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The networkx (python package) was used for network topological analysis60.
Cufflinks package was used to estimate expression profile42, 43.
In the numerical analysis, ANSYS 12.0 software package was used.
For this purpose, the OpenSees computer package was used.
A commercial finite element method package was used.
Echem Analyst 5.0 software package was used for data fitting.
A SPSS package was used to analyze the data.
The Gaussian 03 program package was used [26].
Concord from the Wordsmith Package was used for this purpose.
HighScore Plus software package was used to identify mineral phases.
The PLINK package was used for genetic data analysis.
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