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
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!
│ ├── ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz
│ └── ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi
│ ├── dbNSFP3.4a.txt.gz
│ ├── dbNSFP3.4a.txt.gz.tbi
│ ├── dbscSNV1.1.txt.gz
│ └── dbscSNV1.1.txt.gz.tbi
│ ├── All_20170403.vcf.gz
│ ├── All_20170403.vcf.gz.tbi
│ ├── clinvar.vcf.gz
│ └── clinvar.vcf.gz.tbi
│ ├── DDG2P.csv.gz
│ ├── HI_Predictions_Version3.bed.gz
│ ├── HI_Predictions_Version3.bed.gz.tbi
│ └── population_cnv.txt.gz
│ ├── 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
│ ├── esp6500si.vcf.gz
│ └── esp6500si.vcf.gz.tbi
│ └── GRCh37.75
705 directories, 11839 files
│ ├── miller.vcf.gz
│ ├── NA12878.compound_heterozygous.vcf.gz
│ ├── NA12878.dominant.vcf.gz
│ ├── NA12878.recessive.vcf.gz
│ ├── NA12878.xlinked.vcf.gz
│ └── schinzel_giedion.vcf.gz
How to run it?
Requires at least 65GB of disk space during installation and 35GB after installed.
docker-compose run pynnotator -i pynnotator/tests/sample.1000.vcf
docker-compose run pynnotator -i sample.vcf.gz
# Using Ubuntu 16.04 LTS
sudo apt-get install gcc git python3-dev zlib1g-dev virtualenvwrapper make zip
mkvirtualenv -p /usr/bin/python3 mendelmd
pip install cython
pip install pynnotator
#And them finally:
pynnotator -i sample.vcf
pynnotator -i sample.vcf.gz
- Other Libraries Needed
- OMIM Data
- Manual Installation
- Installing PostgreSQL Database
- Installation on Ubuntu 16.04 LTS (tested)
- Installing the Pynnotator
- Installing Mendel,MD
- Creating a superuser
- Importing Data
- Upload your VCFs using the web interface
- Start the annotation
- Deployment on RedHat/CentOS 7
- Clinical Cases
- Filter Analysis
- One Click
- Family Analysis
- Individuals Options
- VCF Options
- Annovar Options
Getting Genetics Done (GGD) is a blog with tips, reviews, tutorials, and pointers to relevant literature in genetics and bioinformatics research.
It has been claimed that everyone has a different “learning style”.
- If you believe in the existence and validity of learning styles, then you might find some of the following references of interest:
- Claxton & Murrell 1987,
- “Learning Styles” (Wikipedia),
- Keirsey Temperament and Character Web Site,
- William Perry’s Scheme of Intellectual and Ethical Development,
- Holland 1966,
- Kolb 1984,
- Sternberg 1999.
- For some online tools targeted at different learning styles, see “100 Helpful Web Tools for Every Kind of Learner”.
- However, there is no evidence that supports their use! The major study is Pashler et al. 2009; see also Glenn 2009/2010.
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).
Source: HOW TO STUDY
Source: Unsupervised sentiment neuron
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