Wednesday, 12 April 2017

Control a fleet of embedded unix systems (eg Raspberry Pi, Orange Pi) using saltstack

HAHAHA I share the same name as a software project. Bizarre discovery today

https://github.com/unixbigot/kevin
Control a fleet of embedded unix systems (eg Raspberry Pi, Orange Pi) using saltstack

Tuesday, 11 April 2017

github-based, community-maintained list of cancer clinical informatics resources


Sean Davis created a github-based, community-maintained list of cancer clinical informatics resources. 
"Contributions are welcome!" https://lnkd.in/d-uphUc

For now, it's named as
ci4cc-informatics-resources 

Tuesday, 29 November 2016

Verily (Google) is hiring Computational Biologists

https://www.google.com/about/careers/search?src=Online/Job+Board/indeed#!t=jo&jid=228815001&

the role is described as 'hardware engineering' interestingly. the preferred qualifications are very loose...

  • Demonstrated knowledge of core concepts in machine learning or probability and statistics.
  • Willingness to learn molecular and cell biology, computer science, and statistics.
  • Demonstrated effective written and verbal communication skills.


I bet they will be inundated with submissions! 

Wednesday, 9 November 2016

Compiling BWA on Ubuntu 16.04.1 LTS

#install prereq else you will get utils.c:33:18: fatal error: zlib.h: No such file or directory
sudo apt-get install zlib1g-dev

#download the latest version and compile
$ wget http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.12.tar.bz2
$ tar jxvf bwa-0.7.12.tar.bz2
$ cd bwa-0.7.12/
$ make 

Wednesday, 18 May 2016

CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer

CIViC's Role in Precision Medicine

Realizing precision medicine will require this information to be centralized, debated and interpreted for application in the clinic. CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. Our goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations.
CIViC is a community-edited forum for discussion and interpretation of peer-reviewed publications pertaining to the clinical relevance of variants (or biomarker alterations) in cancer. These interpretations may include associations between molecular alterations (or lack of alteration) and one or more drugs, diagnoses, prognoses or other treatment decisions. These interpretations of clinical significance (or lack of clinical significance) are purely for research purposes. A finding of no interpretation does not necessarily indicate lack of relevance for any specific variant or biomarker alteration. Interpretations are not presented in ranked order of potential or predicted importance.These interpretations make no promise or guarantee of any clinical benefit (or lack of clinical benefit).


Thursday, 5 May 2016

Verily Life Sciences new hires

http://www.bizjournals.com/sanfrancisco/blog/biotech/2016/05/google-alphabet-goog-verily-life-sciences-amgen.html

I guess scouting a company's recruitment page to understand the projects is a universally common thing. Interestingly this page even has a word cloud from the LinkedIn Profiles to see where the hires are previously from.


The new hires reflect the scope of the few Verily projects Google/Alphabet has allowed to escape to the public so far: a contact lens venture with Novartis AG for diabetics to track blood glucose levels, its buyout of a company with a spoon that counters shaking by Parkinson's disease patients and the big picture Baseline study, a deep research project designed to define a healthy human being."The future of biotech, medical and tech is going to coalesce. We've seen that with medical sensors that do more than count steps, artificial intelligence and virtual reality," Topol said. "All these things are going to have a big impact in medicine. It's a natural evolution." excerpted from @SFBusinessTimes 


Datanami, Woe be me