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  • FASIMU: Constrained optimization of metabolic networks - Message forums

    Discussion forums: Open Discussion

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    Welcome to Open Discussion
    Submitted by Unset; posted on Wednesday, December 16, 2009
    Welcome to Open Discussion
    Can't find allout2bina, allout2valfiles
    Submitted by Arnab Roy; posted on Friday, March 07, 2014
    Hello, In the FASIMU Manual and Tutorial 'allout2bina' and 'allout2valfiles' have been mentioned to be used to convert the 'allout.txt' output to the corresponding visualization compatible programs. But I could not find any of the two conversion files either in FASIMU package or in CyFluxViz or in BiNA packages. Although the 'All.csv' was already there inside BiNA folder after I ran 'simulate' and it worked well with BiNA, it will be highly appreciable if I have the access of 'allout2bina' and 'allout2valfiles'. It would give the opportunity to view and explore the results in Cytoscape also. Hoping for the best and looking forward to your reply(s). Arnab PhD student Indian Institute of Science Bangalore, INDIA
    Re: Can't find allout2bina, allout2valfiles
    Submitted by Andreas Hoppe; posted on Tuesday, August 19, 2014
    Assuming a simulation with the name "All", allout2bina writes a file All.csv in the BiNA directory. It is overwritten on a subsequent run of allout2bina. "simulate" does not write "BiNA/All.csv", it will hold the result of the previous run of allout2bina. To have an up-dated "All.csv", first call "simulate", then "allout2bina". "allout2valfiles" works in the same way, it writes val/All.txt from the actual allout.txt, the result from the last "simulate". Cheers Andreas Hoppe
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