Software

CSB Framework for Web Applications

  • The CSB scientific content management system is a framework for creating web interfaces for new and existing scientific application.
  • Speckle counting is a 3-step image processing pipeline example that shows how to identify smaller objects (foci) within larger objects (nuclei) using local thresholding and model-controlled flooding algorithms.
  • The BSMHist software for statistical analysis of cellular aggregates in immunofluorescence histology; it uses a Markov Chain Monte Carlo (MCMC) sampler to implement Bayesian inference on immunofluorescence histology stain images and immunofluorescence histology movies.
  • The PriorityWeb application is a web interface for running the Priority application without the need for downloading the software.

Imaging software

Gene circuit simulation software

  • The Dynetica software for graphical construction of kinetic models and automatic generation of the implied differential equations, time course simulations using deteriministic or stochastic algorithms, and sensitivity analyses.

Statistical analysis software relevant for systems biological applications

  • Banjo is a software application and framework for structure learning of static and dynamic Bayesian networks, designed from the ground up to provide efficient structure inference when analyzing large, research-oriented data sets.
  • BFRM software for Bayesian Factor Regression Models - modelling and analysis of sparse latent factor models use in applications in pathway analysis and predictive modelling with large-scale gene expression data sets, with links to studies in gene expression analysis.
  • CLOCCS is a flexible mathematical model that describes the dynamics of population distributions resulting from synchrony loss over time.
  • COMPETE is a software package for calculating the probability of DNA occupancy by a collection of DNA binding factors, including transcription factors, nucleosomes, and the origin recognition complex.
  • Gene Set Association Analysis integrates gene expression analysis with genome wide association studies (GWAS) to determine whether an a priori defined sets of genes shows statistically significant, concordant differences with respect to gene expression profiles and genotypes between two biological states.
  • GGM software for Bayesian analysis and search of graphical/network structures in the framework of Gaussian graphical models, with links to applications in gene expression studies.
  • PIPmiR (Pipeline for the Identification of Plant miRNAs) was developed to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features.
  • The PRIORITY software package for de novo motif discovery based on Bayesian classifiers for identification of transcription factor binding sites.
  • The SMLR is a software package for sparse classification. Its goal is to be simple both to understand and use, while maintaining speed, flexibility, and portability.

General software and visualisation tools that may be of interest for systems biological applications

  • The GraphExplore software for dynamically displaying, exploring and modifying large graphs and networks, with a range of visualisation and interactive analysis facilities
  • GPU software for massively parallel GPU-based computing, enabling mixture modeling of massive datasets on one computer.

General statistical model search and analysis software applications

  • Additional Bayesian analysis software from Alex Hartemink's group, including software for sparse multinomial ligistic regression model search, and for Bayesian network modelling
  • Additional Bayesian analysis software from Mike West's group, including shotgun stochastic search (SSS) for linear and nonlinear regression models with many variables, time series analysis with flexible dynamic models, classification and prediction tree modelling, and others