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The resolution of optimization problems is of great interest nowadays and has encouraged the development of various information technology methods to attempt solving them. There are several problems related to Software E...

UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and gr...

The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing...

In the MDE (Model Driven Engineering) paradigm, models are thought to be the primary conductors in all software development aspects. A PIM (Platform Independent Model) is transformed into one or more PSMs (Platform Speci...

Agents repesent a new paradigm for developing software applications. In spite of the interest of this particular way of looking at problems, there is considerable discrepancy on exactly what is an agent and which are the...

Data quality is a research area strongly investigated during the 90’s. However, few companies in Argentina apply data quality methodologies or tools during the analysis, design or implementation phases of software deve...

Microsoft's .NET Framework, and JAVA platforms, are based in a just-in-time compilation philosophy. Software developed using these technologies is executed in a hardware independent framework, which provides a full objec...

The R package mice imputes incomplete multivariate data by chained equations. The software mice 1.0 appeared in the year 2000 as an S-PLUS library, and in 2001 as an R package. mice 1.0 introduced predictor selection, pa...

Summary The use of both linear and generalized linear mixed‐effects models ( LMM s and GLMM s) has become popular not only in social and medical sciences, but also in biological sciences, especially in the field of eco...

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesi...

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis too...

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been...

Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes cal...

BACKGROUND: RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issu...

Phylogenies are extremely useful tools, not only for establishing genealogical relationships among a group of organisms or their parts (e.g. genes), but also for a variety of research once the phylogenies are estimated. ...

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cg...

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for informatio...

One of the frequent questions by users of the mixed model function lmer of the lme4 package has been: How can I get p values for the F and t tests for objects returned by lmer? The lmerTest package extends the 'lmerMod' ...

The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training...

Materias / palabras clave: computer science, omics, software tools, computational methods, datasets; Science: Mathematics: Instruments and machines: Electronic computers. Computer science

Materias / palabras clave: molecular biology, biotechnology, medical informatics, software tools, databases, data integration; Technology: Chemical technology: Biotechnology

Materias / palabras clave: software tools and applications, applied electromagnetics and electronics, signal processing and multimedia, telecommunications networks, radio communications, communications systems; Technology: Electrical engineering. ...

Materias / palabras clave: information technology and systems, pattern thinking, knowledge processing methods and tools, mathematical modeling, computer engineering and software; Technology: Electrical engineering. Electronics. Nuclear engineering...