GSoC 2024 dingo blog #35
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Thanks @SotirisTouliopoulos! That looks good. A general comment is that the text is more like a gsoc final submission. I would make a few modifications so that it would be more like a blog-post.
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| This figure illustrates a heatmap from a symmetrical correlation matrix without pearson or indicator filtering: | ||
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| <img src="https://sotiristouliopoulos.github.io/dingo/img/corr_matrix_no_cutoffs.png"><br><br> |
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It would be nice to have figures of high resolution; when you are trying to zoom in to check the reaction names you get pixels now.
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General comment: |
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| When an object is initialized from the `PreProcess` class, users can call the `reduce` function on this object to remove three types of reactions: | ||
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| - Blocked reactions: cannot carry a flux in any condition. |
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What is the meaning of "carry a flux"? Is it standard?
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Yes, it is standard. It is mentioned in this article: https://doi.org/10.1038/msb.2010.47
_posts/2024-08-24-GSoC2024-dingo.md
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| removed_reactions, reduced_dingo_model = obj.reduce(extend = False) | ||
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| Reduction with the `PreProcess` class has been tested with various models from the BiGG database <a href="#ref-2">[2]</a>. Figures below show the number of remained reactions, after applying the `reduce` function: |
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Is there a reason to have two instead of one plot?
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For better visibility. Lines overlapped when all reactions were in a single plot
Figures are loaded from my evaluation blog, because i could not find a way to load them from a folder