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Showing posts from June, 2013

A survey of the burgeoning industry of cloud genomics

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I like lists. Here is a list of companies in the cloud genomics industry.

Table 1: Companies acting in the industry of cloud genomics. The list is in no particular order.

Company Products People Founded Link GenoSpace, LLC - GenoSpace platform - John Quackenbush (CEO) 2011 https://www.genospace.com/ DNAnexus, Inc. - DNAnexus Platform - DNAnexus Platform SDK (a.k.a. dx-toolkit) - Serafim Batzoglou (co-founder) - Andreas Sundquist (co-founder and CTO) - a bunch of other famous people in the field 2009 https://dnanexus.com/ Seven Bridges Genomics, Inc. - IGOR - IGOR Python SDK - Igor Bogicevic (CTO) 2009

Spot instances that stop (or reboot) on their own: a new feature in AWS ?

So I have a spot instance for my visualization project. I am using one t1.micro instance in the spot market.

My instance is i-05cabc6a and its spot request is sir-4e01da35. It has a 64 GB EBS volume attached to it (vol-0eba4a7f) and a 8 GB EBS volume for the operating system (vol-b23d42e9).

According to the EC2 Management Console, its launch time was 2013-06-06 11:00 EDT (314 hours). This is a spot instance, it can not be stopped. It can only be terminated, or obviously it can continue to live too.


So today I was showing people my visualization project, but it did not work.

I use http://browser.cloud.raytrek.com/client for the permanent address.

In the DNS:

;; ANSWER SECTION:
browser.cloud.raytrek.com. 14113 IN     CNAME   browser-10.raytrek.com.
browser-10.raytrek.com. 14113   IN      CNAME   ec2-54-226-13-244.compute-1.amazonaws.com.
ec2-54-226-13-244.compute-1.amazonaws.com. 155620 IN A 54.226.13.244

So there was something wrong. I decided from this point to connect to my instance.

I was sur…

Open access doctoral theses on de novo genome assembly

I am presently writing my doctoral thesis.

So far, I have found four open access doctoral thesis on de novo genome assembly.


Table 1: Doctoral theses on de novo assembly in the next-generation sequencing era. Links to citeulike entries are provided on dates.


Date Person Institution January 2008 Mark Chaisson University of California, San Diego, United States of America September 2009 Daniel Robert Zerbino Darwin College, University of Cambridge, United Kingdom July 2012 Rayan Chikhi École normale supérieure de Cachan - Antenne de Bretagne, France September 2012 Jared Thomas Simpson Queens’ College, University of Cambridge, United Kingdom