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Updated requirements for version compatibility
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Update docs
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z-haiman committed Dec 2, 2022
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2 changes: 1 addition & 1 deletion docs/additional/faqs.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.15"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion docs/education/sb2/chapters/sb2_chapter1.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.15"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion docs/education/sb2/chapters/sb2_chapter2.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.15"
}
},
"nbformat": 4,
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168 changes: 73 additions & 95 deletions docs/education/sb2/chapters/sb2_chapter3.ipynb
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2 changes: 1 addition & 1 deletion docs/education/sb2/chapters/sb2_chapter7.ipynb
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.15"
}
},
"nbformat": 4,
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132 changes: 51 additions & 81 deletions docs/education/sb2/chapters/sb2_chapter8.ipynb
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811 changes: 428 additions & 383 deletions docs/education/sb2/chapters/sb2_chapter9.ipynb
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18 changes: 8 additions & 10 deletions docs/gallery/visualization/animating_simulations.ipynb
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129 changes: 72 additions & 57 deletions docs/gallery/visualization/catalytic_potential_visualizations.ipynb
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18 changes: 9 additions & 9 deletions docs/tutorials/cobra_to_mass.ipynb
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" <td>ATP</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td>\n",
" <td>0x07faa782df6a0</td>\n",
" <td>0x07febc9889f70</td>\n",
" </tr><tr>\n",
" <td><strong>Formula</strong></td>\n",
" <td>C10H12N5O13P3</td>\n",
Expand All @@ -113,7 +113,7 @@
" </table>"
],
"text/plain": [
"<MassMetabolite atp_c at 0x7faa782df6a0>"
"<MassMetabolite atp_c at 0x7febc9889f70>"
]
},
"execution_count": 3,
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" <td>glucose-6-phosphate isomerase</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td>\n",
" <td>0x07faa68f6c730</td>\n",
" <td>0x07febc9889fd0</td>\n",
" </tr><tr>\n",
" <td><strong>Subsystem</strong></td>\n",
" <td></td>\n",
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" "
],
"text/plain": [
"<MassReaction PGI at 0x7faa68f6c730>"
"<MassReaction PGI at 0x7febc9889fd0>"
]
},
"execution_count": 6,
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"name": "stdout",
"output_type": "stream",
"text": [
"frozenset({<Gene b4025 at 0x7faa68ffc100>})\n",
"frozenset({<Gene b4025 at 0x7faa68f6c910>})\n"
"frozenset({<Gene b4025 at 0x7febb95c2b80>})\n",
"frozenset({<Gene b4025 at 0x7feba0e93eb0>})\n"
]
}
],
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" <tr>\n",
" <td><strong>Name</strong></td><td>e_coli_core</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td><td>0x07faa69050c40</td>\n",
" <td><strong>Memory address</strong></td><td>0x07feba0e93f70</td>\n",
" </tr><tr>\n",
" <td><strong>Stoichiometric Matrix</strong></td>\n",
" <td>72x95</td>\n",
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" "
],
"text/plain": [
"<MassModel e_coli_core at 0x7faa69050c40>"
"<MassModel e_coli_core at 0x7feba0e93f70>"
]
},
"execution_count": 11,
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.15"
}
},
"nbformat": 4,
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48 changes: 20 additions & 28 deletions docs/tutorials/compartments.ipynb
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22 changes: 11 additions & 11 deletions docs/tutorials/constructing_models.ipynb
