SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Upcoming Workshop - RNA-seq Bioinformatics: A Practical Introduction ecSeq Bioinformatics Events / Conferences 3 02-27-2013 06:30 AM
RNA-Seq: The simple fool's guide to population genomics via RNA-Seq: an introduction Newsbot! Literature Watch 0 08-31-2012 02:00 AM
2012 SciPy Bioinformatics Workshop cmueller Events / Conferences 0 05-03-2012 08:55 AM
ANy info about bioinformatics workshop roshanbernard Bioinformatics 5 01-29-2012 08:14 AM
Introduction - Bioinformatics Graduate Student wesb Introductions 0 07-09-2008 12:00 PM

Reply
 
Thread Tools
Old 01-24-2013, 01:21 AM   #1
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 261
Exclamation Upcoming Workshop - RNA-seq Bioinformatics: A Practical Introduction

RNA-seq Bioinformatics: A Practical Introduction
Mapping, Visualization, Basic Analyses

May 13th - 14th 2013, Leipzig, Germany


Scope and Topics

The purpose of this workshop is to get a deeper understanding in High-Throughput Sequencing (HTS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing machines and their implications on data analysis will be discovered. The participants will be trained on understanding their own HTS data, finding potential problems/errors and finally start writing their own pipelines. In the course we will use a real-life RNA-seq dataset from the current market leader Illumina.

All analyses will be performed using cloud services. By saving their final cloud-images, the participants will be able to reuse all tools/pipelines and to continue their analyses after the workshop(platform independently: Windows, Mac OS, Linux).

Link: http://www.ecseq.com/Workshop_RNAseq_2013.html
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).

Last edited by ecSeq Bioinformatics; 02-20-2013 at 07:00 AM.
ecSeq Bioinformatics is offline   Reply With Quote
Old 01-28-2013, 01:52 AM   #2
Ole Holgersson
Junior Member
 
Location: Denmark

Join Date: Jan 2013
Posts: 2
Default

Quote:
Originally Posted by ecSeq Bioinformatics View Post
All analyses will be performed using cloud services. By saving their final cloud-images, the participants will be able to reuse all tools/pipelines and to continue their analyses after the workshop (platform independently: Windows, Mac OS, Linux).
What exactly does that mean? Can I reuse all programs (mapping, analyses, etc.) for other (internal) datasets than these used in the workshop? Seems insecure to me, uploading internal data to your servers.
Ole Holgersson is offline   Reply With Quote
Old 01-28-2013, 02:16 AM   #3
xied75
Senior Member
 
Location: Oxford

Join Date: Feb 2012
Posts: 129
Default

He means you'll get a Virtual machine image saved for you so that you can start again, with everything still inside. They don't own servers, the Cloud provider does, (e.g. Amazon AWS, Windows Azure), all those Cloud can give you SLA (Service Level Agreement) if you pay them, in theory it was more secure than your own server room, e.g. all servers are loaded into containers, no IT person walking around at all, just a bunch of guards with guns.
xied75 is offline   Reply With Quote
Old 01-28-2013, 03:18 AM   #4
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 261
Default

Thanks for the answer xied75. That is absolutely correct.

All participants will save all results, pipelines and tools. Back at their offices they can connect to the cloud, load their stored virtual machine image, upload their 'internal datasets' and redo the complete analysis with own data. The complete process will be detached from our company. Thus, we do not only train how to do the analysis, but also provide the finished software/pipeline for later analyses.

And the best: You can easily connect to the cloud from all operating systems (also windows). You do no longer need Linux, or expensive cluster machines for your HTS analyses. That saves a lot of time and money!
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).
ecSeq Bioinformatics is offline   Reply With Quote
Old 01-30-2013, 01:26 AM   #5
Ole Holgersson
Junior Member
 
Location: Denmark

Join Date: Jan 2013
Posts: 2
Default

Thanks for the explanations!

I tried to get an idea about the prices for cloud computing, but it completely depends on the virtual machine you want (size of main memory, number of cores, operating system, etc.). What kind of a machine do I have to choose? Does anyone has experiences with cloud computing and can give me some information about the price for the analyses of a typical HTS experiment in the cloud?

