William Poole
William Poole
Sometimes, when simulating interacting lineages with 1 or more cell types, the simulation will stop and the kernel will crash. This is likely a memory/pointer issue but could have another...
In interacting lineage simulations, create the following variables automatically and update them every global sync period: 1. total_cell_count: the total number of cells alive 2. cell_count_{i}: the total number of...
I will describe this problem with a use case: Consider two volumes (internal i and external e) which we are simulating deterministically in bioscrape. We want to model diffusion between...
Hello! I've been finding this simulation tool extremely useful, and think a feature that would enhance this is to be able to have a rule type which will terminate a...
Currently Lineages is a seperate "module" installed on its own. System Identification tools should be too. Bioscrape core has disgustingly long .pyx files which could be split up something like...
This could be complex - quoting Anandh: "When doing simulations with partitioning and delay, the cells' output seems to depend on the timepoint resolution. This might be because there is...
We are still wrestling how to do this correctly. Core functionality is that any lineage model should be simulated [with cell growth, death, and division] in a deterministic way so...
Consider the case when there are two processes A and B which by default each update a store X by setting. Currently, the order A and B are added to...