Thinking Embryo
Projects
Each one opens in its own page. Those marked with a lock ask for a password.
- Cell flux modelpassword The spatial flux network loop (nucleolus, cytoplasm, lysosome, mitochondria and mTORC1) as an interactive cell: fluxes, species pools and perturbations simulated live in the browser, with the model's predictions for budding yeast and HCT116 cells.
- Whole-cell atlaspassword Every gene of a budding yeast cell drawn in its compartment and coloured by evolutionary age, with its reactions, complexes and some 700,000 interactions from public databases. A timeline in years, on a log or a linear scale, walks the cell back through the tree of life to what existed at each stop, and a systems view shows when each complex, pathway and process came together. A metabolic model shows where the cell makes and spends its ATP, era by era. Interactions seen again in other species, from fission yeast to E. coli, date its wiring as well as its parts. A heat layer shows which eras the cell switches off, condenses, or calls on through Hsf1 and Msn2/4 when it is heated, and the frontier, some 20,000 young translated sequences outside the annotated genes, sits beside the genes it was born by. A networks view marks every link by what it does, activates, represses, marks or touches, and finds the signed control network close to monotone, its oldest wiring most of all. Its documentation explains every control, every quantity and every dataset.