SPEDRE is a method for estimating rate constants in a biochemical signaling network, and it is tailored for a special class of data-rich problems with observations of all species — problems that occur mainly when using proteomics technologies such as SILAC.
The QMEAN server provides access to two scoring functions for the quality estimation of protein structure models which allow to rank a set of models and to identify potentially unreliable region within these.
RSEM (RNA-Seq expression estimation by Expectation-Maximization) estimates gene and isoform expression levels from RNA-Seq data with a statistical model that takes into account reads that map to multiple positions.
SBML-PET-MPI is a parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models. The tool allows the user to perform parameter estimation, parameter uncertainty and identifiability analysis by collectively fitting multiple experimental data sets.
BEGFE implements a Markov Chain Monte Carlo algorithm to estimate the posterior probability distribution of the birth and death rate parameters and the numbers of gene copies at the internodes of the phylogenetic tree. In addition, BEGFE can simulate gene family data under the birth and death model.
FRST serves to validate the energy of a protein structure. The server computes both an overall and a per-residue energy profile of a protein structure. The energy profile can be visualized in different ways, including a per-residue plot and a colored structure representation, accessible as a series of dynamic web pages.