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Human 1.18 #735

Merged
merged 140 commits into from
Dec 8, 2023
Merged

Human 1.18 #735

merged 140 commits into from
Dec 8, 2023

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haowang-bioinfo
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@haowang-bioinfo haowang-bioinfo commented Dec 3, 2023

Main improvements in this PR:

mihai-sysbio and others added 30 commits March 23, 2023 11:40
style: merge "Heme biosynthesis" subsystem into "Porphyrin metabolism"
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Updated essentiality evaluation using combined (all) Hart2015 datasets:

version TP TN FP FN accuracy sensitivity specificity F1 MCC
v1.12 40 2333 175 77 0.904000000000000 0.341880341880342 0.930223285486443 0.240963855421687 0.204768560393159
v1.13 40 2334 174 77 0.904380952380952 0.341880341880342 0.930622009569378 0.241691842900302 0.205504558241293
v1.14 40 2334 175 77 0.904036557501904 0.341880341880342 0.930251096054205 0.240963855421687 0.204787829413435
v1.15 40 2342 168 77 0.906737723639132 0.341880341880342 0.933067729083665 0.246153846153846 0.210053956889428
v1.16 41 2308 202 76 0.89417587 0.35042735 0.91952191 0.22777778 0.19220101
v1.17 41 2263 237 75 0.880733944954129 0.353448275862069 0.905200000000000 0.208121827411168 0.172768250444715
v1.18 42 2260 245 74 0.878290728729493 0.362068965517241 0.902195608782435 0.208436724565757 0.174052567331894

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@haowang-bioinfo thank you for updating the essentiality results

I was playing around yesterday with two different solvers on a knockout panel and I got different results, so I am wondering if the same solver has been used in all the evaluations since v1.12.

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Looks good! I've noticed there two commented-out metabolic tasks. I'm not really fond of having them in that state - I would propose that they are outright removed, or whatever underlying issue there is to be reported and ultimately resolved.

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haowang-bioinfo commented Dec 8, 2023

I was playing around yesterday with two different solvers on a knockout panel and I got different results, so I am wondering if the same solver has been used in all the evaluations since v1.12.

good question - for the listed analysis the same solver (gurobi 10) was used except for the results of v1.16, which was copied and I don't know what solver was specifically used

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haowang-bioinfo commented Dec 8, 2023

the PR message was just updated with #740 after its merging into v1.18, which should be enough and probably can move on to a new release?

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Looks good! I've noticed there two commented-out metabolic tasks. I'm not really fond of having them in that state - I would propose that they are outright removed, or whatever underlying issue there is to be reported and ultimately resolved.

@mihai-sysbio, where are the tasks commented out?

@haowang-bioinfo haowang-bioinfo merged commit a128e6e into main Dec 8, 2023
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@mihai-sysbio, where are the tasks commented out?

It's the Cellfie tasks here, specifically the last two commits. It makes sense for them to be commented out, but I still think it would be good to have an issue to at some point resolve this.

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@mihai-sysbio, where are the tasks commented out?

It's the Cellfie tasks here, specifically the last two commits. It makes sense for them to be commented out, but I still think it would be good to have an issue to at some point resolve this.

This most likely refers to the changes made in #697, it was actually discussed but in an atypical way, not via an issue but under a PR (#696)

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7 participants