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Fix maps in GEMs lab #273

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rasools opened this issue Oct 17, 2024 · 0 comments
Open

Fix maps in GEMs lab #273

rasools opened this issue Oct 17, 2024 · 0 comments
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rasools commented Oct 17, 2024

Stefan:
In the GEM lab '03-Pathway-visualization', you can display the map for the E. coli central carbon metabolism by using the following code in cell 3:
b=escher.Builder('e_coli_core.Core metabolism')
escher.Builder.save_html(b, filepath='data/central_carbon_e_coli.html')
The map will then show up as html in your data folder (which you can access from the location where you open the notebook)

This applies to all cells in the subsequent labs where you are trying to visualize maps with escher.Builder(). Assign the builder to a variable (as in e.g b=escher.Builder('e_coli_core.Core metabolism')) and then save it to html (as in escher.Builder.save_html(b, filepath='data/central_carbon_e_coli.html'))

@rasools rasools changed the title Fix Hi @channel, in the GEM lab '03-Pathway-visualization', you can display the map for the E. coli central carbon metabolism by using the following code in cell 3: b=escher.Builder('e_coli_core.Core metabolism') escher.Builder.save_html(b, filepath='data/central_carbon_e_coli.html') The map will then show up as html in your data folder (which you can access from the location where you open the notebook) Stefan Ebmeyer 10:43 AM @channel This applies to all cells in the subsequent labs where you are trying to visualize maps with escher.Builder(). Assign the builder to a variable (as in e.g b=escher.Builder('e_coli_core.Core metabolism')) and then save it to html (as in escher.Builder.save_html(b, filepath='data/central_carbon_e_coli.html')) (edited) maps in GEMs lab Fix maps in GEMs lab Oct 17, 2024
@rasools rasools self-assigned this Oct 17, 2024
@rasools rasools added the bug Something isn't working label Oct 17, 2024
@rasools rasools added this to the omicsint_h25 milestone Oct 17, 2024
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