Computational Tools

The original intent of Marxan and its predecessors was to solve a version of the minimum set reserve design problem (Cocks and Baird 1989; Chapter 3). In this problem, conservation targets are set for a mimber of biodiversity features (eg three populations of each species), and Marxan selects planning units that represent these targets for a minimum total cost, while allowing for more or less emphasis on spatially clustering the selected planning units. Marxan is now used to solve a range of spatial prioritization problems beyond the ...

MIDI Toolbox provides a set of Matlab functions, which together have all the necessary machinery to analyze and visualize MIDI data. The development of the Toolbox has been part of ongoing research involved in topics relating to musical data- mining, modelling music perception and decomposing the data for and from perceptual experiments. Although MIDI data is not necessarily a good representation of music in general, it suffices for many research questions dealing with concepts such as melodic contour, tonality and pulse finding. These concepts are intriguing from the point of view of music perception and the chosen representation greatly affects the way these issues can be approached. MIDI is not able to handle the timbre of music and therefore it unsuitable representation for a number of research questions (for summary, see Hewlett and Selfridge-Field, 1993-94, p. 11-28). All musical signals may be processed from acoustic representation and there are suitable tools available for these purposes (e.g. IPEM toolbox, Leman et al., 2000). However, there is a body of essential questions of music cognition that benefit from a MIDI-based approach. MIDI does not contain notational information, such as phrase and bar markings, and neither is that information conveyed in explicit terms to the ears of music listeners. Consequently, models of music cognition must infer these musical cues from the pitch, timing and velocity information that MIDI provides. Another advantage of the MIDI format is that it is extremely wide-spread among the research community as well as having a wider group of users amongst the music professionals, artists and amateur musicians. MIDI is a common file format between many notation, sequencing and performance programs across a variety of operating systems. Numerous pieces of hardware exist that collect data from musical performances, either directly from the instrument (e.g. digital pianos and other MIDI instruments) or from the movements of the artists (e.g. motion tracking of musician’s gestures, hand movements etc.). The vast majority of this technology is based on MIDI representation. However, the analysis of the MIDI data is often developed from scratch for each research question. The aim of MIDI Toolbox is to provide the core representation and functions that are needed most often. These basic tools are designed to be modular to allow easy further development and tailoring for specific analysis needs. Another aim is to facilitate efficient use and to lower the “threshold of practicalities”. For example, the Toolbox can be used as teaching aid in music cognition courses.

Computational methods play a central role in modern drug discovery process. It includes the design and management of small molecule libraries, initial hit identification through virtual screening, optimization of the affinity as well as selectivity of hits and improving the physicochemical properties of the lead compounds. In this review article, computational drug designing approaches have been elucidated and discussed. The key considerations and guidelines for virtual chemical library design and whole drug discovery process. Traditional approach for discovery of a new drug is a costly and time consuming affair besides not being so productive. A number of potential reasons witness choosing the In-silico method of drug design to be a more wise and productive approach. There is a general perception that applied science has not kept pace with the advances of basic science. Therefore, there is a need for the use of alternative tools to get answers on efficacy and safety faster, with more certainty and at lower cost. In-silico drug design can play a significant role in all stages of drug development from the initial lead designing to final stage clinical development.

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard. org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry. org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This ...

The appearance of more and more complex tools in mathematics classes is not a response to an institutional need of school. It is, rather, the expression within this institution of a huge social phenomenon (the increase in the number of screens and machines) arising from the utilization of computerized tools by certain branches of mathematics and science.

Within the Lexical Constructional Model (LCM), a lexical template (LT) is a meta-entry that codifies the relevant syntactic, semantic, and pragmatic or register features of a predicate. A LT is one of the core elements in the LCM, since the other facets of meaning construction considered by this proposal (cf. traditional implicature, illocutionary meaning and discourse coherence) take templates as their starting point. Therefore, the aim of this paper is to establish the protocol for the creation of such templates, that is, we detail which elements make up the syntactic, semantic and pragmatic/register modules of each LT. Besides, two computational tools are presented. These tools help the linguist in the production of the LTs, assuring they are syntactically correct, as well as allowing us to store them in a database accessible by a user interface that facilitates querying and managing its contents.

Camera calibration is one of the fundamental problems of machine vision. There have been lots of efforts for providing autonomous calibration algorithms. One of the major problems that put up barrier toward autonomy is feature detection and extraction. In this paper, the architecture of an autonomous camera calibration framework is studied. The autonomy of calibration framework originates in its hardware setup. The applied setup makes automatic feature detection and extraction possible. It is shown that the calibration framework is accurate.

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard. org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry. org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This ...

Objective: The study aimed to evaluate the correlation among methylenetetrahydrofolate reductase gene (C677T) polymorphism and Recurrent Pregnancy Loss in Andhra Pradesh women.Methodology: Blood samples were obtained from patients with three or more repeated abortions prior to  22 weeks of pregnancy (n = 128) against control (n = 144) who have no pregnancy complications. DNA was extracted through the standard  Phenol-chloroform method.  PCR was done for gene annealing and samples were tested for MTHFRC677T  polymorphism using the sanger’s di-deoxy method. The functional significance of the observed  C677T  mutation was analyzed using computational tools. Results: The frequency of C677T mutation was CC (63%), CT (29%), TT (8%) in the patient group, and CC (79%), CT (19%), and TT(2%) in the control group (P=0.0025), which indicates significant association.

