93
+ − 1 <macros>
+ − 2
+ − 3 <xml name="options">
+ − 4 <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
+ − 5 <option value="HMRcore" selected="true">HMRcore rules</option>
+ − 6 <option value="Recon">Recon 2.2 rules</option>
+ − 7 <option value="ENGRO2">ENGRO 2 rules</option>
+ − 8 <option value="Custom">Custom rules</option>
+ − 9 </param>
+ − 10 </xml>
+ − 11
+ − 12 <xml name="options_ras_to_bounds_model">
+ − 13 <param name="model_selector" argument="--model_selector" type="select" label="Model:">
+ − 14 <option value="ENGRO2">ENGRO 2</option>
+ − 15 <option value="Custom">Custom model</option>
+ − 16 </param>
+ − 17 </xml>
+ − 18
+ − 19 <xml name="options_ras_to_bounds_medium">
+ − 20 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium:">
+ − 21 <option value="allOpen">Open</option>
+ − 22 <option value="Custom">Custom medium</option>
+ − 23 <option value="RPMI_1640">RPMI 1640</option>
+ − 24 <option value="DMEM">DMEM</option>
+ − 25 <option value="EMEM">EMEM</option>
+ − 26 <option value="DMEM:F12_=_1:1">DMEM:F12 = 1:1</option>
+ − 27 <option value="McCoy's_5A">McCoy's 5A</option>
+ − 28 <option value="IMDM">IMDM</option>
+ − 29 <option value="MEM">MEM</option>
+ − 30 <option value="GMEM">GMEM</option>
+ − 31 <option value="Leibovitz's_L-15">Leibovitz's L-15</option>
+ − 32 <option value="F12">F12</option>
+ − 33 <option value="F10">F10</option>
+ − 34 <option value="AMEM">AMEM</option>
+ − 35 <option value="Waymouth_MB_7521_medium">Waymouth MB 7521 medium</option>
+ − 36 <option value="F12K">F12K</option>
+ − 37 <option value="William's_E_Medium">William's E Medium</option>
+ − 38 <option value="Medium_199">Medium 199</option>
+ − 39 <option value="MCDB_105">MCDB 105</option>
+ − 40 <option value="NEAA">NEAA</option>
+ − 41 <option value="RPMI:F12_=_1:1">RPMI:F12 = 1:1</option>
+ − 42 <option value="RPMI:MEM_=_1:1">RPMI:MEM = 1:1</option>
+ − 43 <option value="RPMI:EMEM_=_1:1">RPMI:EMEM = 1:1</option>
+ − 44 <option value="EMEM:F12_=_1:1">EMEM:F12 = 1:1</option>
+ − 45 <option value="DMEM:RPMI_=_2:1">DMEM:RPMI = 2:1</option>
+ − 46 <option value="DMEM:IMDM_=_1:1">DMEM:IMDM = 1:1</option>
+ − 47 <option value="MCDB_105:Medium_199_=_1:1">MCDB 105:Medium 199 = 1:1</option>
+ − 48 </param>
+ − 49 </xml>
+ − 50
+ − 51 <token name="@CUSTOM_RULES_EXEMPLE@">
+ − 52
+ − 53 +--------------------+-------------------------------+
+ − 54 | id | rule (with entrez-id) |
+ − 55 +====================+===============================+
+ − 56 | SHMT1 | 155060 or 10357 |
+ − 57 +--------------------+-------------------------------+
+ − 58 | NIT2 | 155060 or 100134869 |
+ − 59 +--------------------+-------------------------------+
+ − 60 | GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 |
+ − 61 +--------------------+-------------------------------+
+ − 62
+ − 63 |
+ − 64
+ − 65 </token>
+ − 66
+ − 67 <token name="@DATASET_EXEMPLE1@">
+ − 68
+ − 69 +------------+------------+------------+------------+
+ − 70 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
+ − 71 +============+============+============+============+
+ − 72 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
+ − 73 +------------+------------+------------+------------+
+ − 74 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
+ − 75 +------------+------------+------------+------------+
+ − 76 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
+ − 77 +------------+------------+------------+------------+
+ − 78 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
+ − 79 +------------+------------+------------+------------+
+ − 80 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
+ − 81 +------------+------------+------------+------------+
+ − 82
+ − 83 |
+ − 84
+ − 85 </token>
+ − 86
+ − 87 <token name="@DATASET_EXEMPLE2@">
+ − 88
+ − 89 +-------------+------------+------------+------------+
+ − 90 | Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
+ − 91 +=============+============+============+============+
+ − 92 | A1BG | 0.523167 | 0.371355 | 0.925661 |
+ − 93 +-------------+------------+------------+------------+
+ − 94 | A1CF | 0.568765 | 0.765567 | 0.456789 |
+ − 95 +-------------+------------+------------+------------+
+ − 96 | A2M | 0.876545 | 0.768933 | 0.987654 |
+ − 97 +-------------+------------+------------+------------+
+ − 98 | A4GALT | 0.456788 | 0.876543 | 0.876542 |
+ − 99 +-------------+------------+------------+------------+
+ − 100 | M664Y65 | 0.876543 | 0.786543 | 0.897654 |
+ − 101 +-------------+------------+------------+------------+
+ − 102
+ − 103 |
+ − 104
+ − 105 </token>
+ − 106
+ − 107 <token name="@REFERENCE@">
+ − 108
+ − 109 This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_.
