Chris Villalta Ph.D.

Molecular Biologist and Bioinformatics Scientist with NGS experience


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Setting Up Jupyter Lab Server

I recently decided to try out the alpha version of Jupyter Lab the next step in the Ipython notebook. Below is a screenshot from the Jupyter blog post where Jupyter Lab was announced. I like that now files can be organized easily by date and there can be several windows and it reminds me of ipython notebook meeting pycharm.

jlab-screenshot-nb-con-term-2

There is a link to github where you can download the most up to date alpha version of Jupyter Lab (link here). The instruction on github were easy to follow.

I decided to set up an jupyter lab server using the step below, which I have used to set up ipython notebook servers in the past.

1. Create IPython profile (type command in unix shell)
ipython profile create
2. Activate SSL (type command in unix shell)
openssl req -x509 -nodes -days 365 -newkey rsa:1024 -keyout mycert.pem -  out mycert.pem
3. Add notebook password to config file

Open ipython (type command in unix shell):

ipython

Enter commands below in ipython window:

from IPython.lib import passwd
passwd()

#enter a pw
#verify the  pw
#copy hash key to clipboard

4. Open emacs and make the following file (type command in unix window):
emacs ~/.ipython/profile_default/ipython_notebook_config.py

Input the following into emacs:

c = get_config()
c.NotebookApp.password = u’{paste clipboard a.k.a the hash key}'

5. Start IPython notebook using SSL
ipython notebook --ip='{input your ip address you are using}' --no-browser  --certfile=mycert.pem
6. Start IPython notebook from browser
"https://server/ipaddres:[assigned_port]"

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Search begins for new NGS opportunity. 

I have not updated this blog in 2 years because back in April 2015 I landed a job at Invitae one of the many NGS (next generation sequencing) genetic screening companies trying to change the system and move to more cost efficient multi panel genetic tests for people who have genetic susceptibility or been diagnosed with diseases ranging from cancer to neurological disorders. 
I enjoyed my time at Invitae as a Bioinformacist for the Assay Development team, but now I am looking for a new job, so I will have more time to post on this site as I search for employment. 
I am interested in a job where I can work in the wet lab and use my bioinformatic skills, which would make me a strong researcher. I am also interested in a position where I can continue to be a Bioinformarics specialist. 
I am looking forward to and excited about what new opportunities I will find next!
Thanks,

Chris Villalta Ph.D.


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MAMP (OSX, Apache, MySQL, and Python) installation in OSX Yosemite 10.10 using Brew

iyware

I found this tutorial from iyWare that goes through installing MAMP on OSX Yosemite since a few things have changed since Mavericks. The tutorial uses brew which I think is a great package manager for OSX and has been helpful the last couple of months. It’s pretty cool that the homebrew package manager comes up first when googled considering it has nothing to do with beer making.


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New Penicillium,found on salami during seasoning process, named and described.

Herz_szalámi_plakát(image from wikipedia)

I came across this publication from the Journal of Food Microbiology and it looks like a newly described species, named of course, Penicillium salamii, appears to be found on salami and other cured meats during the seasoning process. While it seems to colonize cured meat the fungus appears to be cosmopolitan and was also found on tea leaves and in soil samples. From scanning the paper looks like the new species does form a distinct clade by maximum parsimony analyses. I hope the next step is to sequence the genome.

Link to the article (Its behind a science direct paywall).


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O’Reilly Books UC Library Subscription

Screen Shot 2014-10-29 at 11.32.43 AM

I was happy to find out that the UC library system has a subscription to all the O’Reilly books. Currently I have began reading the Learning MySQL second edition. The books are on safari books online. Here is the UCSF library link. As a sidenote Safari Books online seems to work ok when not in mobile format, because you can highlight and make notes.