Q&A in E_Coli code

1. why you transponse muD twice?

==============================
muD = net.exp.D; % muD's first column is biased column, row = 'to', col = 'from'
tmp = muD(:,2:end)'; % tmp = transpose of muD, such that in tmp row = 'from', col = 'to'

for j = 1:length(from_idx)

tmp(from_idx(j),to_idx(j)) = double(conn_attr(j))*tmp(from_idx(j),to_idx(j))*mu; % keep it row = 'from', col = 'to'
end

muD(:,2:end) = tmp'; % go back to muD's original format, i.e. row = 'to', col = 'from'
==============================

2. And are the row, column indices in from_idx, to_idx counted with the bias column included?
i.e in the E_coli example from_idx = 27. Does this mean gene 26 (with + 1 from bias column)?

from_idx, to_idx , conn_attr , all derived from the shift network prior:
% hns pp glpC 1
% hns pp glpQ 1
% hns pp cyoD 0
% hns pp cyoE 0
% hns pp cyoB 0
% hns pp cyoA 0
% hns pp sdhB -1
% hns pp arcA 0
% hns pp appY -1
% hns pp cadA -1
% hns pp cadB -1
% hns pp hdeB -1

hns is the 27th gene in common_genereg_names.mat, which is already in the E_Coli.zip, subdirectory 'step1-make_yn_inpn\matdata'.

common_genereg_names.mat is extracted from 'top50&reg.sif' and vsn-normalization.xls. Please refer this post (after Download) for detail.
.
Values in conn_attr.mat are 1 (positive), -1(negative) or 0 (none).