diff --git a/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/README.md b/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/README.md index 1346eba0..8532a2d5 100644 --- a/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/README.md +++ b/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/README.md @@ -19,10 +19,12 @@ The following regulations were modified to ensure consistency of update function ``` @article{bbm-024, - title={Ergodic sets as cell phenotype of budding yeast cell cycle}, - author={Todd, Robert G and Helikar, Tom{\'a}{\v{s}}}, + title={Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle}, + author={Robert G. Todd and Tom{\'a}{\vs} Helikar}, + journal={PLoS ONE}, year={2012}, - publisher={Public Library of Science San Francisco, USA} + volume={7}, + url={https://api.semanticscholar.org/CorpusID:17537524} } ``` diff --git a/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/metadata.json b/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/metadata.json index 11bbd935..ddcc812c 100644 --- a/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/metadata.json +++ b/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/metadata.json @@ -12,5 +12,5 @@ "inputs": 4, "regulations": 42, "notes": "### Modifications\n\nThe following regulations were modified to ensure consistency of update functions with the regulatory graph:\n\n - Regulation `Cdc14 (S_12) -> Sic1 (S_3)` sign set to `unknown`.\n - Regulation `Start (S_9) -> Whi5 (S_14)` sign set to `unknown`.", - "bib": "@article{bbm-024,\n title={Ergodic sets as cell phenotype of budding yeast cell cycle},\n author={Todd, Robert G and Helikar, Tom{\\'a}{\\v{s}}},\n year={2012},\n publisher={Public Library of Science San Francisco, USA}\n}" + "bib": "@article{bbm-024,\n title={Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle},\n author={Robert G. Todd and Tom{\\'a}{\\vs} Helikar},\n journal={PLoS ONE},\n year={2012},\n volume={7},\n url={https://api.semanticscholar.org/CorpusID:17537524}\n}" } \ No newline at end of file diff --git a/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/README.md b/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/README.md index dd325b37..7744dfe2 100644 --- a/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/README.md +++ b/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/README.md @@ -15,8 +15,16 @@ The model is provided without modifications. ### Model citation ``` -@article{bbm-999, - +@article{bbm-170, + title={A logical analysis of the Drosophila gap-gene system}, + author={S{\'a}nchez, Lucas and Thieffry, Denis}, + journal={Journal of theoretical Biology}, + volume={211}, + number={2}, + pages={115--141}, + year={2001}, + publisher={Elsevier} } + ``` diff --git a/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/metadata.json b/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/metadata.json index 5e85957f..a864a026 100644 --- a/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/metadata.json +++ b/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/metadata.json @@ -12,5 +12,5 @@ "inputs": 3, "regulations": 15, "notes": "### Modifications\n\nThe model is provided without modifications.", - "bib": "@article{bbm-999,\n \n}" + "bib": "@article{bbm-170,\n title={A logical analysis of the Drosophila gap-gene system},\n author={S{\\'a}nchez, Lucas and Thieffry, Denis},\n journal={Journal of theoretical Biology},\n volume={211},\n number={2},\n pages={115--141},\n year={2001},\n publisher={Elsevier}\n}\n" } \ No newline at end of file diff --git a/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/README.md b/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/README.md index eb9ab7e4..0bb78e38 100644 --- a/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/README.md +++ b/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/README.md @@ -15,8 +15,16 @@ The model is provided without modifications. ### Model