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489
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1 <macros>
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2
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3 <xml name="options">
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4 <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
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5 <option value="HMRcore">HMRcore tabular</option>
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6 <option value="Recon">Recon3D tabular</option>
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7 <option value="ENGRO2" selected="true">ENGRO 2 tabular</option>
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8 <option value="Custom">Custom rules</option>
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9 </param>
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10 </xml>
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11
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12 <xml name="options_model">
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13 <param name="model_selector" argument="--model_selector" type="select" label="Model:">
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14 <option value="ENGRO2" selected="true">ENGRO 2 tabular</option>
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15 <option value="Recon">Recon3D tabular</option>
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16 <option value="Custom_model">Custom tabular</option>
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17 </param>
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18 </xml>
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19
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20 <xml name="options_ras_to_bounds_model">
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21 <param name="model_selector" argument="--model_selector" type="select" label="Model:">
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22 <option value="ENGRO2" selected="true">ENGRO 2</option>
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23 <option value="Custom">Custom model</option>
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24 </param>
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25 </xml>
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26
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27 <xml name="options_ras_to_bounds_medium">
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28 <param name="medium_selector" argument="--medium_selector" type="select" label="Medium:">
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29 <option value="Default" selected="true">Default (ENGRO2 built-in medium)</option>
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30 <option value="allOpen">Open</option>
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31 <option value="RPMI_1640">RPMI 1640</option>
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32 <option value="DMEM">DMEM</option>
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33 <option value="EMEM">EMEM</option>
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34 <option value="DMEM:F12_=_1:1">DMEM:F12 = 1:1</option>
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35 <option value="adv_DMEM:F12_=_1:1">adv DMEM:F12 = 1:1</option>
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36 <option value="McCoy's_5A">McCoy's 5A</option>
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37 <option value="IMDM">IMDM</option>
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38 <option value="MEM">MEM</option>
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39 <option value="GMEM">GMEM</option>
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40 <option value="Leibovitz's_L-15">Leibovitz's L-15</option>
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41 <option value="F12">F12</option>
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42 <option value="F10">F10</option>
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43 <option value="AMEM">AMEM</option>
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44 <option value="Waymouth_MB_7521_medium">Waymouth MB 7521 medium</option>
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45 <option value="F12K">F12K</option>
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46 <option value="William's_E_Medium">William's E Medium</option>
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47 <option value="Medium_199">Medium 199</option>
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48 <option value="MCDB_105">MCDB 105</option>
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49 <option value="NEAA">NEAA</option>
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50 <option value="mIVC1:adv_DMEM:F12_=_1:1">mIVC1:adv DMEM:F12 = 1:1</option>
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51 <option value="E8_ess">E8 ess</option>
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52 <option value="RPMI:F12_=_1:1">RPMI:F12 = 1:1</option>
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53 <option value="RPMI:MEM_=_1:1">RPMI:MEM = 1:1</option>
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54 <option value="RPMI:EMEM_=_1:1">RPMI:EMEM = 1:1</option>
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55 <option value="EMEM:F12_=_1:1">EMEM:F12 = 1:1</option>
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56 <option value="DMEM:RPMI_=_2:1">DMEM:RPMI = 2:1</option>
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57 <option value="DMEM:IMDM_=_1:1">DMEM:IMDM = 1:1</option>
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58 <option value="MCDB_105:Medium_199_=_1:1">MCDB 105:Medium 199 = 1:1</option>
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59 <option value="mIVC1:adv_DMEM:F12_=_1:1_open">mIVC1:adv DMEM:F12 = 1:1 open</option>
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60 <option value="E8_ess_open">E8 ess open</option>
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61 <option value="open_10">Open 10</option>
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62 <option value="E8_open_10">E8 open 10</option>
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63 </param>
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64 </xml>
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65
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66 <token name="@CUSTOM_RULES_EXEMPLE@">
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67
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68 +--------------------+-------------------------------+
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69 | id | rule (with entrez-id) |
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70 +====================+===============================+
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71 | SHMT1 | 155060 or 10357 |
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72 +--------------------+-------------------------------+
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73 | NIT2 | 155060 or 100134869 |
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74 +--------------------+-------------------------------+
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75 | GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 |
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76 +--------------------+-------------------------------+
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77
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78 |
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79
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80 </token>
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81
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82 <token name="@DATASET_EXEMPLE1@">
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83
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84 +------------+------------+------------+------------+
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85 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
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86 +============+============+============+============+
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87 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
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88 +------------+------------+------------+------------+
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89 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
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90 +------------+------------+------------+------------+
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91 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
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92 +------------+------------+------------+------------+
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93 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
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94 +------------+------------+------------+------------+
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95 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
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96 +------------+------------+------------+------------+
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97
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98 |
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99
