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. [...]
As a common language to represent annotations for models, we have developed, in close collaboration with the COMBINE community, the OMEX metadata specification. This standard provides not only the specification of sharable, RDF formatted annotations, but also detailed examples and a set of recommended biological ontologies to use in those annotations. This standard is [...]
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 [...]
The Simulation Experiment Description Markup Language (SED-ML) is a standardized, community-based format that explicitly describes simulation processes for biochemical models, ensuring that researchers who are interested in a published model can efficiently reproduce and build upon that model. Its use is independent of specific operating systems or versions of software. The CRBM and COMBINE [...]
The Stimulating Peripheral Activity to Relieve Conditions (SPARC) Data and Resource Center is hosting an in-the-cloud codeathon from August 6-8, 2022. Apply by July 25, 2022. Help make SPARC data, tools, and resources more Findable, Accessible, Interoperable, and Reusable in this in-the-cloud codeathon. Over ten projects have made the cut, including: • Leverage AWS Athena and Glue to index, [...]
The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2022 will be a workshop-style event with oral presentations, breakout sessions, and tutorials. The three meeting days will include talks about the COMBINE standards and associated or [...]
We are pleased to announce the 17th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon -- 2022, which will take place between Sunday July 31st and Sunday August 8th, 2022 at Indiana University, Bloomington. For more information, please see the attached flyer or our announcement at https://compucell3d.org/Workshop22. To register, please visit: www.tinyurl.com/CC3D2022. More information on CompuCell3D is available at https://compucell3d.org. [...]
We're glad to share information from a new paper just published in Nucleic Acids Research: BioSimulators: a central registry of simulation engines and services for recommending specific tools. https://academic.oup.com/.../doi/10.1093/nar/gkac331/6582178. “BioSimulators provide streamlined abilities to find, obtain, and use simulation tools for a broad range of modeling frameworks, formats, and algorithms, to help make systems biology, [...]
Click to download Flyer You are invited to attend a week-long summer school on network modeling, which will conclude with a symposium of research and modeling tool talks to demonstrate how the skills you learn are being used in research settings. This summer school is designed to take beginner and intermediate level modelers [...]
Applications for the 2022 PhysiCell workshop/hackathon are now OPEN! This virtual course will teach concepts of agent-based biological simulations, through our open-source PhysiCell package. Sessions include integrating intracellular models, such as Boolean networks, systems of reactions (SBML), flux balance models, and pre-trained deep neural network surrogate models. The organizers also plan to introduce a new [...]
