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Old 07-20-2010, 07:27 PM   #1
thondeboer
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Default 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
  5. Motif detection using the GADEM algorithm
  6. Detection of up- and downstream genes
  7. 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
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Thon de Boer, Ph.D.
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Strand Life Sciences
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deREMOVEMEboer@strandls.com
www.strandls.com
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Old 07-21-2010, 10:59 AM   #2
Lee Sam
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How many samples can you support in a cohort? Tens, hundreds? That's traditionally been the issue when we try and use integrated tools.
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Old 07-21-2010, 11:03 AM   #3
thondeboer
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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?
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Thon de Boer, Ph.D.
Director of Product Management, Software
Strand Life Sciences
548 Market Street, Suite 82804
San Francisco, CA 94104, USA
deREMOVEMEboer@strandls.com
www.strandls.com
Pioneers in Discovery Research Informatics
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Old 07-21-2010, 11:15 AM   #4
NextGenSeq
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How do we sign up? What type of hardware and operating system is needed?
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Old 07-21-2010, 11:18 AM   #5
thondeboer
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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....
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Thon de Boer, Ph.D.
Director of Product Management, Software
Strand Life Sciences
548 Market Street, Suite 82804
San Francisco, CA 94104, USA
deREMOVEMEboer@strandls.com
www.strandls.com
Pioneers in Discovery Research Informatics
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Old 09-03-2010, 07:12 AM   #6
thondeboer
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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....
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Thon
__________________________________
Thon de Boer, Ph.D.
Director of Product Management, Software
Strand Life Sciences
548 Market Street, Suite 82804
San Francisco, CA 94104, USA
deREMOVEMEboer@strandls.com
www.strandls.com
Pioneers in Discovery Research Informatics
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Old 09-03-2010, 11:25 AM   #7
dawe
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Quote:
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
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Old 09-06-2010, 06:36 AM   #8
mgundry
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id like to test it out. let me know what i need to do.
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Old 09-23-2010, 07:01 AM   #9
aunderwo
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Default 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
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