+ − 110
+ − 111 .. _BIMIB: https://bimib.disco.unimib.it/index.php/Home
+ − 112 .. _Department of Informatics, Systems and Communications: https://www.disco.unimib.it/en
+ − 113 .. _University of Milan - Bicocca: https://en.unimib.it/
+ − 114
+ − 115 </token>
+ − 116
+ − 117 <xml name="citations">
+ − 118 <citations> <!--esempio di citazione-->
+ − 119 <citation type="bibtex">
+ − 120 @article{graudenzi2018integration,
+ − 121 title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power},
+ − 122 author={Graudenzi, Alex and Maspero, Davide and Di Filippo, Marzia and Gnugnoli, Marco and Isella, Claudio and Mauri, Giancarlo and Medico, Enzo and Antoniotti, Marco and Damiani, Chiara},
+ − 123 journal={Journal of biomedical informatics},
+ − 124 volume={87},
+ − 125 pages={37--49},
+ − 126 year={2018},
+ − 127 publisher={Elsevier},
+ − 128 url = {https://doi.org/10.1016/j.jbi.2018.09.010},
+ − 129 }
+ − 130 </citation>
+ − 131 <citation type="bibtex">
+ − 132 @article{damiani2020marea4galaxy,
+ − 133 title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy},
+ − 134 author={Damiani, Chiara and Rovida, Lorenzo and Maspero, Davide and Sala, Irene and Rosato, Luca and Di Filippo, Marzia and Pescini, Dario and Graudenzi, Alex and Antoniotti, Marco and Mauri, Giancarlo},
+ − 135 journal={Computational and Structural Biotechnology Journal},
+ − 136 volume={18},
+ − 137 pages={993},
+ − 138 year={2020},
+ − 139 publisher={Research Network of Computational and Structural Biotechnology},
+ − 140 url = {https://doi.org/10.1016/j.csbj.2020.04.008},
+ − 141 }
+ − 142 </citation>
+ − 143 <citation type="bibtex">
+ − 144 @article{ebrahim2013cobrapy,
+ − 145 title={COBRApy: constraints-based reconstruction and analysis for python},
+ − 146 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
+ − 147 journal={BMC systems biology},
+ − 148 volume={7},
+ − 149 pages={1--6},
+ − 150 year={2013},
+ − 151 publisher={Springer}
+ − 152 }
+ − 153 </citation>
+ − 154 </citations>
+ − 155 </xml>
+ − 156
+ − 157 <xml name="citations_fluxes">
+ − 158 <citations>
+ − 159 <citation type="bibtex">
+ − 160 @article{galuzzi2024adjusting,
+ − 161 title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis},
+ − 162 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
+ − 163 journal={Journal of Biomedical Informatics},
+ − 164 volume={150},
+ − 165 pages={104597},
+ − 166 year={2024},
+ − 167 publisher={Elsevier}
+ − 168 }
+ − 169 </citation>
+ − 170 <citation type="bibtex">
+ − 171 @inproceedings{galuzzi2022best,
+ − 172 title={Best practices in flux sampling of constrained-based models},
+ − 173 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
+ − 174 booktitle={International Conference on Machine Learning, Optimization, and Data Science},
+ − 175 pages={234--248},
+ − 176 year={2022},
+ − 177 organization={Springer}
+ − 178 }
+ − 179 </citation>
+ − 180 <citation type="bibtex">
+ − 181 @article{ebrahim2013cobrapy,
+ − 182 title={COBRApy: constraints-based reconstruction and analysis for python},
+ − 183 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
+ − 184 journal={BMC systems biology},
+ − 185 volume={7},
+ − 186 pages={1--6},
+ − 187 year={2013},
+ − 188 publisher={Springer}
+ − 189 }
+ − 190 </citation>
+ − 191 </citations>
+ − 192 </xml>
+ − 193
+ − 194
+ − 195 </macros>