We currently have the following instances available for interactively using the simulator:
A simulator of polymerase dynamics during transcription in the presence of UV damage. Written in Julia and visualised in Javascript/D3.
To model polymerase dynamics numerically, we implemented a process-oriented simulator, continuous in time and location along gene, but discrete in events. So a set of biological events (see supplementary? table [1] for a complete list, but for example repair, transcription completion, polymerase collision with a stalled polymerase) each have a time associated with them. Between events, transcription proceeds in a continuous manner, but when an event occurs an abrupt update is made, and a fresh set of future events is calculated to reflect this.
For each event in temporal turn, the state of the system is updated using the natural mathematical rules (such as a polymerase position being offset by the product of its speed and the time until the event). Then the event is handled (e.g. polymerase's speed is set to zero if the event is a collision). Then the list of events is updated in light of the previous two steps: e.g. in the collision case, the next collision-time is recalculated to be the the time taken for the polymerase immediately prior to the one stalled to reach the it; but time-to-repair is simply reduced by the amount of time elapsed prior to the collision event.
The events are then re-sorted to find the event that is going to happen next in time, and the process is repeated until the required amount of time has elapsed.
The overall state of the system is a small number of representative genes, and a number of polymerases, each either positioned along one of the genes or available for initiation on any of the genes. There is an initial period to achieve steady state, where polymerases are allowed to initiate on the genes (weighted, to allow different proportions of the gene classes) and progress along the gene body without any damage sites. When equilibrium is achieved in terms of initiation and completion, damage sites are introduced at random locations and for random durations (tunable by the user) which will halt any polymerase that encounters them.
Moving polymerases have a probability of being removed from the gene-body at any moment in time; halted polymerases (at a damage site, or in a queue forming to its 3' side) can have an increased risk. Also, upon removal polymerases have a probability of being returned to the pool of polymerases available for initiation, or conversely being degraded. A separate parameter is available to similarly determine the fate of polymerases that have completed transcription.
As the damage sites are stochastic, we run the simulation independently one hundred times to achieve an estimate of polymerase density across the gene bodies of a pool of cells.
The dynamics, and the impact each event has, are tunable by the set of parameters given in table 2.
| Event | Description | Calculation | Impact | Notes |
|---|---|---|---|---|
| initiate | Polymerase attempts to initiate | Exponential-random, depending on baseline rate, and number of existing polymerases | New polymerase added to 5' end of gene | When the event happens, another one is scheduled with the required characteristics. |
| block | Polymerase arrives at damage site | Minimum across polymerase:damage-site pairs of distance/speed | Speed of affected polymerase will be set to zero | A safe lower bound, as events that would alter it will necessarily happen first, inducing a recalculation. |
| bump | Polymerase catches up with 5' neighbour | Minimum across polymerases of delta_distance/delta_speed | " | |
| pause | Polymerase reaches pause site | based on 5'-most polymerase prior to pause site | " | |
| release | Paused polymerase will be released from pause site | User-specified time after it first paused | Affected polymerase will have speed restored to default. | |
| removal | Polymerase removed from gene prematurely | Upon initiation, each polymerase is given an stochastic duration it is allowed to spend on the gene. | Polymerase will either be made available for initiation, or discarded entirely via Bernoulli probability, calculated so that the dissociation and degradation times are satisfied | |
| complete | Polymerase successfully reaches the full gene length | Minimum across polymerases of distance-to-end/speed | " | |
| repair | UV damage site will be removed | At t_0, each (random) damage site is allocated an exponentially-distributed random lifetime. | Speed of 3' (queue of) polymerases restored to default |
| Parameter | Description | Default Value |
|---|---|---|
| gene_length | Number of bases a polymerases must traverse to transcribe a gene | 63kb |
| initiation_period | Expected duration between initiation attempts | 2.5seconds |
| pol_N | The number of polymerases in the pool available for initiation in steady state | 250 |
| pause_site | Distance from TSS where each polymerase will pause | 60bp |
| release_time | How long each polymerase will wait at the pause site | 3seconds |
| pol_speed | Default speed of a polymerase | 2000bp/minutes |
| pol_size | How many bases a polymerase occupies | 33.0bp |
| processivity | Expected duration a moving polymerase can remain on a gene | 2hours |
| degradation | Expected duration a stalled polymerase can remain on a gene | Infinite |
| dissociation | Expected duration a general polymerase can remain on a gene | 10minutes |
| uv_distance | Expected distance between damage sites | 20kb |
| run_length | How long to simulate the dynamics | 240minutes |
| repair_half_life | Time after half the damage sites are expected to have been repaired | 4hours |
| speed_factor_t0 | Polymerases will speed up by this factor when transitioning from steady state to damaged state | 1.0 |
| complete_reuse_p | Probability a polymerase will be available for initiation once it has completed transcription | 1 |
| genome_prop | What proportion of genes in the genome are characterised by this set of parameters | 1 |
| Type | Whether to include stationery polymerases in the calculation of density | Active |
| tally_interval | How frequently to record and draw the density information | 3minutes |
| tally_binsize | How granular to make the density information | 1kb |
Once the package is cloned, a Dockerfile is available to start a web front-end that allows the user to interact with the settings of the simulation and to view the results.
Build and run the local docker file with
docker build --no-cache -t uv_damage .
docker run --rm -p 8080:8000 uv_damageand then point your web-browser at ipaddress:8080/uv_damage to interact with the simulator. You should be given a tour of the interface and will then be able to interact with the simulator.