You can now check the element with BeautifulSoup. You can open the same file with your favorite text editor (Sublime Text 3 for me) and Prism to check the table names and data structure. # read the pzfx file and parse it to bs4 xml data We will replace existing table with new data. The pzfx to start with should already contains the tables and graphs you want. Here is what I did: from bs4 import BeautifulSoup # read and write XML Unfortunately, there is no python module for this purpose yet. It is indeed intended for automated data manipulation. I found out that since version 5, Graphpad Prism stores its data in XML format in its pzfx files. And I often am not sure if I have copy the wrong data or pasted to the right place or not, or whether I completely skipped anything, because the data looks so similar.Īfter a couple of iterations, I realize this has to be automated. It may only take his computer minutes to run, or hours I am not sure (but it is his computer, not his hand.) It takes me a lot of time to redo the copy-and-paste. Every time we change something or have a new idea, my collaborator sends me a new set of simulated data. Soon, as the collaboration progress, I found it is unsustainable. 2 genotypes x 4 residual errors measuring fitting goodness x 100 runs.Īs you can see, I need to put all these data into Prism to make good looking figures.2 genotypes x 10 ( fitted parameters + standard deviations).2 genotypes x 5 cell species x 200 simulated times points.Simulations: 4 simulations, each contains:.Experiment data: 2 genotypes x 5 cell species x 7 times points x 3 replicates. He sends me his model fitting and simulation results in a set of CSV files. I am working on a mathematical modeling figure using Graphpad Prism.
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