Search results for "Computation"
showing 10 items of 7362 documents
Application of model quality evaluation to systems biology
2008
Application of model quality evaluation to the quasispecies models is presented. These models are useful for the analysis of the DNA and RNA evolution and for the description of the population dynamics of viruses and bacteria. An estimate of the parameters together with their interval of variability is computed and the quality evaluation is tested on the basis of the model prediction error capability.
MIPPIE: the mouse integrated protein–protein interaction reference
2020
Abstract Cells operate and react to environmental signals thanks to a complex network of protein–protein interactions (PPIs), the malfunction of which can severely disrupt cellular homeostasis. As a result, mapping and analyzing protein networks are key to advancing our understanding of biological processes and diseases. An invaluable part of these endeavors has been the house mouse (Mus musculus), the mammalian model organism par excellence, which has provided insights into human biology and disorders. The importance of investigating PPI networks in the context of mouse prompted us to develop the Mouse Integrated Protein–Protein Interaction rEference (MIPPIE). MIPPIE inherits a robust infr…
An efficient swap algorithm for the lattice Boltzmann method
2007
During the last decade, the lattice-Boltzmann method (LBM) as a valuable tool in computational fluid dynamics has been increasingly acknowledged. The widespread application of LBM is partly due to the simplicity of its coding. The most well-known algorithms for the implementation of the standard lattice-Boltzmann equation (LBE) are the two-lattice and two-step algorithms. However, implementations of the two-lattice or the two-step algorithm suffer from high memory consumption or poor computational performance, respectively. Ultimately, the computing resources available decide which of the two disadvantages is more critical. Here we introduce a new algorithm, called the swap algorithm, for t…
Stochastic Tension-Stiffening Approach for the Solution of Serviceability Problems in Reinforced Concrete: Constitutive Modeling
2015
A number of studies have indicated that the tension-stiffening law is an important input parameter in a numerical analysis of serviceability (deformations and cracking) problems of reinforced concrete (RC) structures. The stochastic nature of concrete cracking, which results in a large scatter of experimental results, renders the constitutive modeling a very difficult task. Even data obtained from short-term tests are to some degree uncertain due to time-dependent processes occurring in concrete, such as shrinkage and creep relaxation. This article provides statistical analysis tools that can be readily applied to engineering practice. Stochastic principles are applied to modeling of tensio…
An optimization approach for communal home meal delivery service
2009
Abstract: This paper is the first to discuss the communal home meal delivery problem. The problem can be modelled as a multiple travelling salesman problem with time windows, that is closely related to the well-studied vehicle routing problem with time windows. Experimental results are reported for a real-life case study from Central Finland over several alternative scenarios using the SPIDER commercial solver. The comparison with current practice reveals that a significant savings potential can be obtained using off-the-shelf optimization tools. As such, the potential for supporting real-life communal routing problems can be considered to be important for VRP practitioners.
Data Mining in Cancer Research [Application Notes
2010
This article is not intended as a comprehensive survey of data mining applications in cancer. Rather, it provides starting points for further, more targeted, literature searches, by embarking on a guided tour of computational intelligence applications in cancer medicine, structured in increasing order of the physical scales of biological processes.
A reliable and unbiased human protein network with the disparity filter
2017
AbstractThe living cell operates thanks to an intricate network of protein interactions. Proteins activate, transport, degrade, stabilise and participate in the production of other proteins. As a result, a reliable and systematically generated protein wiring diagram is crucial for a deeper understanding of cellular functions. Unfortunately, current human protein networks are noisy and incomplete. Also, they suffer from both study and technical biases: heavily studied proteins (e.g. those of pharmaceutical interest) are known to be involved in more interactions than proteins described in only a few publications. Here, we use the experimental evidence supporting the interaction between protei…
Bioinformatics and Computational Biology
2009
Bioinformatics is a new, rapidly expanding field that uses computational approaches to answer biological questions (Baxevanis, 2005). These questions are answered by means of analyzing and mining biological data. The field of bioinformatics or computational biology is a multidisciplinary research and development environment, in which a variety of techniques from computer science, applied mathematics, linguistics, physics, and, statistics are used. The terms bioinformatics and computational biology are often used interchangeably (Baldi, 1998; Pevzner, 2000). This new area of research is driven by the wealth of data from high throughput genome projects, such as the human genome sequencing pro…
Computer code from Sex roles and the evolution of parental care specialization.
2019
Computer code for the mathematical model in Mathematica
Computer code from Sex roles and the evolution of parental care specialization
2019
Computer code for the mathematical model in Mathematica