citation ``` -@article{bbm-999, - +@article{bbm-171, + title={A logical analysis of the Drosophila gap-gene system}, + author={S{\'a}nchez, Lucas and Thieffry, Denis}, + journal={Journal of theoretical Biology}, + volume={211}, + number={2}, + pages={115--141}, + year={2001}, + publisher={Elsevier} } + ``` diff --git a/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/metadata.json b/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/metadata.json index e726d820..74ccf0fc 100644 --- a/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/metadata.json +++ b/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/metadata.json @@ -12,5 +12,5 @@ "inputs": 2, "regulations": 20, "notes": "### Modifications\n\nThe model is provided without modifications.", - "bib": "@article{bbm-999,\n \n}" + "bib": "@article{bbm-171,\n title={A logical analysis of the Drosophila gap-gene system},\n author={S{\\'a}nchez, Lucas and Thieffry, Denis},\n journal={Journal of theoretical Biology},\n volume={211},\n number={2},\n pages={115--141},\n year={2001},\n publisher={Elsevier}\n}\n" } \ No newline at end of file diff --git a/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/README.md b/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/README.md index 2bccbce3..eb72590a 100644 --- a/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/README.md +++ b/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/README.md @@ -15,8 +15,16 @@ The model is provided without modifications. ### Model citation ``` -@article{bbm-999, - +@article{bbm-172, + title={A logical analysis of the Drosophila gap-gene system}, + author={S{\'a}nchez, Lucas and Thieffry, Denis}, + journal={Journal of theoretical Biology}, + volume={211}, + number={2}, + pages={115--141}, + year={2001}, + publisher={Elsevier} } + ``` diff --git a/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/metadata.json b/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/metadata.json index 617f7285..43499311 100644 --- a/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/metadata.json +++ b/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/metadata.json @@ -12,5 +12,5 @@ "inputs": 2, "regulations": 12, "notes": "### Modifications\n\nThe model is provided without modifications.", - "bib": "@article{bbm-999,\n \n}" + "bib": "@article{bbm-172,\n title={A logical analysis of the Drosophila gap-gene system},\n author={S{\\'a}nchez, Lucas and Thieffry, Denis},\n journal={Journal of theoretical Biology},\n volume={211},\n number={2},\n pages={115--141},\n year={2001},\n publisher={Elsevier}\n}\n" } \ No newline at end of file diff --git a/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/README.md b/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/README.md index b396ed47..299a9ada 100644 --- a/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/README.md +++ b/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/README.md @@ -15,16 +15,14 @@ The model is reproduced based on the table and figure within the paper. ### Model citation ``` -@article {bbm-208, - author = {H{\'e}rault, L{\'e}onard and Poplineau, Mathilde and Duprez, Estelle and Remy, {\'E}lisabeth}, - title = {A novel Boolean network inference strategy to model early hematopoiesis aging}, - year = {2022}, - doi = {10.1101/2022.02.08.479548}, - publisher = {Cold Spring Harbor Laboratory}, - URL = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548}, - eprint = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548.full.pdf}, - journal = {bioRxiv} +@article{bbm-208, + title={A novel Boolean network inference strategy to model early hematopoiesis aging}, + author={L{\'e}onard H{\'e}rault and Mathilde Poplineau and Estelle Duprez and {\'E}lisabeth Remy}, + journal={Computational and Structural Biotechnology Journal}, + year={2022}, + volume={21}, + pages={21 - 33}, + url={https://api.semanticscholar.org/CorpusID:248672123} } - ``` diff --git a/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/metadata.json b/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/metadata.json index cc9376af..11a47c11 100644 --- a/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/metadata.json +++ b/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/metadata.json @@ -10,5 +10,5 @@ "inputs": 0, "regulations": 36, "notes": "### Modifications\n\nThe model is reproduced based on the table and figure within the paper.", - "bib": "@article {bbm-208,\n\tauthor = {H{\\'e}rault, L{\\'e}onard and Poplineau, Mathilde and Duprez, Estelle and Remy, {\\'E}lisabeth},\n\ttitle = {A novel Boolean network inference strategy to model early hematopoiesis aging},\n\tyear = {2022},\n\tdoi = {10.1101/2022.02.08.479548},\n\tpublisher = {Cold Spring Harbor Laboratory},\n\tURL = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548},\n\teprint = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548.full.pdf},\n\tjournal = {bioRxiv}\n}\n" + "bib": "@article{bbm-208,\n title={A novel Boolean network inference strategy to model early hematopoiesis aging},\n author={L{\\'e}onard H{\\'e}rault and Mathilde Poplineau and Estelle Duprez and {\\'E}lisabeth Remy},\n journal={Computational and Structural Biotechnology Journal},\n year={2022},\n volume={21},\n pages={21 - 33},\n url={https://api.semanticscholar.org/CorpusID:248672123}\n}" } \ No newline at end of file diff --git a/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/README.md b/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/README.md index a4aae936..de46ad56 100644 --- a/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/README.md +++ b/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/README.md @@ -52,8 +52,14 @@ The following regulations were updated to fix logical inconsistencies: ### Model citation ``` -@article{bbm-999, - +@article{bbm-222, + title={Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: A computational study}, + author={Ganguli, Piyali and Chowdhury, Saikat and Bhowmick, Rupa and Sarkar, Ram Rup}, + journal={Journal of biosciences}, + volume={40}, + pages={769--789}, + year={2015}, + publisher={Springer} } ``` diff --git a/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/metadata.json b/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/metadata.json index a6182294..a8af3968 100644 --- a/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/metadata.json +++ b/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/metadata.json @@ -12,5 +12,5 @@ "inputs": 39, "regulations": 435, "notes": "### Availability\n\nHonestly, I'm not quite sure where they found the rules, but they are available in the `grn-principles` dataset\nand converted using `rules_to_bnet.py`. In order to be able to properly annotate the logical errors, we then \ncovert the model to `.aeon`.\n\n### Modifications\n\nThe following regulations were updated to fix logical inconsistencies:\n \n - Regulation `ATF2 -> AP1` set as non-essential.\n - Regulation `CRE -> AP1` set as non-essential.\n - Regulation `NUC_ERK1_2 -> AP1` set as non-essential.\n - Regulation `NUC_P38 -> AP1` set as non-essential.\n - Regulation `JNK -> BAD` set as non-essential.\n - Regulation `CALCIPRESSIN -> CALCINEURIN` set as non-essential.\n - Regulation `VAV -> CAM` set as non-essential.\n - Regulation `CBL -> FYN` set as non-essential.\n - Regulation `CD45 -> FYN` set as non-essential.\n - Regulation `AP1 -> GM_CSF` set as non-essential.\n - Regulation `IKK_GAMMA -> IKB_BETA` set as non-essential.\n - Regulation `TAK1_TAB -> IKK_GAMMA` set as non-essential.\n - Regulation `ETS -> IL2` set as non-essential.\n - Regulation `GSK3_BETA -> IL2` set as non-essential.\n - Regulation `GSK3_BETA -> IL4` set as non-essential.\n - Regulation `CBL -> LCK` set as non-essential.\n - Regulation `CD28 -> LCK` set as non-essential.\n - Regulation `CD45 -> LCK` set as non-essential.