[Biopython] Bioinformatics with Python cookbook

[Bo Peng]

BTW, I would like to remind everyone that please leave a review at
amazon.com if you have read the book. This is very important for the
promotion of the book especially for the first few months.

Cheers,
Bo


On Tue, Jul 7, 2015 at 10:19 AM, Tommy Carstensen <
tommy.carstensen at gmail.com> wrote:

> Tiago, congratulations on your book. I already have "Bioinformatics
> Programming Using Python", but it's quite dated. I will buy your book.
>
> On Tue, Jul 7, 2015 at 3:16 PM, Bo Peng <ben.bob at gmail.com> wrote:
> > Hi, Tiago,
> >
> > Congratulations on the publication of the book! I wrote one and know how
> > much it takes to write a book. I am getting a copy right now.
> >
> > Cheers,
> > Bo
> >
> > On Jul 7, 2015 6:42 AM, "Tiago Antao" <tra at popgen.net> wrote:
> >>
> >> Dear all,
> >>
> >>
> >> I would like to announce "Bioinformatics with Python Cookbook" which I
> >> authored. As you might imagine Biopython is discussed heavily in the
> >> book.
> >>
> >> This book is slightly different from the standard books on
> >> Bioinformatics and Python. It is not about teaching Bioinformatics
> >> algorithms, but about solving practical day-to-day problems with
> >> Python, for example:
> >>
> >> Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with
> >> filtering of datasets.
> >>
> >> Genomics: processing reference genomes of both high-quality references
> >> of model species and low-quality non-model species. Also discussed are
> >> genome annotations and gene ontologies.
> >>
> >> Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...
> >>
> >> Genome simulation: mostly forward-time simulations, but also a bit of
> >> coalescent
> >>
> >> Phylogenetics: tree reconstruction and tree drawing
> >>
> >> Proteins: PDB processing and visualization.
> >>
> >> Other topics like processing map data, GBIF, interfacing with
> >> Cytoscape, accessing lots of online databases, ...
> >>
> >> There is a bit on interacting with R/Bioconductor via Python.
> >>
> >> Finally we discuss high-performance in Python: faster algorithms,
> >> clusters, Numba and Cython. Also related technologies like Docker
> >>
> >> The book discusses the usual Python Libraries in the field: Biopython,
> >> PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries
> >> like NumPy, SciPy, matplotlib and scikit-learn.
> >>
> >> The code is fully available for free at github
> >>
> >>
> https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb
> >>
> >> I am keen on maintaining the book code, so if you find any issues
> >> please do contact me.
> >>
> >> The book is available in the usual places (Amazon, etc.) in paperback
> >> and e-book format. The web page of the book is
> >>
> >>
> https://www.packtpub.com/application-development/bioinformatics-python-cookbook
> >>
> >> Regards,
> >> Tiago
> >> _______________________________________________
> >> Biopython mailing list  -  Biopython at mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/biopython
> >
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
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