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Upcoming Workshop - RNA-seq Bioinformatics: A Practical Introduction

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  • 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
    Last edited by ecSeq Bioinformatics; 02-20-2013, 08:00 AM.
    ecSeq Bioinformatics is Europe’s leading provider of hands-on bioinformatics workshops and professional data analysis in the field of Next-Generation Sequencing (NGS).

  • #2
    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.

    Comment


    • #3
      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.

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      • #4
        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).

        Comment


        • #5
          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!

          Comment


          • #6
            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

            Comment


            • #7
              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).

              Comment


              • #8
                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).

                Comment


                • #9
                  !! 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).

                  Comment


                  • #10
                    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).

                    Comment


                    • #11
                      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).

                      Comment


                      • #12
                        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?

                        Comment


                        • #13
                          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).

                          Comment


                          • #14
                            Thanks for the ultrafast response! Already applied.

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