\n - Regulation `CABIN1 -> MEF2` set as non-essential.\n - Regulation `HDAC -> MEF2` set as non-essential.\n - Regulation `PKC -> NCK` set as non-essential.\n - Regulation `GSK3_BETA -> NUC_NFAT` set as non-essential.\n - Regulation `IL1 -> NUC_NFKB` set as non-essential.\n - Regulation `GRB7 -> RAS` set as non-essential.\n - Regulation `NCK_SOS -> RAS` set as non-essential.\n - Regulation `SHC_GRB2_SOS -> RAS` set as non-essential.\n - Regulation `SHP1_GRB2_SOS -> RAS` set as non-essential.\n - Regulation `SHP2_GRB2_GAB1_SOS -> RAS` set as non-essential.\n - Regulation `LYP -> ZAP70` set as non-essential.\n - Regulation `VAV -> ZAP70` set as non-essential.", - "bib": "@article{bbm-999,\n \n}" + "bib": "@article{bbm-222,\n title={Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: A computational study},\n author={Ganguli, Piyali and Chowdhury, Saikat and Bhowmick, Rupa and Sarkar, Ram Rup},\n journal={Journal of biosciences},\n volume={40},\n pages={769--789},\n year={2015},\n publisher={Springer}\n}" } \ No newline at end of file diff --git a/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/README.md b/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/README.md index e5362a0c..43702ee4 100644 --- a/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/README.md +++ b/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/README.md @@ -21,8 +21,13 @@ The model is provided without modifications. ### Model citation ``` -@article{bbm-999, - +@article{bbm-223, + title={A Network Model to Explore the Effect of the Micro-environment on Endothelial Cell Behavior during Angiogenesis}, + author={Nathan Weinstein and Luis Mendoza and Isidoro Gitler and Jaime Klapp}, + journal={Frontiers in Physiology}, + year={2017}, + volume={8}, + url={https://api.semanticscholar.org/CorpusID:12294741} } ``` diff --git a/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/metadata.json b/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/metadata.json index ef810624..ace6dd3c 100644 --- a/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/metadata.json +++ b/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/metadata.json @@ -11,5 +11,5 @@ "inputs": 27, "regulations": 254, "notes": "### Availability\n\nThe models is given as a list of functions in the supplementary material, but these\nare already translated in the `grn-principles` dataset, hence we use those and convert\nto `.bnet`.\n\n### Modifications\n\nThe model is provided without modifications.", - "bib": "@article{bbm-999,\n \n}" + "bib": "@article{bbm-223,\n title={A Network Model to Explore the Effect of the Micro-environment on Endothelial Cell Behavior during Angiogenesis},\n author={Nathan Weinstein and Luis Mendoza and Isidoro Gitler and Jaime Klapp},\n journal={Frontiers in Physiology},\n year={2017},\n volume={8},\n url={https://api.semanticscholar.org/CorpusID:12294741}\n}" } \ No newline at end of file diff --git a/models/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/README.md b/models/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/README.md index bc04ee61..35c9e948 100644 --- a/models/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/README.md +++ b/models/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/README.md @@ -19,7 +19,7 @@ The model is provided without modifications. ### Model citation ``` -@article{ryll2014model, +@article{bbm-228, title={A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models}, author={Ryll, Anke and Bucher, Joachim and Bonin, Anne and Bongard, Sophia and Gon{\c{c}}alves, E and Saez-Rodriguez, Julio and Niklas, Jens and Klamt, Steffen}, journal={Biosystems}, diff --git a/models/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/metadata.json b/models/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/metadata.json index a2553b16..15d69526 100644 --- a/models/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/metadata.json +++ b/models/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/metadata.json @@ -11,5 +11,5 @@ "inputs": 9, "regulations": 107, "notes": "The original model is available in the supplement of the document, but our source is \nfrom `grn-principles` dataset. There seem to be four variants of the model. Here,\nwe consider the `AND_OR` version.