<p dir="ltr">I noticed that as well bow, but it's only for pages that are opened in a new tab.</p>
<p dir="ltr">Really good stuff all in all. </p>
<p dir="ltr">Sent from my phone</p>
<div class="gmail_quote">On Jul 8, 2015 8:07 PM, "Wibowo Arindrarto" <<a href="mailto:w.arindrarto@gmail.com">w.arindrarto@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Tiago,<br>
<br>
Congratulations on publishing the book! +1 as well for using notebooks<br>
and putting them on GitHub (and using many of the up-and-coming<br>
libraries ~ I see e.g. numba and spark there :) ).<br>
<br>
One small note, apparently the direct links to the other notebooks in<br>
the Welcome.ipynb notebook is not working properly in the<br>
GitHub-rendered page. Looks like this is something from GitHub, though<br>
(i.e. the way they render notebook links in notebooks). Anyway, just<br>
in case you haven't noticed :).<br>
<br>
Cheers,<br>
<br>
On Wed, Jul 8, 2015 at 8:02 PM, Iddo Friedberg <<a href="mailto:idoerg@gmail.com">idoerg@gmail.com</a>> wrote:<br>
> Wow, nice going, Tiago. Will buy!<br>
><br>
> On Tue, Jul 7, 2015 at 6:26 AM, Tiago Antao <<a href="mailto:tra@popgen.net">tra@popgen.net</a>> wrote:<br>
>><br>
>> Dear all,<br>
>><br>
>><br>
>> I would like to announce "Bioinformatics with Python Cookbook" which I<br>
>> authored. As you might imagine Biopython is discussed heavily in the<br>
>> book.<br>
>><br>
>> This book is slightly different from the standard books on<br>
>> Bioinformatics and Python. It is not about teaching Bioinformatics<br>
>> algorithms, but about solving practical day-to-day problems with<br>
>> Python, for example:<br>
>><br>
>> Next-Generation Sequencing: FASTQ, BAM and VCF processing. Along with<br>
>> filtering of datasets.<br>
>><br>
>> Genomics: processing reference genomes of both high-quality references<br>
>> of model species and low-quality non-model species. Also discussed are<br>
>> genome annotations and gene ontologies.<br>
>><br>
>> Population Genetics: doing PCA, Admixture/Structure, computing FSTs, ...<br>
>><br>
>> Genome simulation: mostly forward-time simulations, but also a bit of<br>
>> coalescent<br>
>><br>
>> Phylogenetics: tree reconstruction and tree drawing<br>
>><br>
>> Proteins: PDB processing and visualization.<br>
>><br>
>> Other topics like processing map data, GBIF, interfacing with<br>
>> Cytoscape, accessing lots of online databases, ...<br>
>><br>
>> There is a bit on interacting with R/Bioconductor via Python.<br>
>><br>
>> Finally we discuss high-performance in Python: faster algorithms,<br>
>> clusters, Numba and Cython. Also related technologies like Docker<br>
>><br>
>> The book discusses the usual Python Libraries in the field: Biopython,<br>
>> PyVCF, Pysam, simuPOP, DendroPy, Pymol and also scientific libraries<br>
>> like NumPy, SciPy, matplotlib and scikit-learn.<br>
>><br>
>> The code is fully available for free at github<br>
>><br>
>> <a href="https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb" rel="noreferrer" target="_blank">https://github.com/tiagoantao/bioinf-python/blob/master/notebooks/Welcome.ipynb</a><br>
>><br>
>> I am keen on maintaining the book code, so if you find any issues<br>
>> please do contact me.<br>
>><br>
>> The book is available in the usual places (Amazon, etc.) in paperback<br>
>> and e-book format. The web page of the book is<br>
>><br>
>> <a href="https://www.packtpub.com/application-development/bioinformatics-python-cookbook" rel="noreferrer" target="_blank">https://www.packtpub.com/application-development/bioinformatics-python-cookbook</a><br>
>><br>
>> Regards,<br>
>> Tiago<br>
>> _______________________________________________<br>
>> Biopython mailing list - <a href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br>
>> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython" rel="noreferrer" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
><br>
><br>
><br>
><br>
> --<br>
> Iddo Friedberg<br>
> <a href="http://iddo-friedberg.net/contact.html" rel="noreferrer" target="_blank">http://iddo-friedberg.net/contact.html</a><br>
> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.><br>
> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.<br>
> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>><br>
>>>----.<--.>++++++.<<<<------------------------------------.<br>
><br>
> _______________________________________________<br>
> Biopython mailing list - <a href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython" rel="noreferrer" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
_______________________________________________<br>
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</blockquote></div>