WIP: gapfind: Alternative GapFind algorithm which is more robust#209
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jonls wants to merge 1 commit intozhanglab:developfrom
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WIP: gapfind: Alternative GapFind algorithm which is more robust#209jonls wants to merge 1 commit intozhanglab:developfrom
jonls wants to merge 1 commit intozhanglab:developfrom
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Does not depend on v_max, instead sets a maximum flux when solving this problem to 1. This reduces the distance between v_max and epsilon making the problem more robust. This is able to solve larger models that fail with the previous implementation. This respects reaction directionality but ignores any reaction flux limits. This also lowers the maximum flux which scales the solution. This means that some reactions may not be able to produce epsilon flux.
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This is one attempt at finding an alternative implementation of GapFind that works correctly on larger models instead of marking almost all compounds blocked.
Does not depend on v_max, instead sets a maximum flux when solving this problem to 1. This reduces the distance between
v_maxandepsilonmaking the problem more robust. This isable to solve larger models that fail with the previous implementation. This respects reaction directionality but ignores any reaction flux limits. This also lowers the maximum flux which scales the solution. This means that generally there could be some reactions that may not be able to produce epsilon flux.