Powerful Syntax Research Articles

Poetic Harmony In Arif Abdul Mateen’s Naa’atya Poetry

Naa’at is a form of religious poetry that is recited in praise of the Prophet Muhammad (peace be upon him). The word “Naa’at " is derived from the Arabic word "nath," which means "praise. “The content of Naa’ats usually includes descriptions of the Prophet Muhammad's character (seerat), his life, and his teachings. Naa’at can also be used to express the devotion and love that Muslims feel towards the Prophet Muhammad. Arif Abdul Mateen wrote in all forms of poetry and prose but his Naa’at genera have special mental thought process and evolution as a journey from communist thoughts to prospects of religion. He in his Naa’atia poetry, basically initiated a heart touching dialogue with Prophet Muhammad (PBUH) and expected solutions of modern day humanitarian problems from the greatest Reformer and top rank HUMANBEING so he made it a social dialogue rather than mere praise and verbosity. In expression of Naa’at arif’s main focus remained on the philosophical view of developmental, peaceful, progressive and balanced human society as per core Islamic values. His style (Usloob) is having visual and sensory effects embedded with creative, decorated, symbolistic, impressive and articulated treasure of words flavoured with historical imagery. He created Naa’at on the modern poetic norms, which can be seen in each couplet soaked with powerful syntax and images.

Fuzion - Safety through Simplicity

Fuzion is a modern, general purpose programming language that unifies concepts found in structured, functional and object-oriented programming languages into the concept of a Fuzion feature. It combines a powerful syntax and safety features based on the design-by-contract principle with a simple intermediate representation that enables powerful optimizing compilers and static analysis tools to verify correctness aspects. Fuzion maps different concepts into the concept of a Fuzion feature and uses a simple intermediate language that is friendly for static analysis tools as well as for optimizing compilers. Fuzion was influenced by many other languages including Java, Python, Eiffel, Rust, Ada, Go, Lua, Kotlin, C#, F#, Nim, Julia, Clojure, C/C++, Scala, and many more. The goal of Fuzion is to define a language that has the expressive power present in these languages and allow high-performance implementation and powerful analysis tools. Furthermore, Fuzion addresses requirements for safety-critical applications by adding support for contracts that enable formal specification and detailed control over runtime checks.

Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB).

Biologists seek to create increasingly complex molecular regulatory network models. Writing such a model is a creative effort that requires flexible analysis tools and better modeling languages than offered by many of today's biochemical model editors. Our Multistate Model Builder (MSMB) supports multistate models created using different modeling styles that suit the modeler rather than the software. MSMB defines a simple but powerful syntax to describe multistate species. Our syntax reduces the number of reactions needed to encode the model, thereby reducing the cognitive load involved with model creation. MSMB gives extensive feedback during all stages of model creation. Users can activate error notifications, and use these notifications as a guide toward a consistent, syntactically correct model. Any consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB's multistate syntax through realistic models of cell cycle regulation and mRNA transcription. MSMB is an open-source project implemented in Java and it uses the COPASI API. Complete information and the installation package can be found at http://copasi.org/Projects/ .

Design and Analysis of 5G Scenarios with simmer: An R Package for Fast DES Prototyping

Simulation frameworks are important tools for the analysis and design of communication networks and protocols, but they can result extremely costly and/or complex (for the case of very specialized tools), or too naive and lacking proper features and support (for the case of ad-hoc tools). In this paper, we present an analysis of three 5G scenarios using 'simmer', a recent R package for discrete-event simulation that sits between the above two paradigms. As our results show, it provides a simple yet very powerful syntax, supporting the efficient simulation of relatively complex scenarios at a low implementation cost.

Multistate Model Builder (MSMB): a flexible editor for compact biochemical models

BackgroundBuilding models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more flexibility and interactive support than offered by many of today’s biochemical model editors. Our model editor MSMB — Multistate Model Builder — supports multistate models created using different modeling styles.ResultsMSMB provides two separate advances on existing network model editors. (1) A simple but powerful syntax is used to describe multistate species. This reduces the number of reactions needed to represent certain molecular systems, thereby reducing the complexity of model creation. (2) Extensive feedback is given during all stages of the model creation process on the existing state of the model. Users may activate error notifications of varying stringency on the fly, and use these messages as a guide toward a consistent, syntactically correct model. MSMB default values and behavior during model manipulation (e.g., when renaming or deleting an element) can be adapted to suit the modeler, thus supporting creativity rather than interfering with it. MSMB’s internal model representation allows saving a model with errors and inconsistencies (e.g., an undefined function argument; a syntactically malformed reaction). A consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB’s multistate syntax through models of the cell cycle and mRNA transcription.ConclusionsUsing multistate reactions reduces the number of reactions need to encode many biochemical network models. This reduces the cognitive load for a given model, thereby making it easier for modelers to build more complex models. The many interactive editing support features provided by MSMB make it easier for modelers to create syntactically valid models, thus speeding model creation. Complete information and the installation package can be found at http://www.copasi.org/SoftwareProjects. MSMB is based on Java and the COPASI API.

