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| docs/requirements.txt | |
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| examples/fceri_ji/data/hierarchical/params.csv | |
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| examples/fceri_ji/data/hierarchical/params.json | |
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| examples/fceri_ji/data/hierarchical/params.yaml | |
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| examples/fceri_ji/data/modular/binding.csv | |
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| examples/fceri_ji/data/modular/dephosphorylation.csv | |
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| examples/fceri_ji/data/modular/transphosphorylation.csv | |
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| examples/fceri_ji/data/sequential/edits.plist | |
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| examples/fceri_ji/data/sequential/params.yaml | |
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| examples/fceri_ji/original_model/contact_map.gml | |
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| examples/fceri_ji/original_model/dimer.gml | |
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| examples/fceri_ji/original_model/fceri_ji.txt | |
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| examples/fceri_ji/original_model/model_description.png | |
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| requirements.txt | |
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| setup.cfg | |
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| wc_rules/VERSION | |
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| wc_rules/expressions/expression.lark | |
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| wc_rules/glossary.txt | |
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| wc_rules/graph/templates/template_exprgraph.html | |
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| wc_rules/matcher/DOCUMENTATION | |
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| docs/conf.py | 90 |
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| examples/fceri_ji/__init__.py | 0 |
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| examples/fceri_ji/load_data.py | 21 |
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| examples/fceri_ji/model.py | 30 |
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| examples/fceri_ji/schema/molecules.py | 9 |
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| examples/fceri_ji/schema/sites.py | 20 |
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| examples/fceri_ji/submodels/LigandReceptorBinding.py | 53 |
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| examples/fceri_ji/submodels/LynKinase.py | 44 |
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| examples/fceri_ji/submodels/LynReceptorBinding.py | 51 | A 1 hr |
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| examples/fceri_ji/submodels/SykKinase.py | 24 |
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| examples/fceri_ji/submodels/SykReceptorBinding.py | 26 | A 35 mins |
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| examples/fceri_ji/submodels/dephosphorylation.py | 26 |
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| examples/fceri_ji/submodels/naive.py | 76 | A 1 hr |
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| examples/fceri_ji/submodels2/LigandReceptorBinding.py | 39 |
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| examples/fceri_ji/submodels2/LynKinase.py | 45 |
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| examples/fceri_ji/submodels2/LynReceptorBinding.py | 36 |
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| examples/fceri_ji/submodels2/SykKinase.py | 24 |
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| examples/fceri_ji/submodels2/SykReceptorBinding.py | 25 |
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| examples/fceri_ji/submodels2/dephosphorylation.py | 22 |
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| examples/fceri_ji/submodels2/graphs.py | 67 | D 2 days |
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| examples/fceri_ji/submodels2/templates.py | 53 |
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| examples/fceri_ji/templates/graphs.py | 63 |
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| examples/fceri_ji/templates/rules.py | 46 |
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| examples/simple_addremove/model.py | 50 |
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