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m-philippsm-philipps
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Merge pull request #202 from paulflang/pl/Lang_PLOSComputBiol2024
- add new model Lang_PLOSComputBiol2024 - close #210
2 parents 31e3ac8 + b4c68c6 commit e50299b

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‎.github/workflows/python.yml‎

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name: Python CI
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‎.github/workflows/tests.yml‎

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name: Tests
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‎Benchmark-Models/Lang_PLOSComputBiol2024/Lang_PLOSComputBiol2024.yaml‎

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format_version: 1
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parameter_file: parameters_Lang_PLOSComputBiol2024.tsv
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problems:
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- condition_files:
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- experimentalCondition_Lang_PLOSComputBiol2024.tsv
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measurement_files:
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- measurementData_Lang_PLOSComputBiol2024.tsv
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observable_files:
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- observables_Lang_PLOSComputBiol2024.tsv
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sbml_files:
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- model_Lang_PLOSComputBiol2024.xml
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visualization_files:
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- visualizationSpecification_Lang_PLOSComputBiol2024.tsv

‎Benchmark-Models/Lang_PLOSComputBiol2024/experimentalCondition_Lang_PLOSComputBiol2024.tsv‎

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conditionId _Cyt__CCND _Cyt__CCNE_CDKN1A_B_ _Cyt__E2F_DBD_RB1_Ser332u_ _Cyt__E2F_DBD_RB1_Ser332p_ _Cyt__CCNA_CDKN1A_B_ _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ _Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ _Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ _Cyt__RB1_E2F_Ser807_Ser811u_ _Cyt__RB1_E2F_Ser807_Ser811p_ _Cyt__PPP2R2B_ENSA_ARPP19_ _Cyt__APC_FBXO5_FZR1_CDC20_Ser355u_ _Cyt__CDC20_APC_ _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ _Cyt__APC_FBXO5_FZR1_CDC20_Ser355p_ _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ _Cyt__FZR1_APC_FBXO5_nTermu_ _Cyt__FZR1_APC_FBXO5_nTermp_ _Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ _Cyt__FBXO5_APC_FZR1_Ser182u_ _Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ _Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ _Cyt__FBXO5_APC_FZR1_Ser182p_ _Cyt__FOXM1_DBD_Thr600u_ _Cyt__FOXM1_DBD_Thr600p_ _Cyt__WEE1_Ser123u_ _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ _Cyt__WEE1_Ser123p_ _Cyt__CDC25_pSitesp_ _Cyt__CDC25_pSitesu_ _Cyt__MASTL_Thr198u_ _Cyt__MASTL_Thr198p_ _Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ _Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ _Cyt__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ _Cyt__SKP2 _Cyt__TP53_DBD_Ser15p_ _Cyt__FOXO_DBD_ _Num__NUP_pSitesu_ _Nuc__CCND _Nuc__CCNE_CDKN1A_B_ _Nuc__E2F_DBD_RB1_Ser332u_ _Nuc__E2F_DBD_RB1_Ser332p_ _Nuc__CCNA_CDKN1A_B_ _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ _Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ _Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ _Nuc__RB1_E2F_Ser807_Ser811u_ _Nuc__RB1_E2F_Ser807_Ser811p_ _Nuc__PPP2R2B_ENSA_ARPP19_ _Nuc__APC_FBXO5_FZR1_CDC20_Ser355u_ _Nuc__CDC20_APC_ _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ _Nuc__APC_FBXO5_FZR1_CDC20_Ser355p_ _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ _Nuc__FZR1_APC_FBXO5_nTermu_ _Nuc__FZR1_APC_FBXO5_nTermp_ _Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ _Nuc__FBXO5_APC_FZR1_Ser182u_ _Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ _Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ _Nuc__FBXO5_APC_FZR1_Ser182p_ _Nuc__FOXM1_DBD_Thr600u_ _Nuc__FOXM1_DBD_Thr600p_ _Nuc__CCNB_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ _Nuc__CCNB_promoter_FOXM1_ _Nuc__CDC20_promoter_FOXM1_ _Nuc__CDC20_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ _Nuc__WEE1_Ser123u_ _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ _Nuc__WEE1_Ser123p_ _Nuc__CDC25_pSitesp_ _Nuc__CDC25_pSitesu_ _Nuc__MASTL_Thr198u_ _Nuc__MASTL_Thr198p_ _Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ _Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ _Nuc__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ _Nuc__CCNE_promoter_E2F_ _Nuc__CCNA_promoter_E2F_ _Nuc__E2F_promoter_E2F_ _Nuc__FBXO5_promoter_E2F_ _Nuc__FOXM1_promoter_E2F_ _Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ _Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ _Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ _Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ _Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_ _Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ _Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ _Nuc__E2F_DBD_1_RB1_Ser332p__E2F_promoter_E2F_1_ _Nuc__E2F_DBD_1_RB1_Ser332p__FBXO5_promoter_E2F_1_ _Nuc__E2F_DBD_1_RB1_Ser332p__FOXM1_promoter_E2F_1_ _Nuc__SKP2 _Nuc__TP53_DBD_Ser15p_ _Nuc__CDKN1A_promoter_TP53_ _Nuc__FOXO_DBD_ _Nuc__CDKN1B_promoter_FOXO_ _Nuc__CDKN1A_promoter_TP53_1__TP53_DBD_1_Ser15p_ _Cyt__CDKN1A_CCNE_A_B_Ser130u_ _Nuc__CDKN1B_promoter_FOXO_1__FOXO_DBD_1_ _Cyt__CDKN1B_CCNE_A_Thr187u_ _Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Cyt__CDKN1A_CCNE_A_B_Ser130p_ _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ _Cyt__CDKN1B_CCNE_A_Thr187p_ _Nuc__CDKN1A_CCNE_A_B_Ser130u_ _Nuc__CDKN1B_CCNE_A_Thr187u_ _Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ _Nuc__CDKN1A_CCNE_A_B_Ser130p_ _Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ _Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ _Nuc__CDKN1B_CCNE_A_Thr187p_ _Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ _Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_
2+
wt ic_wt_Cyt__CCND ic_wt_Cyt__CCNE_CDKN1A_B_ ic_wt_Cyt__E2F_DBD_RB1_Ser332u_ ic_wt_Cyt__E2F_DBD_RB1_Ser332p_ ic_wt_Cyt__CCNA_CDKN1A_B_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ ic_wt_Cyt__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Cyt__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Cyt__RB1_E2F_Ser807_Ser811u_ ic_wt_Cyt__RB1_E2F_Ser807_Ser811p_ ic_wt_Cyt__PPP2R2B_ENSA_ARPP19_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_Ser355u_ ic_wt_Cyt__CDC20_APC_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_Ser355p_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Cyt__FZR1_APC_FBXO5_nTermu_ ic_wt_Cyt__FZR1_APC_FBXO5_nTermp_ ic_wt_Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Cyt__FBXO5_APC_FZR1_Ser182u_ ic_wt_Cyt__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Cyt__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Cyt__FBXO5_APC_FZR1_Ser182p_ ic_wt_Cyt__FOXM1_DBD_Thr600u_ ic_wt_Cyt__FOXM1_DBD_Thr600p_ ic_wt_Cyt__WEE1_Ser123u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ ic_wt_Cyt__WEE1_Ser123p_ ic_wt_Cyt__CDC25_pSitesp_ ic_wt_Cyt__CDC25_pSitesu_ ic_wt_Cyt__MASTL_Thr198u_ ic_wt_Cyt__MASTL_Thr198p_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ ic_wt_Cyt__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ ic_wt_Cyt__SKP2 