UNLABELLED We introduce a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets, with the aim of a low memory footprint and ease of integration within bioinformatics pipelines. We provide the libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave and C++. The ...

We developed a freeware for the analysis of neuromagnetic epileptic discharges and named it "hns_meg." It works as an executable standalone application, compatible with 32/64 bit Microsoft Windows Vista or Mac OSX 10.6. The program is designed for recordings from planar gradiometers and includes the following functions: listing of topographies of maximum gradient magnetic field ((partial differ...

Bone is formed through the processes of endochondral and intramembranous ossification. In endochondral ossification primary mesenchymal cells differentiate to chondrocytes and then are progressively substituted by bone, while in intramembranous ossification mesenchymal stem cells (MSCs) differentiate directly into osteoblasts to form bone. The steps of osteogenic proliferation, differentiation,...

TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq da...

In structural biology, management of a large number of Protein Data Bank (PDB) files and raw X-ray diffraction images often presents a major organizational problem. Existing software packages that manipulate these file types were not designed for these kinds of file-management tasks. This is typically encountered when browsing through a folder of hundreds of X-ray images, with the aim of rapidl...

Platelet-derived growth factors (PDGFs) play important roles in skeletal development and bone fracture healing, yet how PDGFs execute their functions remains incompletely understood. Here we show that PDGF-AA, but not -AB or -BB, could activate the BMP-Smad1/5/8 pathway in mesenchymal stem cells (MSCs), which requires BMPRIA as well as PDGFRα. PDGF-AA promotes MSC osteogenic differentiation thr...

jModelTest is a new program for the statistical selection of models of nucleotide substitution based on ‘‘Phyml’’ (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696–704.). It implements 5 different selection strategies, including ‘‘hierarchical and dynamical likelihood ratio tests,’’ the ‘‘Akaike information c...

UNLABELLED Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using ...