Monday, 21 April 2014

Fwd: Welcome to the Google Genomics Preview

Sweet!!

---------- Forwarded message ----------



Welcome to the Google Genomics Preview! You've been approved for early access to the API.

The goal of the Genomics API is to encourage interoperability and build a foundation to store, process, search, analyze and share tens of petabytes of genomic data.


We've loaded sample data from public BAM files:

* The complete 1000 Genomes Project

* Selections from the Personal Genome Project


How to get started:

* Follow the instructions in the developer documentation

* Try the sample genome browser which calls the API

* Try out the other open source examples -- an R script, Python MapReduce, and a Java file-based implementation

* Write your own code to call the API and explore new uses


This is only the beginning. Your feedback will be essential to make the API useful. Please submit feature requests, bugs and suggestions on our GitHub page.


Thank you for being part of the first wave. If you'd rather join with a different email address (Gmail or Google Apps domain), please fill out the request form with that address too, and we'll grant access soon. Thank you for your interest!


Sincerely,

The Google Genomics team


Friday, 18 April 2014

GEN | News Highlights:A Chromosomal Rearrangement by Any Other Name

http://www.genengnews.com/gen-news-highlights/a-chromosomal-rearrangement-by-any-other-name/81249761/?kwrd=Next-Generation%20Sequencing

A standard way of describing chromosomal rearrangements would help clarify an already perplexing problem

Tuesday, 25 March 2014

Monocle is a R toolkit for analyzing single cell expression experiments



---------- Forwarded message ----------
From: Cole Trapnell <cole cs.umd.edu>
Date: Mon, Mar 24, 2014 at 11:51 PM
Subject: [Bowtie-bio-announce] Monocle 0.99.0
To: bowtie-bio-announce lists.sourceforge.net


I am proud to announce the first release of the Monocle analysis toolkit for single-cell RNA-Seq and qPCR.  Monocle performs differential expression and time series analysis for single-cell expression experiments.  You can read about Monocle and its “pseudo time” analysis of biological processes in the paper, which just appeared on Nature Biotech’s AOP list:


http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2859.html


The Monocle source code and support site is also live:


http://monocle-bio.sourceforge.net/index.html


I hope you will consider using Monocle for your single-cell expression analysis workflow!  Please report any issues on the new Monocle google group:


https://groups.google.com/forum/#!forum/monocle-users


Note that Monocle is currently considered an ALPHA release - new features and interfaces changes will be coming in future releases, along with significant new functionality. The release announcement for Monocle v 0.99.0 is below.


Best,


Cole


0.99.0 release - 3/23/2014

The first public release of Monocle is now available for download. Monocle is a toolkit for analyzing single cell expression experiments. It runs on the R statistical computing platform.

Monocle takes as input a matrix of gene or transcript expression values, along with information about each cell in the experiment, and some annotation about each gene/transcript, both provided as simple tables. It is designed for single-cell RNA-Seq experiments, but in principle Monocle can be used with other data types such as qPCR. For RNA-Seq, you can useCufflinks to estimate your expression values.

This software is a work in progress - it is a beta release, and new features will continue to be added over the next couple of weeks. To suggest a feature or report a bug, please post your comments on the Monocle user's group.


-- 
Cole Trapnell

https://lists.sourceforge.net/lists/listinfo/bowtie-bio-announce


Wednesday, 5 March 2014

Google Genomics -- Google Developers

https://developers.google.com/genomics/ Google genomics limited preview is out.
Been wondering when and how they might do genomics.
Now suddenly it's scarier to link all ur google accounts together. 

Maybe we will see gene association studies with different online surfing habits very soon! *chuckles*

Thursday, 27 February 2014

It's been a while ... Python 3 print is now a function

Gosh it's definitely telling that I haven't been coding in Python 3 for a while.

I didn't know that they have changed the print statement to a function. So now I need parentheses

for details see
http://stackoverflow.com/questions/937491/invalid-syntax-when-using-print

Tuesday, 28 January 2014

Growth slows in cloud business

Has the cloud hype died down? Seagate reportedly misses analyst's estimates as growth slowed in it's cloud storage business. With the exception of Galaxy or Basespace, it's hard to get researchers to buy into the cloud analysis paradigm even though their sporadic usage pattern would fit nicely for the economics of cloud usage. Maybe the cost of storage space / moving files into the cloud is the biggest hurdle.  My two cents.


Datanami, Woe be me