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comparison COBRAxy/marea_macros.xml @ 93:7e703e546998 draft

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author luca_milaz
date Sun, 13 Oct 2024 11:41:34 +0000
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92:fdf713bb5772 93:7e703e546998
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>