Photorespiration causes a substantial decrease in crop yield because of mitochondrial decarboxylation. Alternative pathways (APs) have been designed to relocate the decarboxylation step or even fix additional carbon. To improve success transferring those engineered APs from model species crops, we must understand how they will interact with metabolism and plant physiology affects their performance. Here, used multiple mathematical modeling techniques analyze compare existing AP designs. We...

Hackathons are collaborative, fast-paced events where participants from various fields work together to solve real-world problems. The term combines "hack" and "marathon", reflecting both the creative intensive nature of these activities. Emerging evidence highlights benefits hackathons as educational tools, particularly in engineering, software development, social sciences, they enhance problem-solving skills, teamwork, engagement. Here, we extend this body by presenting our experience...

During photosynthesis, organisms respond to their energy demand and ensure the supply of redox equivalents that sustain metabolism. Hence, photosynthetic apparatus can, in fact should, be treated as an integrated supply-demand system. Any imbalance produced consumed can lead adverse reactions, such production reactive oxygen species (ROS). Reaction centres both photosystems are known sites ROS production. Here, we investigate particular central role Photosystem I (PSI) this tightly regulated...

Photosynthetic organisms use photosynthesis to harvest sunlight and convert the solar energy into chemical energy, which is then used reduce atmospheric carbon dioxide organic molecules. This process forms basis of all life on Earth, stands at beginning food chain feeds world population. Not surprisingly, many research efforts are currently ongoing aiming improving growth product yield photosynthetic organisms, several these activities directly target pathways. Metabolic Control Analysis...

Abstract Background Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding various regulatory processes, metabolic fluxes, effects drug therapies, disease evolution transmission. Unfortunately, despite community efforts leading the development SBML BioModels database, many published not fully exploited, largely due a lack proper documentation or dependence on proprietary software. To facilitate reuse further biology...

Photorespiration causes a significant decrease in crop yield due to mitochondrial decarboxylation. Alternative pathways (APs) have been designed relocate the decarboxylating step or even fix additional carbon. To improve success of transferring those engineered APs from model species crops we must understand how they will interact with metabolism and plant physiology affects their performance. Here used multiple mathematical modelling techniques analyse compare existing AP designs. We show...

Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles metabolism and growth. Such approaches include, among others, differential-equation-based systems, constraint-based network expansion networks. Most these methods are well established implemented in numerous software packages, but scattered between different programming languages, packages syntaxes. This complicates establishing straight forward pipelines integrating model construction...

COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose to facilitate the integration modern high performance computing environments with processing metabolic models challenging complexity. We report architecture package, demonstrate how design promotes scalability on several use-cases multi-organism community models.https://doi.org/10.17881/ZKCR-BT30.Supplementary data are available...

The modelbase package is a free expandable Python for building and analysing dynamic mathematical models of biological systems. Originally it was designed the simulation metabolic systems, but can be used virtually any deterministic chemical processes. provides easy construction methods to define reactions their rates. Based on rates stoichiometries, system differential equations assembled automatically. minimises constraints imposed user, allowing access all variables, including derived...

Abstract Studies show the advantage of active versus passive learning formats in delivering complicated concepts (Minocha and Clarke, 2009; Pluta et al., 2013). Hence, interactive teaching tools are not only more often positively evaluated by students but also contribute to better life-long outcomes (Ang 2021). Following this evidence, we created ComPhot, a stand-alone platform for motivated researchers. It guides user studying photosynthesis as well-known biological process with support...

Terpenoids make up the largest class of specialized metabolites with over 180,000 reported compounds currently across all kingdoms life. Their synthesis accentuates one natures most choreographed enzymatic and non-reversible chemistries, leading to an extensive range structural functionality diversity. Current terpenoid repositories provide a seemingly endless landscape systematically survey for information regarding structure, sourcing, synthesis. Efforts here investigate entries 20-carbon...

The modelbase package is a free expandable Python for building and analysing dynamic mathematical models of biological systems. Originally it was designed the simulation metabolic systems, but can be used virtually any deterministic chemical processes. provides easy construction methods to define reactions their rates. Based on rates stoichiometries, system differential equations assembled automatically. minimises constraints imposed user, allowing access all variables, including derived...

Abstract Background Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding various regulatory processes, metabolic fluxes, effects drug therapies disease evolution or transmission. Unfortunately, despite community efforts leading the development SBML BioModels database, many published not fully exploited, largely due lack proper documentation dependence on proprietary software. To facilitate synergies within emerging...

Summary COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose to facilitate the integration modern high performance computing environments with processing metabolic models challenging complexity. We report architecture package, demonstrate how design promotes scalability on several use-cases multi-organism community Availability implementation https://doi.org/10.17881/ZKCR-BT30 ....

Plants use photosynthesis to harvest sunlight and convert the solar energy into chemical energy, which is then used reduce atmospheric carbon dioxide organic molecules. This process forms basis of all life on Earth, stands at beginning food chain feeds world population. Not surprisingly, many research efforts are currently ongoing aiming improving plant growth crop yield, several these activities directly target photosynthetic pathways. Metabolic Control Analysis (MCA) shows that, in...

Several commercially important secondary metabolites are produced and accumulated in high amounts by glandular trichomes, giving the prospect of using them as metabolic cell factories. Due to extremely fluxes through previous research focused on how such flows achieved. The question regarding their bioenergetics became even more interesting with discovery photosynthetic activity some trichomes. Despite recent advances, primary metabolism contributes trichomes is still not fully elucidated....

Abstract Summary dismo is a Python package for building and analysing discrete spatial models based on ordinary differential equations. Its primary purpose to allow arbitrarily complex internal transport processes easily be mapped over multiple different regular grids. For this it features one, two threedimensional layouts, with standard non-standard (e.g. hexagonal or triangular) Availability implementation https://gitlab.com/qtb-hhu/dismo Contact oliver.ebenhoeh@hhu.de

Abstract Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles metabolism and growth. Such approaches include, amongst others, differential equation based systems, constraint topological analysis networks. Most these methods are well established implemented in numerous software packages, but scattered between different programming languages, packages syntaxes. This complicates establishing straight forward pipelines integrating model...

Abstract Several commercially important secondary metabolites are produced and accumulated in high amounts by glandular trichomes, giving the prospect of using them as metabolic cell factories. Due to extremely fluxes through previous research focused on how such flows achieved. The question regarding their bioenergetics became even more interesting with discovery photosynthetic activity some trichomes. Despite recent advances, primary metabolism contributes trichomes is still not fully...

Plants use light energy to produce ATP and redox equivalents for metabolism. Since during the course of a day plants are exposed constantly fluctuating light, supply is also fluctuating. Further, if metabolism cannot all supplied energy, excess absorbed can damage plant in form reactive oxygen species. It thus reasonable assume that downstream dynamic as being capable dampening sudden spikes advantageous, it further immediate flexible well. A input unlikely be metabolic steady-state, yet lot...