[Biopython] Bioinformatics with Python cookbook

[Fields, Christopher J]

Nice Tiago, congrats!

Chris

> On Jul 7, 2015, at 8:47 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
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