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comparison COBRAxy/flux_simulation.xml @ 14:c10d8b38de84 draft

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author luca_milaz
date Wed, 18 Sep 2024 12:37:06 +0000
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13:73be0702f1a2 14:c10d8b38de84
125 **TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10. 125 **TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10.
126 **TIP**: The Thinning parameter of the OPTGP algorithm is useful to converge to a stationary distribution (see cited articles by Galuzzi, Milazzo and Damiani). 126 **TIP**: The Thinning parameter of the OPTGP algorithm is useful to converge to a stationary distribution (see cited articles by Galuzzi, Milazzo and Damiani).
127 127
128 ]]> 128 ]]>
129 </help> 129 </help>
130 130 <expand macro="citations_fluxes" />
131
132 <citations>
133 <citation type="bibtex">
134 @article{galuzzi2024adjusting,
135 title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis},
136 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
137 journal={Journal of Biomedical Informatics},
138 volume={150},
139 pages={104597},
140 year={2024},
141 publisher={Elsevier}
142 }
143 </citation>
144 <citation type="bibtex">
145 @inproceedings{galuzzi2022best,
146 title={Best practices in flux sampling of constrained-based models},
147 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
148 booktitle={International Conference on Machine Learning, Optimization, and Data Science},
149 pages={234--248},
150 year={2022},
151 organization={Springer}
152 }
153 </citation>
154 <citation type="bibtex">
155 @article{ebrahim2013cobrapy,
156 title={COBRApy: constraints-based reconstruction and analysis for python},
157 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
158 journal={BMC systems biology},
159 volume={7},
160 pages={1--6},
161 year={2013},
162 publisher={Springer}
163 }
164 </citation>
165 </citations>
166 131
167 </tool> 132 </tool>