Spatial Calculus of Looping Sequences

This paper presents Spatial CLS, an extension of the Calculus of Looping Sequences (CLS) with spatial features. Spatial CLS allows keeping track of the position of biological elements in a continuous space (2D or 3D) as time passes. The movement of elements in the space can be precisely described, and elements can interact when constraints on their positions are satisfied such as, for example, if two elements are close enough. As for CLS, membranes and elements inside them can be directly modeled in the syntax. Spatial CLS allows describing the space occupied by elements and membranes. The space occupied by different objects is always kept disjoint. The validity of this constraint is ensured at all times by the semantics of the calculus. In order to model specific behaviors, the modeler can provide an algorithm to rearrange the position of objects in case of a space conflict. Being an extension of CLS, Spatial CLS provides a simple and powerful syntax, based on rewrite rules, for describing the possible reactions among elements of a system. Moreover, rewrite rules are endowed with a stochastic reaction rate parameter. The aim of Spatial CLS is to enable a more accurate description of those biological processes whose behavior depends on the exact position of the elements. As example applications of the calculus, we present a model of cell proliferation, and a model of the quorum sensing process in Pseudomonas aeruginosa.

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

BackgroundAccurately modeling the sequence substitution process is required for the correct estimation of evolutionary parameters, be they phylogenetic relationships, substitution rates or ancestral states; it is also crucial to simulate realistic data sets. Such simulation procedures are needed to estimate the null-distribution of complex statistics, an approach referred to as parametric bootstrapping, and are also used to test the quality of phylogenetic reconstruction programs. It has often been observed that homologous sequences can vary widely in their nucleotide or amino-acid compositions, revealing that sequence evolution has changed importantly among lineages, and may therefore be most appropriately approached through non-homogeneous models. Several programs implementing such models have been developed, but they are limited in their possibilities: only a few particular models are available for likelihood optimization, and data sets cannot be easily generated using the resulting estimated parameters.ResultsWe hereby present a general implementation of non-homogeneous models of substitutions. It is available as dedicated classes in the Bio++ libraries and can hence be used in any C++ program. Two programs that use these classes are also presented. The first one, Bio++ Maximum Likelihood (BppML), estimates parameters of any non-homogeneous model and the second one, Bio++ Sequence Generator (BppSeqGen), simulates the evolution of sequences from these models. These programs allow the user to describe non-homogeneous models through a property file with a simple yet powerful syntax, without any programming required.ConclusionWe show that the general implementation introduced here can accommodate virtually any type of non-homogeneous models of sequence evolution, including heterotachous ones, while being computer efficient. We furthermore illustrate the use of such general models for parametric bootstrapping, using tests of non-homogeneity applied to an already published ribosomal RNA data set.

BioRuby: Open-Source Bioinformatics Library

BioRuby [1] is an open-source project which aims to provide a reusable library for biological tasks for the Ruby language [4]. Ruby is an interpreted object-oriented scripting language with a simple and powerful syntax and native object-oriented programming support. Ruby is developed by a Japanese author and is now accepted not only by Japanese but also by many professional programmers around the world as a highly productive language. Ruby has many advantageous features to process text files and for system management tasks, which are frequently needed for bioinformatics tools. Compared to other languages, it has native support for object-oriented programming with a simple but powerful syntax, with which we can easily describe and manipulate complicated biological data structures efficiently. These are the main reason why we decided to implement a bioinformatics library in Ruby, even though BioPerl [2], BioJava, and BioPython were developed previously. BioRuby is available as free software and is licensed under the GNU Lesser General Public License. It is available for download at http://bioruby.org/.

BioRuby: Object Oriented Open Source Library for Bioinformatics

BioRuby [6] is the project to bulid useful library for bioinformatics tasks with the object oriented scripting language Ruby, started in late 2000. Ruby is made in Japan and is getting popularity by its simple and powerful syntax in recent years. For Perl, Java and Python programmers, there are already existing BioPerl [4], BioJava [3] and BioPython [5] projects as precedent efforts, and organized by the open bio foundation [7, 2, 1]. However, they tend to be complicated unnecessarily because of the limitation of each language characteristics and historical reasons that they have gradually developed. Taking these state into consideration, we find the ruby language is suitable for constructing simple and easy to use open bio library. In 2002, the first invited-only Open Bio* developers meeting called BioHackathon was held in Arizona and Cape Town, and we have agreed on five new ways to retrieve a record given an identifier from the biological sequence databases. These methods are named OBDA (open bio sequence database access) and include flatfile indexing (simple, Berkeley DB), BioFetch (CGI/HTTP), BioSQL (MySQL, PostgreSQL, Oracle), XEMBL and Corba described below.

Inductive expansion: A calculus for verifying and synthesizing functional and logic programs

Guarded Horn clauses over a many-sorted polymorphic signature provide a powerful syntax for design specifications. Expressed as a set of positive Gentzen clauses with a common guard, requirements to such a specification can be proved top-down by inductive expansion: conclusions and generators of the clauses are transformed via resolution and paramodulation upon axioms, lemmas and induction hypotheses into the guard. Case distinctions are generated when axioms or lemmas are applied in parallel. They split the proof into subexpansions, which are later rejoined by applying disjunctive lemmas. Induction orderings need not be selected before redices for induction hypotheses have been created.

APAREL—A parse-request language

APAREL is described: this language is an extension to an algorithmic language (PL/I) that provides the pattern-matching capabilities normally found only in special purpose languages such as SNOBOL4 and TMG. This capability is provided through parse-requests stated in a BNF-like format. These parse-requests form their own programming language with special sequencing rules. Upon successfully completing a parse-request, an associated piece of PL/I code is executed. This code has available for use, as normal PL/I strings, the various pieces (at all levels) of the parse. It also has available, as normal PL/I variables, the information concerning which of the various alternatives were successful. Convenient facilities for multiple input-output streams, the initiation of sequences of parse-requests as a subroutine, and parse-time semantic checks are also included. APAREL has proven convenient in building a powerful SYNTAX and FUNCTION macro system, an algebraic language preprocessor debugging system, an on-line command parser, a translator for Dataless Programming, and as a general string manipulator.