Thanks a lot for your help!
Ole Holgersson is offline   Reply With Quote
Old 01-30-2013, 02:29 AM   #6
xied75
Senior Member
 
Location: Oxford

Join Date: Feb 2012
Posts: 129
Default

Hi, Ole,

Not sure about what size will ecSeq provide. In my case I need to run BWA and samtools on Windows so I need at least 4 cores 8GB machine. I use Windows Azure, there is the price calculator here http://www.windowsazure.com/en-us/pr...?scenario=full

Costing on cloud is not difficult to calculate, but you need to consider all the small text. What is chargable what is not, how does one hour count. e.g. in Azure Cloud Service, the hour starts from an exact hour say 11:00am, so if you start your instance at 10:59am, and remove your instance at 11:01am, you'll be charged 2 hours even you only used 2 mins (this is in theory, there is some grey area loosing ofcause.)

A real cost example I've done before: 10 1x human paired end in 58 files, run BWA ALN, run BWA SAMPE, run SAMTOOLS VIEW, with 25 Large (4 core, total 100 core), get bam file in the end, it can finish in about 1hour40mins, so chargable hours is 2.
2 x 25 x £0.291 = £14.55

(note: this is only CPU hours, for storage I assume you'll upload and run and download and delete everything from storage account, upload is free, download is not.)

Hope helps,

dong
xied75 is offline   Reply With Quote
Old 02-04-2013, 04:23 AM   #7
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 261
Default

Dear Ole,

cloud computing costs highly depend on the requirements of the employed tools and data sets, and of course of the provider and the time needed for analysis. Using a high main memory (70GB) instance, that we currently consider to allow testing several read aligners, costs ~$100 for 40 hours usage (without data transfer) at AWS (amazon).
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).
ecSeq Bioinformatics is offline   Reply With Quote
Old 02-11-2013, 03:45 AM   #8
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 261
Exclamation

UPDATE:

There are only two weeks left to register for the workshop! The number of participants increases every day.

Keep in mind: The sooner you register, the higher the chance to be selected!
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).
ecSeq Bioinformatics is offline   Reply With Quote
Old 02-20-2013, 05:19 AM   #9
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 261
Exclamation !! Last call !!

This is a reminder that registration for the workshop
"RNA-seq Bioinformatics: A Practical Introduction"
will close within the next days.

Deadline: February 22nd 2013

Workshop Website: http://www.ecseq.com/Workshop_RNAseq_2013.html
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).
ecSeq Bioinformatics is offline   Reply With Quote
Old 02-21-2013, 05:42 AM   #10
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 261
Default Academic discount and postponed deadline

ATTENTION:
Due to the many requests for an academic rate we decided to offer a 20% discount for attendees with non-commercial background (documentary proof must be provided upon acceptance). Accordingly, we postponed the registration deadline to March 1st 2013.
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).
ecSeq Bioinformatics is offline   Reply With Quote
Old 02-27-2013, 06:31 AM   #11
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 261
Lightbulb Last call

LAST CALL
Registration Deadline: March 1st 2013
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).
ecSeq Bioinformatics is offline   Reply With Quote
Old 02-28-2013, 01:22 AM   #12
LarsB
Junior Member
 
Location: France

Join Date: Feb 2013
Posts: 9
Default

Quote:
Originally Posted by ecSeq Bioinformatics View Post
Due to the many requests for an academic rate we decided to offer a 20% discount for attendees with non-commercial background (documentary proof must be provided upon acceptance).

Does the academic discount also apply to hospital staff?
LarsB is offline   Reply With Quote
Old 02-28-2013, 07:53 AM   #13
ecSeq Bioinformatics
Senior Member
 
Location: Leipzig, Germany

Join Date: May 2012
Posts: 261
Default

Dear Lars,

I think that depends on what exactly you are working on.... but I'm pretty sure we would give you the academic discount.
__________________
ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).
ecSeq Bioinformatics is offline   Reply With Quote
Old 03-01-2013, 01:47 AM   #14
LarsB
Junior Member
 
Location: France

Join Date: Feb 2013
Posts: 9
Default

Thanks for the ultrafast response! Already applied.
LarsB is offline   Reply With Quote
Reply

Tags
bioinformatics, rna-seq, workshop

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:36 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO