Reaction balancer functionality in Metapenta
This project introduces a new functionality focused on reaction balance within the pre-existing MetaPenta software, with the purpose of automating a crucial step in the reconstruction of genome-scale networks. The novel module allows the generation of a complete report pointing out unbalanced reacti...
- Autores:
-
García Cárdenas, Gabriela
- Tipo de recurso:
- Trabajo de grado de pregrado
- Fecha de publicación:
- 2024
- Institución:
- Universidad de los Andes
- Repositorio:
- Séneca: repositorio Uniandes
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.uniandes.edu.co:1992/73495
- Acceso en línea:
- https://hdl.handle.net/1992/73495
- Palabra clave:
- Genome-scale metabolic reconstruction
Reaction balance
MetaPenta
Ingeniería
- Rights
- openAccess
- License
- Attribution-NonCommercial 4.0 International
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Reaction balancer functionality in Metapenta |
| title |
Reaction balancer functionality in Metapenta |
| spellingShingle |
Reaction balancer functionality in Metapenta Genome-scale metabolic reconstruction Reaction balance MetaPenta Ingeniería |
| title_short |
Reaction balancer functionality in Metapenta |
| title_full |
Reaction balancer functionality in Metapenta |
| title_fullStr |
Reaction balancer functionality in Metapenta |
| title_full_unstemmed |
Reaction balancer functionality in Metapenta |
| title_sort |
Reaction balancer functionality in Metapenta |
| dc.creator.fl_str_mv |
García Cárdenas, Gabriela |
| dc.contributor.advisor.none.fl_str_mv |
Duitama Castellanos, Jorge Alexander |
| dc.contributor.author.none.fl_str_mv |
García Cárdenas, Gabriela |
| dc.subject.keyword.eng.fl_str_mv |
Genome-scale metabolic reconstruction Reaction balance MetaPenta |
| topic |
Genome-scale metabolic reconstruction Reaction balance MetaPenta Ingeniería |
| dc.subject.themes.spa.fl_str_mv |
Ingeniería |
| description |
This project introduces a new functionality focused on reaction balance within the pre-existing MetaPenta software, with the purpose of automating a crucial step in the reconstruction of genome-scale networks. The novel module allows the generation of a complete report pointing out unbalanced reactions from the target metabolic network. This report also details the successfully balanced reactions, specifying modifications made on both sides of each reaction and the method that was used. The motivation for this development emerges from the observed limitations in current tools available designed for genome-scale metabolic reconstruction, which still lack the capability to autonomously curate the first draft. Consequently, researchers currently have to verify manually which reactions are not balanced by calculating the stoichiometry of each reaction. Therefore, the introduced reaction balancer functionality automates the evaluation of each reaction in the metabolic network aiming to balance as many reactions as feasible. In this way, the automation improves the curation process by augmenting the performance and reliability of genome-scale metabolic reconstructions. |
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2024 |
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2024-01-25T21:50:50Z |
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2024-01-25T21:50:50Z |
| dc.date.issued.none.fl_str_mv |
2024-01-14 |
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Trabajo de grado - Pregrado |
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info:eu-repo/semantics/bachelorThesis |
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info:eu-repo/semantics/acceptedVersion |
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Text |
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https://hdl.handle.net/1992/73495 |
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instname:Universidad de los Andes |
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reponame:Repositorio Institucional Séneca |
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repourl:https://repositorio.uniandes.edu.co/ |
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eng |
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eng |
| dc.relation.references.none.fl_str_mv |
Angione, C. (2019). Human systems biology and metabolic modelling: a review—from disease metabolism to precision medicine. BioMed research international, 2019 Parra, V. (2020). MetaPenta: visualizacion y analisis de redes metabolicas Cho, J. S., Gu, C., Han, T. H., Ryu, J. Y., & Lee, S. Y. (2019). Reconstruction of context-specific genome-scale metabolic models using multiomics data to study metabolic rewiring. Current Opinion in Systems Biology, 15, 1-11. Oberhardt, M. A., Palsson, B. Ø., & Papin, J. A. (2009). Applications of genome‐scale metabolic reconstructions. Molecular systems biology, 5(1), 320. Mendoza, S. N., Olivier, B. G., Molenaar, D., & Teusink, B. (2019). A systematic assessment of current genome-scale metabolic reconstruction tools. Genome biology, 20(1), 1-20. Hari, A., & Lobo, D. (2020). Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks. Nucleic acids research, 48(W1), W427-W435. Thiele, I., & Palsson, B. Ø. (2010). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature protocols, 5(1), 93-121. Marmiesse, L., Peyraud, R., & Cottret, L. (2015). FlexFlux: combining metabolic flux and regulatory network analyses. BMC systems biology, 9(1), 1-13. BiGG models. (n.d.). http://bigg.ucsd.edu/models |
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Attribution-NonCommercial 4.0 International |
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http://creativecommons.org/licenses/by-nc/4.0/ |
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16 páginas |
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application/pdf |
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Universidad de los Andes |
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Ingeniería de Sistemas y Computación |
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Facultad de Ingeniería |
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Departamento de Ingeniería Sistemas y Computación |
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Universidad de los Andes |
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Universidad de los Andes |
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Duitama Castellanos, Jorge AlexanderGarcía Cárdenas, Gabriela2024-01-25T21:50:50Z2024-01-25T21:50:50Z2024-01-14https://hdl.handle.net/1992/73495instname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/This project introduces a new functionality focused on reaction balance within the pre-existing MetaPenta software, with the purpose of automating a crucial step in the reconstruction of genome-scale networks. The novel module allows the generation of a complete report pointing out unbalanced reactions from the target metabolic network. This report also details the successfully balanced reactions, specifying modifications made on both sides of each reaction and the method that was used. The motivation for this development emerges from the observed limitations in current tools available designed for genome-scale metabolic reconstruction, which still lack the capability to autonomously curate the first draft. Consequently, researchers currently have to verify manually which reactions are not balanced by calculating the stoichiometry of each reaction. Therefore, the introduced reaction balancer functionality automates the evaluation of each reaction in the metabolic network aiming to balance as many reactions as feasible. In this way, the automation improves the curation process by augmenting the performance and reliability of genome-scale metabolic reconstructions.Ingeniero de Sistemas y ComputaciónPregrado16 páginasapplication/pdfengUniversidad de los AndesIngeniería de Sistemas y ComputaciónFacultad de IngenieríaDepartamento de Ingeniería Sistemas y ComputaciónAttribution-NonCommercial 4.0 Internationalhttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Reaction balancer functionality in MetapentaTrabajo de grado - Pregradoinfo:eu-repo/semantics/bachelorThesisinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_7a1fTexthttp://purl.org/redcol/resource_type/TPGenome-scale metabolic reconstructionReaction balanceMetaPentaIngenieríaAngione, C. (2019). Human systems biology and metabolic modelling: a review—from disease metabolism to precision medicine. BioMed research international, 2019Parra, V. (2020). MetaPenta: visualizacion y analisis de redes metabolicasCho, J. S., Gu, C., Han, T. H., Ryu, J. Y., & Lee, S. Y. (2019). Reconstruction of context-specific genome-scale metabolic models using multiomics data to study metabolic rewiring. Current Opinion in Systems Biology, 15, 1-11.Oberhardt, M. A., Palsson, B. Ø., & Papin, J. A. (2009). Applications of genome‐scale metabolic reconstructions. Molecular systems biology, 5(1), 320.Mendoza, S. N., Olivier, B. G., Molenaar, D., & Teusink, B. (2019). A systematic assessment of current genome-scale metabolic reconstruction tools. Genome biology, 20(1), 1-20.Hari, A., & Lobo, D. (2020). Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks. Nucleic acids research, 48(W1), W427-W435.Thiele, I., & Palsson, B. Ø. (2010). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature protocols, 5(1), 93-121.Marmiesse, L., Peyraud, R., & Cottret, L. (2015). FlexFlux: combining metabolic flux and regulatory network analyses. BMC systems biology, 9(1), 1-13.BiGG models. 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