Related papers: Asterias: a parallelized web-based suite for the a…
Due to the complexity of many decision making problems, tree search algorithms often have inadequate information to produce accurate transition models. This results in ambiguities (uncertainties for which there are multiple plausible…
In situ hybridisation gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information are often both incomplete and inconsistent. This paper examines a…
Spatial transcriptomics (ST) is a novel technology that enables the observation of gene expression at the resolution of individual spots within pathological tissues. ST quantifies the expression of tens of thousands of genes in a tissue…
Nowadays, software artifacts are ubiquitous in our lives being an essential part of home appliances, cars, cell phones, and even in more critical activities like aeronautics and health sciences. In this context software failures may produce…
Constraint-based applications attempt to identify a solution that meets all defined user requirements. If the requirements are inconsistent with the underlying constraint set, algorithms that compute diagnoses for inconsistent constraints…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
Genetic Algorithms (GAs) are used to solve search and optimization problems in which an optimal solution can be found using an iterative process with probabilistic and non-deterministic transitions. However, depending on the problem's…
The Statistical Toolkit is an open source system specialized in the statistical comparison of distributions. It addresses requirements common to different experimental domains, such as simulation validation (e.g. comparison of experimental…
Regression analysis is used for prediction and to understand the effect of independent variables on dependent variables. Symbolic regression (SR) automates the search for non-linear regression models, delivering a set of hypotheses that…
Gene expression analysis aims at identifying the genes able to accurately predict biological parameters like, for example, disease subtyping or progression. While accurate prediction can be achieved by means of many different techniques,…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
PHAST is a software package written in standard Fortran, with MPI and CUDA extensions, able to efficiently perform parallel multicanonical Monte Carlo simulations of single or multiple heteropolymeric chains, as coarse-grained models for…
Genetic Algorithms (GAs) are powerful metaheuristic techniques mostly used in many real-world applications. The sequential execution of GAs requires considerable computational power both in time and resources. Nevertheless, GAs are…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…
GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based…
Daisy (Data Analysis Integrated Software System) has been designed for the analysis and visualization of the X-ray experiments. To address an extensive range of Chinese radiation facilities community's requirements from purely algorithmic…
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
Assessing journal legitimacy during literature reviews, publication venue selection, and citation verification requires consulting information scattered across multiple incompatible data-sets. This paper introduces Aletheia-Probe, an…
In this paper, we introduce an efficient and money-saving automatic parallel strategies search framework on heterogeneous GPUs: Astra. First, Astra searches for the efficiency-optimal parallel strategy in both GPU configurations search…