introduced to non‐specialists, and might even become a part of elementary educatio
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