Release of IPython 6.0

It is with great pleasure that today we released IPython 6.0 — almost a year after the 5.0 version. Users on Python 3.3 and above can get this latest version with all its new features by asking your package manager to upgrade IPython. If you are using pip:

Source: Release of IPython 6.0

New Pynnotator released!

Pynnotator New Release!

This new release brings a lot more stability for this annotation pipeline!

Now you can use Docker for running in any machine and also it accepts .vcf and .vcf.gz files as an input.

I updated all the tools (Ex. snpeff and vep) and databases (decipher, 1000genomes, dbsnp and dbnfsp)
Data and Lib Files are now hosted on Google Cloud!

├── 1000genomes
│   ├── ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz
│   └── ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi
├── dbnsfp
│   ├── dbNSFP3.4a.txt.gz
│   ├── dbNSFP3.4a.txt.gz.tbi
│   ├── dbscSNV1.1.txt.gz
│   └── dbscSNV1.1.txt.gz.tbi
├── dbsnp
│   ├── All_20170403.vcf.gz
│   ├── All_20170403.vcf.gz.tbi
│   ├── clinvar.vcf.gz
│   └── clinvar.vcf.gz.tbi
├── decipher
│   ├── DDG2P.csv.gz
│   ├── HI_Predictions_Version3.bed.gz
│   ├── HI_Predictions_Version3.bed.gz.tbi
│   └── population_cnv.txt.gz
├── ensembl
│   ├── Homo_sapiens_clinically_associated.vcf.gz
│   ├── Homo_sapiens_clinically_associated.vcf.gz.tbi
│   ├── Homo_sapiens_phenotype_associated.vcf.gz
│   └── Homo_sapiens_phenotype_associated.vcf.gz.tbi
├── esp6500
│   ├── esp6500si.vcf.gz
│   └── esp6500si.vcf.gz.tbi
├── snpeff_data
│   └── GRCh37.75
└── vep_cache
└── homo_sapiens
└── 88_GRCh37

705 directories, 11839 files

├── annotation.validated.vcf.gz
├── examples
│   ├── miller.vcf.gz
│   ├── NA12878.compound_heterozygous.vcf.gz
│   ├── NA12878.dominant.vcf.gz
│   ├── NA12878.recessive.vcf.gz
│   ├── NA12878.xlinked.vcf.gz
│   └── schinzel_giedion.vcf.gz
└── sample.1000.vcf

How to run it?

Requires at least 65GB of disk space during installation and 35GB after installed.

1º Method::

docker-compose run pynnotator -i pynnotator/tests/sample.1000.vcf
docker-compose run pynnotator -i sample.vcf.gz

2º Method::

# Using Ubuntu 16.04 LTS

sudo apt-get install gcc git python3-dev zlib1g-dev virtualenvwrapper make zip
source /etc/bash_completion.d/virtualenvwrapper
mkvirtualenv -p /usr/bin/python3 mendelmd
pip install cython
pip install pynnotator
pynnotator install

#And them finally:
pynnotator -i sample.vcf
pynnotator -i sample.vcf.gz

Welcome to Mendel,MD’s documentation! — 0.2 documentation

Indices and tables

Source: Welcome to Mendel,MD’s documentation! — 0.2 documentation


1. Introduction

It has been claimed that everyone has a different “learning style”.

But everyone surely has a different “studying style”.

More importantly, the way that you are studying right now might not be the best for you:
How would you know? Easy: If your grades aren’t what you’d like them to be, then you probably need to change how you study!

One important clarification before we begin:

“Studying” is not the same thing as “doing homework”!

Studying may include doing homework, but it is also a lot more, as you will see.
(So, if you say that you have no homework and that therefore you can’t, or you don’t have to, study, you’re mistaken!)

I am going to give you some suggestions on how to study efficiently. They worked for me when I was in high school, college, and graduate school.
Not only that, but they worked equally well for me in humanities courses (like philosophy and literature) and in science courses (like math and computer science).

But, to the extent that everyone’s learning style may be different, some of my suggestions may not work for you, at least not without some individual modifications.
Nevertheless, I urge you to try them. Most successful students use them (or some slight variation of them).


Jupyter Notebook 5.0

We are pleased to announce the release of Jupyter Notebook version 5.0. This is the first major release of the Jupyter Notebook since version 4.0 and the “Big Split” of IPython and Jupyter. This release adds some long-awaited features, such as cell tagging, customizing keyboard shortcuts, copying &

Source: Jupyter Notebook 5.0