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{
"data": {
"text/plain": [
"{<MassMetabolite adp_c at 0x7fc90922c130>: 0.4,\n",
" <MassMetabolite atp_c at 0x7fc90922c190>: 1.6,\n",
" <MassMetabolite amp_c at 0x7fc90922c1c0>: 0.1,\n",
" <MassMetabolite B at 0x7fc8e9469cd0>: 2.0,\n",
" <MassMetabolite BP at 0x7fc8e9469c70>: 8.0}"
"{<MassMetabolite adp_c at 0x7f8368c373a0>: 0.4,\n",
" <MassMetabolite atp_c at 0x7f8368c377c0>: 1.6,\n",
" <MassMetabolite amp_c at 0x7f8368c37f70>: 0.1,\n",
" <MassMetabolite B at 0x7f8359672160>: 2.0,\n",
" <MassMetabolite BP at 0x7f8359672b50>: 8.0}"
]
},
"execution_count": 26,
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"output_type": "stream",
"text": [
"Millimolar:\n",
"<Unit at 0x7fc9194fcd00 kind: liter; exponent: -1; scale: 1; multiplier: 1>\n",
"<Unit at 0x7fc9194fca30 kind: mole; exponent: 1; scale: -3; multiplier: 1>\n"
"<Unit at 0x7f835967d1c0 kind: mole; exponent: 1; scale: -3; multiplier: 1>\n",
"<Unit at 0x7f835967dbe0 kind: liter; exponent: -1; scale: 1; multiplier: 1>\n"
]
}
],
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"output_type": "stream",
"text": [
"min\n",
"[<Unit at 0x7fc9194ec9a0 kind: second; exponent: 1; scale: 1; multiplier: 60>]\n"
"[<Unit at 0x7f8309bbea90 kind: second; exponent: 1; scale: 1; multiplier: 60>]\n"
]
}
],
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{
"data": {
"text/plain": [
"[<UnitDefinition Millimolar \"mM\" at 0x7fc919500f70>,\n",
" <UnitDefinition Minute \"min\" at 0x7fc8e944feb0>]"
"[<UnitDefinition Millimolar \"mM\" at 0x7f8318e6b970>,\n",
" <UnitDefinition Minute \"min\" at 0x7f8309bbe8b0>]"
]
},
"execution_count": 43,
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.15"
}
},
"nbformat": 4,
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70 changes: 31 additions & 39 deletions docs/tutorials/dynamic_simulation.ipynb
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68 changes: 33 additions & 35 deletions docs/tutorials/enzyme_modules.ipynb
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54 changes: 27 additions & 27 deletions docs/tutorials/getting_started_with_masspy.ipynb
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" <tr>\n",
" <td><strong>Name</strong></td><td>RBC_PFK</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td><td>0x07faa982ae520</td>\n",
" <td><strong>Memory address</strong></td><td>0x07fe87832e850</td>\n",
" </tr><tr>\n",
" <td><strong>Stoichiometric Matrix</strong></td>\n",
" <td>68x76</td>\n",
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" "
],
"text/plain": [
"<MassModel RBC_PFK at 0x7faa982ae520>"
"<MassModel RBC_PFK at 0x7fe87832e850>"
]
},
"execution_count": 3,
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" <td>Diphosphoglycerate phosphatase</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td>\n",
" <td>0x07faa61e50ac0</td>\n",
" <td>0x07fe8c9882910</td>\n",
" </tr><tr>\n",
" <td><strong>Subsystem</strong></td>\n",
" <td>Hemoglobin</td>\n",
Expand All @@ -209,7 +209,7 @@
" "
],
"text/plain": [
"<MassReaction DPGase at 0x7faa61e50ac0>"
"<MassReaction DPGase at 0x7fe8c9882910>"
]
},
"execution_count": 4,
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" <td>ATP</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td>\n",
" <td>0x07faa58a4d490</td>\n",
" <td>0x07fe8c9834430</td>\n",
" </tr><tr>\n",
" <td><strong>Formula</strong></td>\n",
" <td>C10H12N5O13P3</td>\n",
Expand All @@ -265,12 +265,12 @@
" <td>1.2338626826140733</td>\n",
" </tr><tr>\n",
" <td><strong>In 16 reaction(s)</strong></td>\n",
" <td>PFK_R01, PFK_R41, PFK_T3, PFK_T1, ADK1, PFK_R31, PFK_R11, PFK_T4, ATPM, ADNK1, PFK_R21, PYK, PFK_T2, HEX1, PRPPS, PGK</td>\n",
" <td>PRPPS, PFK_R31, PFK_R11, ATPM, PFK_R21, PFK_T2, PFK_T4, PFK_T1, ADNK1, ADK1, PFK_R41, PYK, PFK_R01, HEX1, PGK, PFK_T3</td>\n",
" </tr>\n",
" </table>"
],
"text/plain": [
"<MassMetabolite atp_c at 0x7faa58a4d490>"
"<MassMetabolite atp_c at 0x7fe8c9834430>"
]
},
"execution_count": 5,
