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How can I get the dataset for all the 43 metabolic networks for this paper: https://www.nature.com/articles/35036627

It looks like the WIT database does not exist anymore.

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It seems like there are some files related to the databases at the ftp site: http://ftp.mcs.anl.gov/pub/WIT2/. The related files were last updated on 2002.

I found it via searching at google: site:*.mcs.anl.gov/ WIT.

Which reports also a page about the database. There seems to be a project to develop WIT3, because there is a mailing list for developers, maybe you can ask them more details if you have problems with the database.

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