The Karr Lab published a perspective on how researchers are beginning to leverage recent progress in measurement technology, bioinformatics, data sharing, rule-based modeling, and multi-algorithmic simulation to build the first whole-cell models.
The Karr Lab proposed a plan for a project, termed the Human Whole-Cell Modeling Project, to achieve human whole-cell models. The foundations of the plan include technology development, standards development, and interdisciplinary collaboration.
To develop a plan for achieving human whole-cell models, the Karr Lab analyzed the existing models of individual cellular pathways, surveyed the biomodeling community, and reflected on theirr experience developing whole-cell models of bacteria.
Prof. Karr has his team have released an early version of their kinetic_datanator software tool for finding experimental data for building and calibrating dynamical models of cellular biochemistry. kinetic_datanator helps users find data such as metabolite, RNA, and protein abundances; protein complex compositions; transcription factor binding motifs; and kinetic parameters. kinetic_datanator is particularly useful for building large models, [...]
We released a new version (4.0) of the SemGen platform that includes a new user interface and new model merging capabilities.
Prof. Sauro released an updated version (1.3.7) of the Tellurium modeling and reproducibility platform.
Prof. Sauro released an updated version (1.4.18) of the libRoadRunner high-performance simulation engine.
Prof. Sauro has released an updated version of his textbook "Systems Biology: Introduction to Pathway Modeling"
Prof. Sauro has released an updated version of his textbook "Enzyme Kinetics for Systems Biology"
Profs. Karr and Goldberg are writing a comprehensive primer on whole-cell modeling, both to train their lab and teach the community. It covers the fundamentals of cell modeling, including data aggregation and organization; model design, calibration, representation, annotation, and composition; model testing; logging, organizing, and analyzing simulation results; and software engineering. It emphasizes practical skills, [...]