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" <td>Glucose-6-phosphate isomerase</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td>\n",
" <td>0x07faa58a5d7c0</td>\n",
" <td>0x07fe8c9841760</td>\n",
" </tr><tr>\n",
" <td><strong>Subsystem</strong></td>\n",
" <td>Glycolysis</td>\n",
Expand All @@ -378,7 +378,7 @@
" "
],
"text/plain": [
"<MassReaction PGI at 0x7faa58a5d7c0>"
"<MassReaction PGI at 0x7fe8c9841760>"
]
},
"execution_count": 7,
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" <td>D-Glucose 6-phosphate</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td>\n",
" <td>0x07faa78bf4d30</td>\n",
" <td>0x07fe8c97f8ca0</td>\n",
" </tr><tr>\n",
" <td><strong>Formula</strong></td>\n",
" <td>C6H11O9P</td>\n",
Expand All @@ -820,12 +820,12 @@
" <td>0.16501847288094948</td>\n",
" </tr><tr>\n",
" <td><strong>In 3 reaction(s)</strong></td>\n",
" <td>HEX1, G6PDH2r, PGI</td>\n",
" <td>G6PDH2r, HEX1, PGI</td>\n",
" </tr>\n",
" </table>"
],
"text/plain": [
"<MassMetabolite g6p_c at 0x7faa78bf4d30>"
"<MassMetabolite g6p_c at 0x7fe8c97f8ca0>"
]
},
"execution_count": 19,
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{
"data": {
"text/plain": [
"frozenset({<Gene New_Gene at 0x7faaa8fcf2e0>})"
"frozenset({<Gene New_Gene at 0x7fe8b99e9070>})"
]
},
"execution_count": 28,
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" <td><strong>Name</strong></td><td></td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td>\n",
" <td>0x07faaa8fcf2e0</td>\n",
" <td>0x07fe8b99e9070</td>\n",
" </tr><tr>\n",
" <td><strong>Functional</strong></td><td>True</td>\n",
" </tr><tr>\n",
Expand All @@ -1188,7 +1188,7 @@
" </table>"
],
"text/plain": [
"<Gene New_Gene at 0x7faaa8fcf2e0>"
"<Gene New_Gene at 0x7fe8b99e9070>"
]
},
"execution_count": 29,
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" <td><strong>Name</strong></td><td></td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td>\n",
" <td>0x07faaa8fcf2e0</td>\n",
" <td>0x07fe8b99e9070</td>\n",
" </tr><tr>\n",
" <td><strong>Functional</strong></td><td>True</td>\n",
" </tr><tr>\n",
Expand All @@ -1248,7 +1248,7 @@
" </table>"
],
"text/plain": [
"<Gene New_Gene at 0x7faaa8fcf2e0>"
"<Gene New_Gene at 0x7fe8b99e9070>"
]
},
"execution_count": 30,
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" <tr>\n",
" <td><strong>Name</strong></td><td>PFK</td>\n",
" </tr><tr>\n",
" <td><strong>Memory address</strong></td><td>0x07faab8f14040</td>\n",
" <td><strong>Memory address</strong></td><td>0x07fe8a93ff940</td>\n",
" </tr><tr>\n",
" <td><strong>Stoichiometric Matrix</strong></td>\n",
" <td>26x24</td>\n",
Expand Down Expand Up @@ -1320,7 +1320,7 @@
" "
],
"text/plain": [
"<EnzymeModuleDict PFK at 0x7faab8f14040>"
"<EnzymeModuleDict PFK at 0x7fe8a93ff940>"
]
},
"execution_count": 31,
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{
"data": {
"text/plain": [
"[<MassMetabolite h_c at 0x7faa58a4d5b0>,\n",
" <MassMetabolite fdp_c at 0x7faa78bf4df0>,\n",
" <MassMetabolite adp_c at 0x7faa58a4d460>]"
"[<MassMetabolite h_c at 0x7fe8c9834550>,\n",
" <MassMetabolite fdp_c at 0x7fe8c97f8d90>,\n",
" <MassMetabolite adp_c at 0x7fe8c9834400>]"
]
},
"execution_count": 35,
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{
"data": {
"text/plain": [
"[<UnitDefinition Millimolar \"mM\" at 0x7faa61e72550>,\n",
" <UnitDefinition hour \"hr\" at 0x7faa78bf4cd0>]"
"[<UnitDefinition Millimolar \"mM\" at 0x7fe8c98a3eb0>,\n",
" <UnitDefinition hour \"hr\" at 0x7fe8c97f8c70>]"
]
},
"execution_count": 38,
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"name": "stdout",
"output_type": "stream",
"text": [
"kind: litre; exponent: -1; scale: 0; multiplier: 1\n",
"kind: mole; exponent: 1; scale: -3; multiplier: 1\n"
"kind: mole; exponent: 1; scale: -3; multiplier: 1\n",
"kind: litre; exponent: -1; scale: 0; multiplier: 1\n"
]
}
],
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.9.15"
}
},
"nbformat": 4,
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