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100 </token>
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101
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102 <token name="@DATASET_EXEMPLE2@">
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103
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104 +-------------+------------+------------+------------+
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105 | Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
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106 +=============+============+============+============+
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107 | A1BG | 0.523167 | 0.371355 | 0.925661 |
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108 +-------------+------------+------------+------------+
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109 | A1CF | 0.568765 | 0.765567 | 0.456789 |
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110 +-------------+------------+------------+------------+
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111 | A2M | 0.876545 | 0.768933 | 0.987654 |
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112 +-------------+------------+------------+------------+
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113 | A4GALT | 0.456788 | 0.876543 | 0.876542 |
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114 +-------------+------------+------------+------------+
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115 | M664Y65 | 0.876543 | 0.786543 | 0.897654 |
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116 +-------------+------------+------------+------------+
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117
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118 |
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119
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120 </token>
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121
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122 <token name="@REFERENCE@">
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123
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124 This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_.
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125
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126 .. _BIMIB: https://bimib.disco.unimib.it/index.php/Home
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127 .. _Department of Informatics, Systems and Communications: https://www.disco.unimib.it/en
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128 .. _University of Milan - Bicocca: https://en.unimib.it/
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129
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130 </token>
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131
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132 <xml name="citations">
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133 <citations> <!--esempio di citazione-->
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134 <citation type="bibtex">
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135 @article{graudenzi2018integration,
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136 title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power},
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137 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},
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138 journal={Journal of biomedical informatics},
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139 volume={87},
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140 pages={37--49},
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141 year={2018},
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142 publisher={Elsevier},
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143 url = {https://doi.org/10.1016/j.jbi.2018.09.010},
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144 }
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145 </citation>
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146 <citation type="bibtex">
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147 @article{damiani2020marea4galaxy,
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148 title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy},
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149 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},
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150 journal={Computational and Structural Biotechnology Journal},
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151 volume={18},
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152 pages={993},
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153 year={2020},
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154 publisher={Research Network of Computational and Structural Biotechnology},
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155 url = {https://doi.org/10.1016/j.csbj.2020.04.008},
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156 }
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157 </citation>
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158 <citation type="bibtex">
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159 @article{ebrahim2013cobrapy,
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160 title={COBRApy: constraints-based reconstruction and analysis for python},
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161 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
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162 journal={BMC systems biology},
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163 volume={7},
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164 pages={1--6},
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165 year={2013},
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166 publisher={Springer}
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167 }
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168 </citation>
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169 </citations>
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170 </xml>
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171
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172 <xml name="citations_fluxes">
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173 <citations>
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174 <citation type="bibtex">
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175 @article{galuzzi2024adjusting,
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176 title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis},
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177 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
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178 journal={Journal of Biomedical Informatics},
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179 volume={150},
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180 pages={104597},
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181 year={2024},
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182 publisher={Elsevier}
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183 }
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184 </citation>
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185 <citation type="bibtex">
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186 @inproceedings{galuzzi2022best,
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187 title={Best practices in flux sampling of constrained-based models},
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188 author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
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189 booktitle={International Conference on Machine Learning, Optimization, and Data Science},
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190 pages={234--248},
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191 year={2022},
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192 organization={Springer}
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193 }
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194 </citation>
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195 <citation type="bibtex">
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196 @article{ebrahim2013cobrapy,
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197 title={COBRApy: constraints-based reconstruction and analysis for python},
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198 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
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199 journal={BMC systems biology},
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200 volume={7},
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201 pages={1--6},
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202 year={2013},
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203 publisher={Springer}
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204 }
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205 </citation>
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206 </citations>
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207 </xml>
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208
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209
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210 </macros>
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