[Biopython] Bioinformatics with Python cookbook

[Tiago Antao]

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