Colored Petri Net: Its application to Sucrose Biosynthesis Pathway in Plasmodium falciparum

Sucrose plays major role as macromolecule used in organisms including Plasmodium falciparum (P.f.) to generate glucose for energy production in the glycolysis pathway. A metabolic pathway is a series of chemical reactions, which goes through various intermediate compounds to transform input compounds into a product. In this work, we modelled a metabolic pathway in Plasmodium falciparum using Colored Petri Net Markup Language (CPNML). The model was used to examine the dynamic behavior of the sucrose biosynthesis pathway which shows the interactions between the metabolites and the reactions in the sucrose biosynthesis pathway of Plasmodium falciparum. We further analyzed the model for its structural and quantitative properties using Petri Net theory. Our model gives more insight to the structure of the pathway and helps to improve our understanding of the biological processes within this pathway.Keywords: Sucrose, Colored Petri Net, Plasmodium falciparu

Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets

Malaria is one of the deadly diseases, which affects a large number of the world’s population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. falci-parum is one of the important metabolic pathways of the parasite because the parasite is entirely dependent on it for energy. Also, several glycolytic enzymes have been proposed as drug targets. Petri nets (PNs) have been recognized as one of the important models for representing biological pathways. In this work, we built a qualitative PN model for the glycolysis pathway in P. falciparum and analyzed the model for its structural and quantitative properties using PN theory. From PlasmoCyc files, a total of 11 reactions were extracted; 6 of these were reversible and 5 were irreversible. These reactions were catalyzed by a total number of 13 enzymes. We extracted some of the essential reactions in the pathway using PN model, which are the possible drug targets without which the pathway cannot function. This model also helps to improve the understanding of the biological processes within this pathway

Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets

Malaria is one of the deadly diseases, which affects a large number of the world’s population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. falci-parum is one of the important metabolic pathways of the parasite because the parasite is entirely dependent on it for energy. Also, several glycolytic enzymes have been proposed as drug targets. Petri nets (PNs) have been recognized as one of the important models for representing biological pathways. In this work, we built a qualitative PN model for the glycolysis pathway in P. falciparum and analyzed the model for its structural and quantitative properties using PN theory. From PlasmoCyc files, a total of 11 reactions were extracted; 6 of these were reversible and 5 were irreversible. These reactions were catalyzed by a total number of 13 enzymes. We extracted some of the essential reactions in the pathway using PN model, which are the possible drug targets without which the pathway cannot function. This model also helps to improve the understanding of the biological processes within this pathway

Representing and Comparing Metabolic Pathways as Petri Nets with MPath2PN and CoMeta

We present two tools, MPath2PN and CoMeta, which are part of an ongoing project for representing and comparing metabolic pathways as Petri Nets. MPath2PN is intended to support an automatic translation of metabolic pathways from the major biological databases into corresponding Petri nets expressed in the input formalisms for Petri net tools. CoMeta is devised to compare metabolic pathways of different organisms through their Petri net representation produced by MPath2PN. CoMeta automatically takes the data from the KEGG database and, in the comparison, it con- siders both homology of reactions and behavioural aspects of the pathways as expressed by the T-invariants of the underlying Petri nets

Bidirektionale Abbildung zwischen Geschäftsprozessmodellen und IT-Kommunikationssystemen

Wie können Menschen mit verschiedenen Kenntnissen und Erfahrungen Prozessmodelle in der digitalen Kommunikation verwenden und zugleich Systemunterstützung durch die beschriebenen Prozesse erhalten? Diese Fragestellung wird mit einer beidseitigen Transformation auf Basis natürlicher Sprache gelöst und mit praxisnahen Beispielen erläutert. So können IT-gestützte Workflows über bisher schwer überwindbare Systemgrenzen hinweg umgesetzt werden

Bidirektionale Abbildung zwischen Geschäftsprozessmodellen und IT-Kommunikationssystemen

How can people with different knowledge and experience use process models in the digital communication and at the same time how can they receive system support through the described processes? This question is solved by a mutual transformation based on natural language which is illustrated with practical examples. Thus, more widespread workflows can be implemented by incorporating system boundaries that were previously hard to overcome