Comments (7)
I've implemented two variants for this, one working on the model itself, and one as a callback only acting on the optimization model. So far I think both might have their merits, depending on their use context.
This version here acts on the model and will delete reactions in-place:
function knockout!(model::StandardModel, gene_id::String)
function knockout!(model::StandardModel, gene_ids::Array{String})
The other one uses the callback scheme and just sets the upper and lower bound of the corresponding reactions to 0.
function knockout_callback(gene_id::String)
function knockout_callback(gene_ids::Array{String,1})
You can check them both out in d58ef65
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I'm in no way clingy to the name knockout_callback
by the way. It could also just be knockout
for example, but I get too easily confused when working with similar-sounding functions, so for development I named them like this
from cobrexa.jl.
I'm in no way clingy to the name
knockout_callback
by the way. It could also just beknockout
for example, but I get too easily confused when working with similar-sounding functions, so for development I named them like this
No problem, but in the merge iteration they should be called knockout!
since dispatch will take care of the thinking for you :)
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But it's not an inplace operation. It returns a function, just like the other callbacks. In all of these cases (change_sense
, change_objective
, ..), we also (correctly) did not use the !
, so I think this would lead to confusion at best.
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But it's not an inplace operation. It returns a function, just like the other callbacks. In all of these cases (
change_sense
,change_objective
, ..), we also (correctly) did not use the!
, so I think this would lead to confusion at best.
yeah without the !
is better :)
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@marvinvanaalst I guess this is now done by merging the knockouts?
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@marvinvanaalst I guess this is now done by merging the knockouts?
yes, I think so. Closing!
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Related Issues (20)
- Add support for ME models HOT 4
- Drop OSQP and use Clarabel instead for QPs HOT 4
- tINIT algorithm HOT 7
- Parse common attributes from notes HOT 3
- Collect package download information HOT 5
- .mat model not loading HOT 6
- Conversion from MATModel produces opaque errors if fields are missing HOT 3
- Incorrect gene reaction rule parsing HOT 7
- JSON model format incompatible with escher HOT 8
- Mapping through delimited IDs into inner models HOT 2
- `removeReaction!` etc. doesn't update all fields in a `CoreModel` HOT 1
- Pretty print model semantics HOT 2
- Check that function return types inferred in documentation make sense HOT 2
- `check_duplicate_reaction` does not consider reaction directionality HOT 2
- Implement Tables.jl interface for `ModelWithResult` HOT 1
- Document forwarding the `--project` exeflag with ClusterManagers HOT 1
- Warning when reaction is added with metabolites not yet in model HOT 2
- inconsistent parsing of subsystems HOT 9
- JUMP time limit HOT 5
- Genes not parsed if they have an "@" symbol HOT 1
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