ic_wt_Cyt__TP53_DBD_Ser15p_ ic_wt_Cyt__FOXO_DBD_ ic_wt_Num__NUP_pSitesu_ ic_wt_Nuc__CCND ic_wt_Nuc__CCNE_CDKN1A_B_ ic_wt_Nuc__E2F_DBD_RB1_Ser332u_ ic_wt_Nuc__E2F_DBD_RB1_Ser332p_ ic_wt_Nuc__CCNA_CDKN1A_B_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_ ic_wt_Nuc__E2F_DBD_RB1_1_Ser332u__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Nuc__E2F_DBD_RB1_1_Ser332p__RB1_E2F_1_Ser807_Ser811u_ ic_wt_Nuc__RB1_E2F_Ser807_Ser811u_ ic_wt_Nuc__RB1_E2F_Ser807_Ser811p_ ic_wt_Nuc__PPP2R2B_ENSA_ARPP19_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_Ser355u_ ic_wt_Nuc__CDC20_APC_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__CDC20_APC_1_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_Ser355p_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355u__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Nuc__FZR1_APC_FBXO5_nTermu_ ic_wt_Nuc__FZR1_APC_FBXO5_nTermp_ ic_wt_Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355u__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Nuc__FBXO5_APC_FZR1_Ser182u_ ic_wt_Nuc__APC_FBXO5_1_FZR1_CDC20_2_Ser355p__FBXO5_APC_1_FZR1_3_Ser182u__FZR1_APC_2_FBXO5_3_nTermu_ ic_wt_Nuc__APC_FBXO5_FZR1_CDC20_1_Ser355p__FZR1_APC_1_FBXO5_nTermu_ ic_wt_Nuc__FBXO5_APC_FZR1_Ser182p_ ic_wt_Nuc__FOXM1_DBD_Thr600u_ ic_wt_Nuc__FOXM1_DBD_Thr600p_ ic_wt_Nuc__CCNB_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ ic_wt_Nuc__CCNB_promoter_FOXM1_ ic_wt_Nuc__CDC20_promoter_FOXM1_ ic_wt_Nuc__CDC20_promoter_FOXM1_1__FOXM1_DBD_1_Thr600p_ ic_wt_Nuc__WEE1_Ser123u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_ ic_wt_Nuc__WEE1_Ser123p_ ic_wt_Nuc__CDC25_pSitesp_ ic_wt_Nuc__CDC25_pSitesu_ ic_wt_Nuc__MASTL_Thr198u_ ic_wt_Nuc__MASTL_Thr198p_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67u_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_Ser62_Ser67p_ ic_wt_Nuc__ENSA_ARPP19_PPP2R2B_1_Ser62_Ser67p__PPP2R2B_ENSA_ARPP19_1_ ic_wt_Nuc__CCNE_promoter_E2F_ ic_wt_Nuc__CCNA_promoter_E2F_ ic_wt_Nuc__E2F_promoter_E2F_ ic_wt_Nuc__FBXO5_promoter_E2F_ ic_wt_Nuc__FOXM1_promoter_E2F_ ic_wt_Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332u_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__E2F_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__FBXO5_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332u__FOXM1_promoter_E2F_1_ ic_wt_Nuc__CCNE_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ ic_wt_Nuc__CCNA_promoter_E2F_1__E2F_DBD_1_RB1_Ser332p_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__E2F_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FBXO5_promoter_E2F_1_ ic_wt_Nuc__E2F_DBD_1_RB1_Ser332p__FOXM1_promoter_E2F_1_ ic_wt_Nuc__SKP2 ic_wt_Nuc__TP53_DBD_Ser15p_ ic_wt_Nuc__CDKN1A_promoter_TP53_ ic_wt_Nuc__FOXO_DBD_ ic_wt_Nuc__CDKN1B_promoter_FOXO_ ic_wt_Nuc__CDKN1A_promoter_TP53_1__TP53_DBD_1_Ser15p_ ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130u_ ic_wt_Nuc__CDKN1B_promoter_FOXO_1__FOXO_DBD_1_ ic_wt_Cyt__CDKN1B_CCNE_A_Thr187u_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Cyt__CDKN1A_CCNE_A_B_Ser130p_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CDKN1B_CCNE_A_Thr187p_ ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130u_ ic_wt_Nuc__CDKN1B_CCNE_A_Thr187u_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15u_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CCNB_CDK1_Thr14_Tyr15p_CDKN1A_1__CDKN1A_CCNE_A_B_1_Ser130u_ ic_wt_Nuc__CDKN1A_CCNE_A_B_Ser130p_ ic_wt_Cyt__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Cyt__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187u_ ic_wt_Nuc__CDKN1B_CCNE_A_Thr187p_ ic_wt_Nuc__CCNA_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_ ic_wt_Nuc__CCNE_CDKN1A_B_1__CDKN1B_CCNE_A_1_Thr187p_

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