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  • Looking for Beta testers for Strand NGS module

    Hi,

    We at Strand Life Sciences are currently working on an application for the analysis of ChIP-SEQ, RNA-SEQ and DNA Variation data and we are looking for BETA TESTERS!

    The application starts with pre-aligned NGS data (in SAM/BAM format) and is built on the same platform as Agilent GeneSpring (and can be fully integrated with GeneSpring) and allows for the following analysis

    ChIP-SEQ
    1. Import of SAM/BAM file of aligned data
    2. The detection of peaks in the coverage by two algorithms
    3. PICS
    4. MACS
  • Motif detection using the GADEM algorithm
  • Detection of up- and downstream genes
  • GO and Pathway analysis of the affected genes


  • RNA-SEQ
    The RNA-SEQ experiment type allows for the measurement of expression levels of known transcripts and the detection of novel genes. It supports alternative splicing analysis as well as statistical analysis of differentially expressed genes.

    DNA Variant analysis
    The DNA Variant analysis experiment type allows for the detection of SNPs, MNPs, large and small InDels and large structural variants, such as translocations and inversions etc. Annotation of the found variants with previously published variants from dbSNPs as well as the analysis of the effect of the variants on the coding regions of the genes, such as frameshifts, insertions/deletions, etc.

    Let me know if you are interested in BETA testing and once we release this product, we give you 6 months free access!

    Sincerely yours,

    Thon de Boer
    Dir. of Product Manager
    Strand Life Sciences
Thon
__________________________________
Thon de Boer, Ph.D.
Director of Product Management, Software
Strand Life Sciences
548 Market Street, Suite 82804
San Francisco, CA 94104, USA
[email protected]
www.strandls.com
Pioneers in Discovery Research Informatics
_______________________________________

  • #2
    How many samples can you support in a cohort? Tens, hundreds? That's traditionally been the issue when we try and use integrated tools.

    Comment


    • #3
      We are aiming and designed it for being able to do hundreds, but frankly have not found these kinds of data sets but simulations are in the works...What kind of data sets do you have access to? Hundreds of what kind of coverage and is it whole genome or targeted?
      Thon
      __________________________________
      Thon de Boer, Ph.D.
      Director of Product Management, Software
      Strand Life Sciences
      548 Market Street, Suite 82804
      San Francisco, CA 94104, USA
      [email protected]
      www.strandls.com
      Pioneers in Discovery Research Informatics
      _______________________________________

      Comment


      • #4
        How do we sign up? What type of hardware and operating system is needed?

        Comment


        • #5
          Just let me know you are interested and send me a private message with your email address and I will send you the info once we are ready to start the beta (in about a week or so).

          The NGS Module is a desktop application at the moment (we are working on a cloud version as well) and will run on Windows, Linux and Mac OSX at although it can run in 2 GB, we recommend 64bit machines with at least 4 GB of memory....
          Thon
          __________________________________
          Thon de Boer, Ph.D.
          Director of Product Management, Software
          Strand Life Sciences
          548 Market Street, Suite 82804
          San Francisco, CA 94104, USA
          [email protected]
          www.strandls.com
          Pioneers in Discovery Research Informatics
          _______________________________________

          Comment


          • #6
            We have finally started the beta program for Avadis NGS by Strand.
            If you are interested to participate, please send me a private message here and I will add you to the list....
            Thon
            __________________________________
            Thon de Boer, Ph.D.
            Director of Product Management, Software
            Strand Life Sciences
            548 Market Street, Suite 82804
            San Francisco, CA 94104, USA
            [email protected]
            www.strandls.com
            Pioneers in Discovery Research Informatics
            _______________________________________

            Comment


            • #7
              Originally posted by thondeboer View Post
              Hi,

              We at Strand Life Sciences are currently working on an application for the analysis of ChIP-SEQ, RNA-SEQ and DNA Variation data and we are looking for BETA TESTERS!

              The application starts with pre-aligned NGS data (in SAM/BAM format) and is built on the same platform as Agilent GeneSpring (and can be fully integrated with GeneSpring) and allows for the following analysis
              We had a really bad experience with GeneSpring GX and its development road. Does this suite need an Oracle DB backend?

              d

              Comment


              • #8
                id like to test it out. let me know what i need to do.

                Comment


                • #9
                  I'd be happy to test

                  I am a bioinfomatician but have many users who would like to try software with an intuitive UI. Tried to pm you but this seemed to be disabled.

                  Please get in touch if looking for a beta tester

                  Anthony

                  Comment

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