Friday, November 28, 2014

Continuous integration servers


Jenkins
http://jenkins-ci.org/

Bamboo
https://confluence.atlassian.com/display/BAMBOO/Bamboo+Documentation+Home

Wednesday, November 26, 2014

PLOS Computational Biology: Translational Bioinformatics

http://www.ploscollections.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcol.v03.i11

Education Articles

Chapter 2: Data-Driven View of Disease Biology

Casey S. Greene, Olga G. Troyanskaya

Chapter 4: Protein Interactions and Disease

Mileidy W. Gonzalez, Maricel G. Kann

Chapter 5: Network Biology Approach to Complex Diseases

Dong-Yeon Cho, Yoo-Ah Kim, Teresa M. Przytycka

Chapter 7: Pharmacogenomics

Konrad J. Karczewski, Roxana Daneshjou, Russ B. Altman

Chapter 9: Analyses Using Disease Ontologies

Nigam H. Shah, Tyler Cole, Mark A. Musen

Chapter 10: Mining Genome-Wide Genetic Markers

Xiang Zhang, Shunping Huang, Zhaojun Zhang, Wei Wang

Chapter 11: Genome-Wide Association Studies

William S. Bush, Jason H. Moore

Chapter 12: Human Microbiome Analysis

Xochitl C. Morgan, Curtis Huttenhower

Chapter 14: Cancer Genome Analysis

Miguel Vazquez, Victor de la Torre, Alfonso Valencia

Chapter 16: Text Mining for Translational Bioinformatics

K. Bretonnel Cohen, Lawrence E. Hunter

Chapter 17: Bioimage Informatics for Systems Pharmacology

Fuhai Li, Zheng Yin, Guangxu Jin, Hong Zhao, Stephen T. C. Wong

Thursday, November 20, 2014

threejs - makes WebGL - 3D in the browser - very easy

http://threejs.org/docs/index.html#Manual/Introduction/Creating_a_scene

Three.js is a library that makes WebGL - 3D in the browser - very easy. While a simple cube in raw WebGL would turn out hundreds of lines of Javascript and shader code, a Three.js equivalent is only a fraction of that.

Google Genomics

https://cloud.google.com/genomics/v1beta2/visualization

Google Genomics provides an API to store, process, explore, and share DNA sequence reads, reference-based alignments, and variant calls, using Google's cloud infrastructure.

    Store alignments and variant calls for one genome or a million.
    Process genomic data in batch by running principal component analysis or Hardy-Weinberg equilibrium, in minutes or hours, by using parallel computing frameworks like MapReduce.
    Explore data by slicing alignments and variants by genomic range across one or multiple samples -- for your own algorithms or for visualization; or interactively process entire cohorts to find transition/transversion ratios, allelic frequency, genome-wide association and more using BigQuery.
    Share genomic data with your research group, collaborators, the broader community, or the public. You decide.

Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

Cluster computing
https://spark.apache.org/downloads.html

Google BigQuery
https://cloud.google.com/bigquery/what-is-bigquery

Thursday, November 13, 2014

10 New Breakthrough Technologies 2014

http://www.technologyreview.com/lists/technologies/2014/


Agricultural Drones
Ultraprivate Smartphones
Brain Mapping
Neuromorphic Chips
Genome Editing
Microscale 3-D Printing
Mobile Collaboration
Oculus Rift
Agile Robots
Smart Wind and Solar Power

Monday, November 10, 2014

Alzheimer's drug sneaks through blood–brain barrier

Neurobiologist Ryan Watts and his colleagues at the biotechnology company Genentech in South San Francisco have sought to break through the barrier by exploiting transferrin, a protein that sits on the surface of blood vessels and carries iron into the brain. The team created an antibody with two ends. One end binds loosely to transferrin and uses the protein to transport itself into the brain. And once the antibody is inside, its other end targets an enzyme called β-secretase 1 (BACE1), which produces amyloid-β. Crucially, the antibody binds more tightly to BACE1 than to transferrin, and this pulls it off the blood vessel and into the brain. It locks BACE1 shut and prevents it from making amyloid-β.

http://www.nature.com/news/alzheimer-s-drug-sneaks-through-blood-brain-barrier-1.16291