With the growing complexity and quantity of biosimulation models, annotation tools that can accommodate a variety of modeling languages and simulation environments were needed to encourage models which could be easily understood and uniquely identified. The COMBINE community developed a consensus on the utilities required for this open-source, cross-platform software library for model annotation. [...]
The Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories(NLIMED) was developed by Yuda Munarko to convert natural language queries into the SPARQL syntax which is typically used to search semantic annotations encoded in RDF. The SPARQL syntax is complex and rigid, making it difficult to understand and use for many modeling [...]
SemGen is an experimental software tool for automating the modular composition and decomposition of biosimulation models. SemGen facilitates the construction of complex, integrated models, and the swift extraction of reusable sub-models from larger ones. SemGen relies on the semantically-rich SemSim model description format to help automate these modeling tasks. With SemGen, users can: Visualize [...]