Location: Chen, Calzone, Csikasznagy, Cross, Novak, Tyson, 2004 @ 433bd6bdd21f / chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml

Author:
Mathieu Deneux <mathieu.deneux@gmail.com>
Date:
2016-07-29 17:19:42+12:00
Desc:
Added a SEDML file
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