Orodja za analizo in vizualizacijo metabolnih omrežij

Miha Moškon21. 11. 2016

Rekonstrukcija metabolnih omrežij

Vir: Nishu Goyal et al. A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane, Mol. BioSyst., 2014, 10, 1043-1054.

Matematične metode

N. E. Lewis et al. Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silicomethods, Nature Reviews Microbiology, Vol. 10, pp. 291-305, 2014.

Na vseh korakih rekonstrukcije in analize!

Unbiased metode: okarakterizirajo vse možne pretoke, ki vodijo v ravnovesno stanje.

Biased metode: uporaba kriterijske funkcije –določitev optimalnega stanja.

Računalniška orodja – RAVEN

R. Agren et al. The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicilliumchrysogenum, Vol. 9, No. 3, pp. 291-305, 2014.

Reconstruction, Analysis, and Visualization of Metabolic Networks

Računalniška orodja - COBRA

http://cobramethods.wikidot.com/Približno 200 metod:

Constraint Based Reconstruction and Analysis

Računalniška orodja – COBRA

https://opencobra.github.io/cobrapy/https://opencobra.github.io/cobratoolbox/https://opencobra.github.io/cobratoolbox/docs/ https://cobrapy.readthedocs.io/

Cobra Matlab

Tutorial: http://systemsbiology.usu.edu/cobra_toolbox.php

Postopek dela: Schellenberger, J., R. Que, et al. (2011). "Quantitative prediction ofcellular metabolism with constraint-based models: the COBRA Toolbox v2.0." Nature protocols 6(9): 1290-1307.

COBRApy

Osnovne funkcije – glej zgleda:• createModel.py• modelFBA.py

Dokumentacija na strani https://cobrapy.readthedocs.io/

Google group (za obe okolji): https://groups.google.com/forum/#!forum/cobra-toolbox

Orodja za vizualizacijo

Paint4Net (Matlab Cobra)• http://biosystems.lv/index.php/software/paint4net/15-paint4net-download-and-installation• A. Kostromins and E. Stalidzans, Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models

of metabolism, Biosystems, Vol. 109, Issue 2, pp. 233–239, 2012

Escher• https://escher.github.io/• Z. A. King et al. Escher: A web application for building, sharing, and embedding data-rich visualizations of

biological pathways, PLOS Computational Biology, Vol. 11, No. 8, 2015.

MetDraw• http://www.metdraw.com/• P. A. Jensen and J. A. Papin, MetDraw: automated visualization of genome-scale metabolic network

reconstructions and high-throughput data, Bioinformatics, Vol. 30, No. 9, pp. 1327-8, 2014.

Escher

Vhod: JSON datoteka (generiramo v CobraPy)

Izhod: JSON datoteka, ki vsebuje podatke za vizualizacijo.

Ogled vsebine JSON datoteke: http://jsonviewer.stack.hu/

Demonstracija uporabe na primeru.

Primeri vizualizacij (ReconMap)https://vmh.uni.lu/MapViewer/index.xhtml

Primeri vizualizacij (ReconMap)https://vmh.uni.lu/MapViewer/index.xhtml

Na osnovi modela Recon 2.04

CellDesigner

MINERVA (Molecular InteractionNEtwoRks VisuAlization) + Google MapsAPI (navigacija po zemljevidu)

Povezava z bazo VMH (VirtualMetabolic Human, http://vmh.uni.lu) + ostale baze (npr. CHEMBL)

Omogoča poganjanje OpenCobra skript (tutorial) – potrebna registracija.

N., Alberto,…, Thiele, Ines, and Fleming, Ronan MT: ReconMap: An interactive visualisation of human metabolism, in Bioinformatics (in press)

Primeri vizualizacij (KEGG)

1) Pojdi na http://www.genome.jp/kegg/pathway.html2) Izberi organizem, npr. cge (Cricetulus griseus)3) Ključne besede lahko pustiš prazne "Go"

http://www.kegg.jp/kegg-bin/search_pathway_text?map=cge&keyword=&mode=1&viewImage=true