Open Access Highly Accessed Research article

Parkinson’s disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein

Finja Büchel1*, Sandra Saliger1, Andreas Dräger12, Stephanie Hoffmann1, Clemens Wrzodek1, Andreas Zell1 and Philipp J Kahle3

Author Affiliations

1 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany

2 Bioengineering Department, University of California, San Diego, La Jolla, CA 92093-0412, USA

3 Laboratory of Functional Neurogenetics, Department of Neurodegeneration, Hertie Institute for Clinical Brain Research and German Center for Neurodegenerative Diseases, University of Tuebingen, 72076 Tübingen, Germany

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BMC Neuroscience 2013, 14:136  doi:10.1186/1471-2202-14-136

Published: 6 November 2013

Additional files

Additional file 1:

SBML model of the dopaminergic nerve cell. The SBML file contains the annotated SBML model of the dopaminergic nerve cell.

Format: XML Size: 191KB Download file

Open Data

Additional file 2:

Reactions of the dopaminergic nerve cell model. This table describes all reactions of the dopaminergic nerve cell model in detail with name and flux ranges.

Format: PDF Size: 164KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 3:

Entities of the dopaminergic nerve cell model. This spreadsheet lists all model entities that are used in the dopaminergic nerve cell model. It also includes a description for each entity, as well as identifiers to commonly used databases.

Format: PDF Size: 110KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 4:

Comparison of the mathematical model by Bestet al. to the dopamine sub-model of the dopaminergic nerve cell. This file presents the comparison of the mathematical model by Best et al. to the sub-model of the dopaminergic nerve cell containing dopamine synthesis, metabolism, and transport. It lists in detail the adjusted flux ranges of the initial model and the result of the FBA of this sub-model.

Format: PDF Size: 411KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 5:

Detailed model of the dopaminergic nerve cell. This file contains the visualization of the dopaminergic nerve cell model with its 139 reactions and 111 metabolites in detail. The metabolites are depicted as circles and the reactions as rectangles. Red circles visualize all reagents and products, whereas pink circles visualize units of currency. Reactions are colored blue. Reactions with the suffix ‘IN’ represent input reactions transporting metabolites in the cell (light green) and reactions with the suffix ‘OUT’ represent the corresponding output reactions (dark green).

Format: TIFF Size: 12.6MB Download file

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