[Biopython] Bioinformatics with Python cookbook

[Wibowo Arindrarto]

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
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