Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB).
Methods Mol Biol
; 1945: 119-139, 2019.
Article
en En
| MEDLINE
| ID: mdl-30945244
Biologists seek to create increasingly complex molecular regulatory network models. Writing such a model is a creative effort that requires flexible analysis tools and better modeling languages than offered by many of today's biochemical model editors. Our Multistate Model Builder (MSMB) supports multistate models created using different modeling styles that suit the modeler rather than the software. MSMB defines a simple but powerful syntax to describe multistate species. Our syntax reduces the number of reactions needed to encode the model, thereby reducing the cognitive load involved with model creation. MSMB gives extensive feedback during all stages of model creation. Users can activate error notifications, and use these notifications as a guide toward a consistent, syntactically correct model. Any consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB's multistate syntax through realistic models of cell cycle regulation and mRNA transcription. MSMB is an open-source project implemented in Java and it uses the COPASI API. Complete information and the installation package can be found at http://copasi.org/Projects/ .
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Biología Computacional
/
Biología de Sistemas
/
Modelos Biológicos
Idioma:
En
Revista:
Methods Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2019
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
Estados Unidos