libBioLCCC v.1.2.0 is released
Anton Goloborodko
Today the new version of libBioLCCC was released. This time the
improvements targeted the speed and accuracy of calculations.
Firstly, we changed the way we integrate the main equation of
chromatography. Usually we replaced the integral with a sum of small
terms dV / Vp / Kd and calculated this expression until it was greater
than 1.0. The problem with this approach was that the whole last term
was added, regardless of how much it was needed to reach 1.0. Now we
have fixed this annoying behaviour and add the last term
proportionally to remaining amount of the sum. As a result, the
dependence of calculated retention time on the value of dV is much
smaller for conventional gradients. As a matter of fact, dV = flow
rate / 10 is now enough for most of the peptides.
Secondly, in this version of libBioLCCC we introduce the fast version
of calculateRT function. Previously, we invoked the full equations to
calculate coefficient of distribution in each new concentration of
second solvent. Now we calculate Kd in two steps. At first, we
tabulate the value of Kd for several points uniformly distributed all
over the concentration range. Then we use this values to reconstruct
the whole function with cubic spline interpolation. This routine works
up to ten times faster without a significant loss of accuracy.
The further information regarding the introduced features can be found
in the chapter "Changing the precision of calculation" of libBioLCCC
documentation (http://theorchromo.ru/lib/advanced.html#changing-the-precision-of-calculation).
Note, that all these improvements are especially useful for
calibration routines. The increased calculation speed is essential
there due to the great search space.
Sincerely yours,
libBioLCCC development team.
Michael Gorshkov
Anton Goloborodko
> Great! What would be helpful then is making the calibration available for
> the users.
> MVG
The calibration function is almost ready for release. I think, it will
be published in a separate repository within a month.
Anton Goloborodko.