Background With the decrease of DNA sequencing costs, sequence-based typing methods
are rapidly becoming the gold standard for epidemiological surveillance. These methods …

Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models, …

The logical (or logic) formalism is increasingly used to model regulatory and signaling
networks. Complementing these applications, several groups contributed various methods and …

The YEASTRACT+ information system ( http://YEASTRACT-PLUS.org/ ) is a wide-scope tool
for the analysis and prediction of transcription regulatory associations at the gene and …

The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT—
www.yeastract.com ) information system has been, for 11 years, a key tool for the analysis …

Background Qualitative frameworks, especially those based on the logical discrete formalism,
are increasingly used to model regulatory and signalling networks. A major advantage of …

The Yeast search for transcriptional regulators and consensus tracking (YEASTRACT)
information system ( www.yeastract.com ) was developed to support the analysis of transcription …

Analysing models of biological networks typically relies on workflows in which different software
tools with sensitive parameters are chained together, many times with additional manual …

The logical formalism is well adapted to model large cellular networks, in particular when
detailed kinetic data are scarce. This tutorial focuses on this well-established qualitative …

The identification of large regulatory and signalling networks involved in the control of
crucial cellular processes calls for proper modelling approaches. Indeed, models can help …