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Ten-year challenge: Reproduction of An allosteric model of calmodulin [PNAS 105(31), 10768 (2008)] #38

Open MelanieIStefan opened 4 years ago

MelanieIStefan commented 4 years ago

Original article: M.I. Stefan, S.J. Edelstein, N. Le Novère (2008). An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. PNAS 105(31), 10768.

PDF URL: https://github.com/MelanieIStefan/calmodulin_reproduction/blob/master/ReScience_Calmodulin.pdf Metadata URL:
Code URL: https://github.com/MelanieIStefan/calmodulin_reproduction

Scientific domain: Systems neuroscience Programming language: SBML, R Suggested editor: This is part of the 10-year challenge, so should be handled by the challenge organisers

rougier commented 4 years ago

Thanks for your submission, I will edit it.

@apdavison Could you review this submission for the Ten Years Reproducibility Challenge?

apdavison commented 4 years ago

yes, I can review it

rougier commented 4 years ago

@apdavison Wonderful, thanks. No hard deadline for the review but the sooner the better...

rougier commented 4 years ago

@apdavison Gentle reminder

apdavison commented 4 years ago

Hi @MelanieIStefan I'm struggling a bit with this, as I haven't used Copasi before. I've got as far as loading "Figure3.cps" and running a parameter scan, but I can't figure out how to save the results (i.e. to try to recreate Figure3.txt). Please can you help me out with a detailed description of what to click on/select?

MelanieIStefan commented 4 years ago

Hi @apdavison - when you run the parameter scan, a separate window should be created by Copasi where the results are plotted. In that window, you can select "Save Data" from the menu above the plot.

Save

This should bring up a menu allowing you to save the data as a .txt file. Please let me know if this doesn't work.

apdavison commented 4 years ago

This is a well-written article, which serves as an excellent example of why reproducibility of modelling studies requires not only the model specification but also the simulation configuration and data analysis scripts to be stored.

I was able to re-run the simulations, and reproduce the data files in the repository.

Major issues:

comparison_figure3

comparison_figure4

On the basis of this, I don't think that the original parameters have been correctly recovered. I recommend an attempt is made to obtain a closer fit to the original curves (perhaps using automated parameter fitting). This might also result in a successful reproduction of Figure 5. Otherwise, I think this has to be labelled an unsuccessful reproduction and the manuscript amended accordingly.

Minor issues:

MelanieIStefan commented 4 years ago

Thank you for your thoughtful comments!

rougier commented 4 years ago

@apdavison Thanks for the detailed review. @MelanieIStefan Did you have time to address the comments ?

rougier commented 3 years ago

@MelanieIStefan Sorry for the delay. Did you have time to take comments into account?

rougier commented 2 years ago

@MelanieIStefan Should we close this submission?

MelanieIStefan commented 2 years ago

Hello! Please don't close it just yet. I know it's been a while, but I would like a chance to figure this out please.

rougier commented 11 months ago

@MelanieIStefan Any update (after 1.5 years :))