\n\n### Modifications\n\nThe model is provided without modifications.", - "bib": "@article{ryll2014model,\n title={A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models},\n author={Ryll, Anke and Bucher, Joachim and Bonin, Anne and Bongard, Sophia and Gon{\\c{c}}alves, E and Saez-Rodriguez, Julio and Niklas, Jens and Klamt, Steffen},\n journal={Biosystems},\n volume={124},\n pages={26--38},\n year={2014},\n publisher={Elsevier}\n}" + "bib": "@article{bbm-228,\n title={A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models},\n author={Ryll, Anke and Bucher, Joachim and Bonin, Anne and Bongard, Sophia and Gon{\\c{c}}alves, E and Saez-Rodriguez, Julio and Niklas, Jens and Klamt, Steffen},\n journal={Biosystems},\n volume={124},\n pages={26--38},\n year={2014},\n publisher={Elsevier}\n}" } \ No newline at end of file diff --git a/sources/024_BUDDING-YEAST-CELL-CYCLE/citation.bib b/sources/024_BUDDING-YEAST-CELL-CYCLE/citation.bib index d77a3e1b..c3a1252a 100644 --- a/sources/024_BUDDING-YEAST-CELL-CYCLE/citation.bib +++ b/sources/024_BUDDING-YEAST-CELL-CYCLE/citation.bib @@ -1,6 +1,8 @@ @article{bbm-024, - title={Ergodic sets as cell phenotype of budding yeast cell cycle}, - author={Todd, Robert G and Helikar, Tom{\'a}{\v{s}}}, + title={Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle}, + author={Robert G. Todd and Tom{\'a}{\vs} Helikar}, + journal={PLoS ONE}, year={2012}, - publisher={Public Library of Science San Francisco, USA} + volume={7}, + url={https://api.semanticscholar.org/CorpusID:17537524} } \ No newline at end of file diff --git a/sources/170_DROSOPHILA-GAP-B/citation.bib b/sources/170_DROSOPHILA-GAP-B/citation.bib index b917a0d0..85816735 100644 --- a/sources/170_DROSOPHILA-GAP-B/citation.bib +++ b/sources/170_DROSOPHILA-GAP-B/citation.bib @@ -1,3 +1,10 @@ -@article{bbm-999, - -} \ No newline at end of file +@article{bbm-170, + title={A logical analysis of the Drosophila gap-gene system}, + author={S{\'a}nchez, Lucas and Thieffry, Denis}, + journal={Journal of theoretical Biology}, + volume={211}, + number={2}, + pages={115--141}, + year={2001}, + publisher={Elsevier} +} diff --git a/sources/171_DROSOPHILA-GAP-C/citation.bib b/sources/171_DROSOPHILA-GAP-C/citation.bib index b917a0d0..1c6654bc 100644 --- a/sources/171_DROSOPHILA-GAP-C/citation.bib +++ b/sources/171_DROSOPHILA-GAP-C/citation.bib @@ -1,3 +1,10 @@ -@article{bbm-999, - -} \ No newline at end of file +@article{bbm-171, + title={A logical analysis of the Drosophila gap-gene system}, + author={S{\'a}nchez, Lucas and Thieffry, Denis}, + journal={Journal of theoretical Biology}, + volume={211}, + number={2}, + pages={115--141}, + year={2001}, + publisher={Elsevier} +} diff --git a/sources/172_DROSOPHILA-GAP-D/citation.bib b/sources/172_DROSOPHILA-GAP-D/citation.bib index b917a0d0..0cf190f1 100644 --- a/sources/172_DROSOPHILA-GAP-D/citation.bib +++ b/sources/172_DROSOPHILA-GAP-D/citation.bib @@ -1,3 +1,10 @@ -@article{bbm-999, - -} \ No newline at end of file +@article{bbm-172, + title={A logical analysis of the Drosophila gap-gene system}, + author={S{\'a}nchez, Lucas and Thieffry, Denis}, + journal={Journal of theoretical Biology}, + volume={211}, + number={2}, + pages={115--141}, + year={2001}, + publisher={Elsevier} +} diff --git a/sources/208_HEMATOPOIESIS-AGING/citation.bib b/sources/208_HEMATOPOIESIS-AGING/citation.bib index 2490512c..3abdeaa8 100644 --- a/sources/208_HEMATOPOIESIS-AGING/citation.bib +++ b/sources/208_HEMATOPOIESIS-AGING/citation.bib @@ -1,10 +1,9 @@ -@article {bbm-208, - author = {H{\'e}rault, L{\'e}onard