Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of …
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers …
Synthetic Biology is an emerging discipline which uses engineering principles to shape biological behavior. The Synthetic Biology Open Language (SBOL) is a standard for describing biological constructs which enables engineering workflows that …
This paper presents pySBOL, a software library for computer-aided design of synthetic biological systems in the Python scripting language. This library provides an easy-to-use, object-oriented, application programming interface (API) with low barrier …
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form …
Biology is a very noisy field. Experiments are difficult to reproduce, the mechanisms behind life are not well understood, and data that we do obtain is difficult to make sense of. Much like traditional engineering fields where engineers draw from a …
Data standards are integral for interoperability between software applications, since they provide guidelines for how data can be meaningfully exchanged and in a uniform manner. While standards provide a bridge for applications to share and translate …
This book presents outstanding contributions in an exciting, new and multidisciplinary research area: the application of formal, automated reasoning techniques to analyse complex models in systems biology and systems medicine. Automated reasoning is …
Synthetic biology, as a field of research, applies electrical engineering, systems biology, and bioinformatics to genetic circuit design. Software tools are leveraged to provide rapid iteration through the design space, and data standards are used to …
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form …