The traditional methods of bacterial identification are based on observation of either the morphology of single cells or colony characteristics. However, the adoption of newer and automated methods offers advantage in terms of rapid and reliable identification of bacterial species. The review provides a comprehensive appreciation of new and improved technologies such fatty acid profiling, sequence analysis of the 16S rRNA gene, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), metabolic finger profiling using BIOLOG, ribotyping, together with the computational tools employed for querying the databases that are associated with these identification tools and high-throughput genomic sequencing in bacterial identification. It is evident that with the increase in the adoption of new technologies bacterial identification is becoming easier.

Computational methods play a central role in modern drug discovery process. It includes the design and management of small molecule libraries, initial hit identification through virtual screening, optimization of the affinity as well as selectivity of hits and improving the physicochemical properties of the lead compounds. In this review article, computational drug designing approaches have been elucidated and discussed. The key considerations and guidelines for virtual chemical library design and whole drug discovery process. Traditional approach for discovery of a new drug is a costly and time consuming affair besides not being so productive. A number of potential reasons witness choosing the In-silico method of drug design to be a more wise and productive approach. There is a general perception that applied science has not kept pace with the advances of basic science. Therefore, there is a need for the use of alternative tools to get answers on efficacy and safety faster, with mo...

Abstract In this paper we proposed a novel feature fusion technique in Saliency-Based Visual Attention Model, presented in [Itti, 1998]. There are three conspicuity maps in Saliency-Based Visual Attention Model, which are linearly combined from 12 color maps, ...

In property development, the view quality contributes significantly to the property value. In many cases, the architect is constrained by the property developer to take full advantage of the view by designing large glazed facades ignoring the consequence on the energy consumption of the building caused by the conflicting orientation of the view. This paper presents a design tool to help the architect interactively explore different building and window geometries that trade-off energy consumption (kWh) and view quality (€). This design tool allows interaction with parametric building geometry, simulation of energy consumption and view quality, and an optimisation search engine. The simulation of the view quality quantifies a view according to the visibility and quality of its contents by using a novel view-scoring method. The design tool is tested with both north-oriented and south-oriented views and produces a Pareto front from which resulting geometries are visualised.

Papaya (Carica papaya) fruits contain components that can increase the total antioxidant power in blood and reduce the lipid per-oxidation level. Antioxidant proteins are a special group of nutritional supplements that scavenge free radicals. Free radicals impair the proper functioning of the immune system leading to various disease conditions. In this study, a bioinformatics and molecular modeling approach was adopted to explore properties and structure of papaya antioxidant proteins. These antioxidant proteins include ascorbic peroxidase (APX), dehydro ascorbate reductase (DHAR), beta carotene hydroxylase (BCHD), and lycopene beta-cyclase (LBC). Physico-chemical characterization interprets properties such as pI, EC, AI, GRAVY and instability index and provides data about these proteins and their properties. Prediction of motifs, patterns, disulfide bridges and secondary structure were performed for functional characterization. Three dimensional structures for these proteins were not available as yet at PDB. Therefore, homology models for these antioxidant proteins were developed. The modeling of the three dimensional structure of these proteins shows that models generated by Modeller 9.10 were more acceptable in comparison to that by Geno 3D and Swiss Model. The models were validated using protein structure checking tools PROCHECK and WHAT IF. These structures will provide a good foundation for functional analysis of experimentally derived crystal structures.

Computational methods play a central role in modern drug discovery process. It includes the design and management of small molecule libraries, initial hit identification through virtual screening, optimization of the affinity as well as selectivity of hits and improving the physicochemical properties of the lead compounds. In this review article, computational drug designing approaches have been elucidated and discussed. The key considerations and guidelines for virtual chemical library design and whole drug discovery process. Traditional approach for discovery of a new drug is a costly and time consuming affair besides not being so productive. A number of potential reasons witness choosing the In-silico method of drug design to be a more wise and productive approach. There is a general perception that applied science has not kept pace with the advances of basic science. Therefore, there is a need for the use of alternative tools to get answers on efficacy and safety faster, with mo...

This presentation interrogates how a particular conception of creativity: ‘wise humanising creativity’ (WHC) is manifest within a virtual learning environment (VLE) with children and young people.  WHC is creativity guided by ethical action, meaning it is mindful of its consequences and is empowering, offering far greater shared hope for the future than the competitive mentality that pervades most education systems.  It reports on the outcomes of C2Learn, a three-year European Commission funded project, which introduced innovative digital gaming activities to foster co-creativity in the VLE between players and between players and machines.  In particular this presentation focuses on the bespoke co-creativity assessment methodology developed for the project.  In order to evidence WHC, this methodology opted to document developments in lived experience via qualitative methods including teacher and student interviews, fieldnotes, video capture, observation and student self-assessment tools.  The presentation, drawing on data from England, Austria and Greece, articulates how WHC manifests in C2Learn’s unique VLE or C2Space, and its potential to develop more nuanced understandings of creativity across digital environments.

... II. COMPOUND K-DISTRIBUTION MODEL Several researches on modelling sea clutter returns, proved that the observed intensity of the data fit the compound K-distribution model characterized by a shape Amar Mezache, Mohamed Sahed, and Toufik Laroussi ...

Camera calibration is one of the fundamental problems of machine vision. There have been lots of efforts for providing autonomous calibration algorithms. One of the major problems that put up barrier toward autonomy is feature detection and extraction. In this paper, the architecture of an autonomous camera calibration framework is studied. The autonomy of calibration framework originates in its hardware setup. The applied setup makes automatic feature detection and extraction possible. It is shown that the calibration framework is accurate.