Introduction to Kappa, a rule-based language for modeling protein-protein and gene-protein networks based on the DNA repair model
Anton Kulaga
1. ILA (International Longevity Alliance)
2. IRIF (Institute of fundamental research in Informatics), PPS team (Proofs, Programs and Systems), Université Paris Diderot, Paris, France
3. Computer Science Department of École normale supérieure, Paris, France
DNA damage accumulation is an important hallmark of biological aging. Once a certain level of DNA damage is reached, cells may undergo a wide range of phenotypic changes, from cell cycle arrest, apoptosis, or cellular senescence [1]. Understanding DNA repair process is also important for the development of genetic therapies against aging and other diseases because Homology Directed Repair (HDR) is actively used for insertions of DNA sequences and Base excision repair (BER) is required for targeted nucleotide editing method [2].
According to PubMed there are more than 10 000 papers dealing with mutations and aging and this number is growing rapidly due to increasing interest in the topic and extensive use of high-throughput methods in experiments. As a consequence, it became hard for researchers to remain up-to-date with all relevant information. To counter this problem, about 2000 review paper has been written in the field...
As an alternative to classical reviews, which are static objects with a natural obsolescence, we propose to use kappa rule-based modeling to designing formal updatable reviews that are at the same time executable [3]. Kappa is a rule-based language for modeling protein-protein and gene-protein interactions.
I will present Kappa-Notebook, an open-source software, that allows to collaboratively develop executable models by linking kappa code to papers, databases, plasmid maps and other artifacts.
In my presentation, using DNA-repair model, I will:
* demonstrate core features of Kappa language
* highlight the ways how researchers can benefit from kappa modeling and will show its limitations
* share intermediate results of the ongoing HDR modeling project (in collaboration with Maurice Kanbar center of biomedical engineering )
REFERENCES
1. Erol, A., 2011. Deciphering the intricate regulatory mechanisms for the cellular choice between cell repair apoptosis or senescence in response to damaging signals. Cell. Signal. 23, 1076–1081.
2. Nishida K. et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems //Science. – 2016. – С. Aaf8729., 2-3
3. Danos, V., Feret, J., Fontana, W., Krivine, J.: Scalable simulation of cellular signaling networks. In: Proceedings of APLAS 2007. Volume 4807 of LNCS. (2007) 139–157
Anton Kulaga
1. ILA (International Longevity Alliance)
2. IRIF (Institute of fundamental research in Informatics), PPS team (Proofs, Programs and Systems), Université Paris Diderot, Paris, France
3. Computer Science Department of École normale supérieure, Paris, France
DNA damage accumulation is an important hallmark of biological aging. Once a certain level of DNA damage is reached, cells may undergo a wide range of phenotypic changes, from cell cycle arrest, apoptosis, or cellular senescence [1]. Understanding DNA repair process is also important for the development of genetic therapies against aging and other diseases because Homology Directed Repair (HDR) is actively used for insertions of DNA sequences and Base excision repair (BER) is required for targeted nucleotide editing method [2].
According to PubMed there are more than 10 000 papers dealing with mutations and aging and this number is growing rapidly due to increasing interest in the topic and extensive use of high-throughput methods in experiments. As a consequence, it became hard for researchers to remain up-to-date with all relevant information. To counter this problem, about 2000 review paper has been written in the field...
As an alternative to classical reviews, which are static objects with a natural obsolescence, we propose to use kappa rule-based modeling to designing formal updatable reviews that are at the same time executable [3]. Kappa is a rule-based language for modeling protein-protein and gene-protein interactions.
I will present Kappa-Notebook, an open-source software, that allows to collaboratively develop executable models by linking kappa code to papers, databases, plasmid maps and other artifacts.
In my presentation, using DNA-repair model, I will:
* demonstrate core features of Kappa language
* highlight the ways how researchers can benefit from kappa modeling and will show its limitations
* share intermediate results of the ongoing HDR modeling project (in collaboration with Maurice Kanbar center of biomedical engineering )
REFERENCES
1. Erol, A., 2011. Deciphering the intricate regulatory mechanisms for the cellular choice between cell repair apoptosis or senescence in response to damaging signals. Cell. Signal. 23, 1076–1081.
2. Nishida K. et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems //Science. – 2016. – С. Aaf8729., 2-3
3. Danos, V., Feret, J., Fontana, W., Krivine, J.: Scalable simulation of cellular signaling networks. In: Proceedings of APLAS 2007. Volume 4807 of LNCS. (2007) 139–157
