[Biopython] Bioinformatics with Python cookbook

[Chris Mitchell]

I noticed that as well bow, but it's only for pages that are opened in a
new tab.

Really good stuff all in all.

Sent from my phone
On Jul 8, 2015 8:07 PM, "Wibowo Arindrarto" <w.arindrarto at gmail.com> wrote:

> Hi Tiago,
>
> Congratulations on publishing the book! +1 as well for using notebooks
> and putting them on GitHub (and using many of the up-and-coming
> libraries ~ I see e.g. numba and spark there :) ).
>
> One small note, apparently the direct links to the other notebooks in
> the Welcome.ipynb notebook is not working properly in the
> GitHub-rendered page. Looks like this is something from GitHub, though
> (i.e. the way they render notebook links in notebooks). Anyway, just
> in case you haven't noticed :).
>
> Cheers,
>
> On Wed, Jul 8, 2015 at 8:02 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
> > Wow, nice going, Tiago. Will buy!
> >
> > On Tue, Jul 7, 2015 at 6:26 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
> >
> >
> >
> >
> > --
> > Iddo Friedberg
> > http://iddo-friedberg.net/contact.html
> > ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> > ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> > .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
> >>>----.<--.>++++++.<<<<------------------------------------.
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
> _______________________________________________
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