Latex

Anyway, one of the things our group has been up to in the last two weeks, is writing a book to support of the free, online Pharmaceutical Bioinformatics course. The material includes a good deal of cheminformatics (molecular representation: chemical graph theory, 3D geometries, file formats, line notations, InChI), bioinformatics (sequence analysis), and statistics (PLS, PCA, proteochemometrics). All in light of drug discovery. Of course, we’re using LaTeX, and I asked around here and there about related things. For example, on StackOverflow on educational book styles. But also on FriendFeed on tautomerism in relation to drug activity.

Bioclipse

I also hacked up a Bioclipse plugin that allows me to convert a Bioclipse matrix resource into LaTeX source code, but that will not be part of the Bioclipse 2.2 release, as it requires quite some updating of the statistics functionality. BTW, the LaTeX plugin is hosted at Gitorious, which is an GitHub alternative, but does not seem to have post-commit hooks :(

Also, the Bioclipse2 paper “Bioclipse 2: A scriptable integration platform for the life sciences” has been published now in BMC Bioinformatics (DOI:10.1186/1471-2105-10-397)!

New student

I am also happy to have a second student starting in January, who will work primarily on an RDF version of the ChEMBL data. Her work will extend on the excellent work being done right now by Samuel on comparing Prolog with DL reasoning.

CDK Licensing

Another thing that required my attention was the problem brought up by Andew on licensing. There was considerable out-of-date problems with the statements the CDK makes on the license and copyright informations certain CDK modules use, and the implications that has on what the CDK project is required to do (e.g. link to source code of third party libraries) and for downstream CDK distributors, like the Debian and Ubuntu projects. For example, it became apparent that the Debian package cannot distribute the XML Schema of CML, which is CC-BY-ND which is not DSFG-compatible. A few bugs have been reported, and work is ongoing to fix the issues.

But wait, LaTeX can do more; why not have a color and a grayscale option? Here comes optional.sty. By adding \usepackage{optional} I can add to the source (from book.tex):

\begin{figure}[bt]
\begin{center}
  \subfigure[]{
    \label{fig:benzene:a}
    \opt{color}{\includegraphics[width=0.4\textwidth]{intro/benzoCompounds_color}}
    \opt{grayscale}{\includegraphics[width=0.4\textwidth]{intro/benzoCompounds}}
  }
  \hspace{2cm}
  \subfigure[]{
    \label{fig:benzene:b}
    \includegraphics[width=0.18\textwidth]{intro/Ferrocene-2D}
  }
\end{center}
\caption{a) 2D diagrams of the two possible resonance structures of a compound
with a phenyl ring. Both diagrams refer to the same compounds, but the depicted
graph representations are not identical. b) 2D diagram of ferrocene, which,
like all organometallic compounds,
is difficult to represent with classical chemoinformatics approaches.}
\label{fig:benzene}
\end{figure}

Ferrocene was already black-and-white, so no worry about that. And, it is just the red colored hydroxyl group. But it serves the point :)

Which then allows me to run pdflatex to create a color version and a grayscale version:

pdflatex "\def\UseOption{color}\input{book}"
pdflatex "\def\UseOption{grayscale}\input{book}"

/me is happy