and Poplineau, Mathilde and Duprez, Estelle and Remy, {\'E}lisabeth}, - title = {A novel Boolean network inference strategy to model early hematopoiesis aging}, - year = {2022}, - doi = {10.1101/2022.02.08.479548}, - publisher = {Cold Spring Harbor Laboratory}, - URL = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548}, - eprint = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548.full.pdf}, - journal = {bioRxiv} -} +@article{bbm-208, + title={A novel Boolean network inference strategy to model early hematopoiesis aging}, + author={L{\'e}onard H{\'e}rault and Mathilde Poplineau and Estelle Duprez and {\'E}lisabeth Remy}, + journal={Computational and Structural Biotechnology Journal}, + year={2022}, + volume={21}, + pages={21 - 33}, + url={https://api.semanticscholar.org/CorpusID:248672123} +} \ No newline at end of file diff --git a/sources/222_TEMPORAL-PROTEIN-EXPRESSION/citation.bib b/sources/222_TEMPORAL-PROTEIN-EXPRESSION/citation.bib index b917a0d0..ed2e860e 100644 --- a/sources/222_TEMPORAL-PROTEIN-EXPRESSION/citation.bib +++ b/sources/222_TEMPORAL-PROTEIN-EXPRESSION/citation.bib @@ -1,3 +1,9 @@ -@article{bbm-999, - +@article{bbm-222, + title={Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: A computational study}, + author={Ganguli, Piyali and Chowdhury, Saikat and Bhowmick, Rupa and Sarkar, Ram Rup}, + journal={Journal of biosciences}, + volume={40}, + pages={769--789}, + year={2015}, + publisher={Springer} } \ No newline at end of file diff --git a/sources/223_ANGIOGENESIS-MICROENVIRONMENT/citation.bib b/sources/223_ANGIOGENESIS-MICROENVIRONMENT/citation.bib index b917a0d0..c2ed42a7 100644 --- a/sources/223_ANGIOGENESIS-MICROENVIRONMENT/citation.bib +++ b/sources/223_ANGIOGENESIS-MICROENVIRONMENT/citation.bib @@ -1,3 +1,8 @@ -@article{bbm-999, - +@article{bbm-223, + title={A Network Model to Explore the Effect of the Micro-environment on Endothelial Cell Behavior during Angiogenesis}, + author={Nathan Weinstein and Luis Mendoza and Isidoro Gitler and Jaime Klapp}, + journal={Frontiers in Physiology}, + year={2017}, + volume={8}, + url={https://api.semanticscholar.org/CorpusID:12294741} } \ No newline at end of file diff --git a/sources/228_INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS/citation.bib b/sources/228_INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS/citation.bib index 35ff2cf9..bb278bc6 100644 --- a/sources/228_INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS/citation.bib +++ b/sources/228_INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS/citation.bib @@ -1,4 +1,4 @@ -@article{ryll2014model, +@article{bbm-228, title={A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models}, author={Ryll, Anke and Bucher, Joachim and Bonin, Anne and Bongard, Sophia and Gon{\c{c}}alves, E and Saez-Rodriguez, Julio and Niklas, Jens and Klamt, Steffen}, journal={Biosystems}, diff --git a/sync.py b/sync.py index 7e0151d2..d3ded690 100644 --- a/sync.py +++ b/sync.py @@ -26,7 +26,7 @@ def read_dir_name(dir_name): print("ERROR: Invalid source directory:", dir_name) return (int(result.group(1)), result.group(2)) -def check_metadata(id, name, metadata): +def check_metadata(id, name, metadata, bib): if (not 'id' in metadata) or metadata['id'] != id: print("ERROR: Invalid id in metadata of", name) sys.exit(128) @@ -47,6 +47,10 @@ def check_metadata(id, name, metadata): print("ERROR: Missing keywords attribute in", name) sys.exit(128) + if (not f'bbm-{int(id):03d}' in bib): + print(f"ERROR: Missing a `bbm-{int(id):03d}` key in the `citation.bib` file.") + sys.exit(128) + def check_unused_variables(model): graph = model.graph() for var in graph.variables(): @@ -139,7 +143,7 @@ def fix_variable_names(model): with open(metadata_file) as file: metadata = json.load(file) - check_metadata(model_id, model_name, metadata) + check_metadata(model_id, model_name, metadata, bib) # Load the model (including syntactic check)