Tibco Spotfire has recently released Integromics Biomarker Discovery for
their new software platform:
http://spotfire.tibco.com/news/press_releases/detail.cfm?id=7597
You can check the product at: http://www.integromics.com/IBD.php
Regards,
Alberto
----- Original Message -----
From: "Vered Caspi" <[email protected]>
To: "'Harry Mangalam'" <[email protected]>; "'General Forum at
Bioinformatics.Org'" <[email protected]>
Sent: Wednesday, December 24, 2008 2:57 PM
Subject: Re: [BiO BB] gene expression software for mere biologists?
Dear Harry,
Does Spotfire still support gene expression?
It seems they do.
I am using SpotFire DecisionSite for Functional Genomics:
http://spotfire.tibco.com/products/decisionsite_functional_genomics.cfm
They also have a newer software with more advanced statistics for
microarray analysis:
SpotFire DecisionSite for Microarray Analysis:
http://spotfire.tibco.com/solutions/life_sciences/biomarker_discovery.cfm
With best regards,
Vered
______________________________________________________________
Vered Caspi, Ph.D.
Bioinformatics Core Facility, Head
National Institute for Biotechnology in the Negev
Building 39, room 214
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel
Email: [email protected]
Tel: 08-6479034 054-7915969
Fax: 08-6472983
http://bioinfo.bgu.ac.il
______________________________________________________________
-----Original Message-----
From: Harry Mangalam [mailto:[email protected]]
Sent: Wednesday, December 24, 2008 12:23 AM
To: [email protected]
Cc: Vered Caspi
Subject: Re: [BiO BB] gene expression software for mere biologists?
Thanks very much for taking the time to comment.
Does Spotfire still support gene expression? I went to their website
but couldn't find anything related - it looks like they're trying to
become SAS (business intelligence, decision support) just as SAS is
trying to be Spotfire (with JMP/Genomics).
Expander <http://acgt.cs.tau.ac.il/expander/> looks interesting - the
1st time I've heard of it.
hjm
On Monday 22 December 2008, Vered Caspi wrote:
Hello,
I highly recommend Partek, Spotfire (both commercial), Expander
(mainly clustering and functional analysis) and GSEA (functional
analysis) Vered
______________________________________________________________
Vered Caspi, Ph.D.
Bioinformatics Core Facility, Head
National Institute for Biotechnology in the Negev
Building 39, room 214
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel
Email: [email protected]
Tel: 08-6479034 054-7915969
Fax: 08-6472983
http://bioinfo.bgu.ac.il
______________________________________________________________
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Harry Mangalam
Sent: Monday, December 22, 2008 8:40 PM
To: BBB
Subject: [BiO BB] gene expression software for mere biologists?
Hi All,
This may be a difficult query for this group to answer as the
readership is canted heavily in the geek direction, but what gene
expression software are you and your users relying on for gene
expression and pathway analysis?
I tilt heavily towards R/Bioconductor and other free software, so
I'm aware of the advantages of it, but we have non-commandline tool
researchers who are in need of tools they can use to examine the
results of gene expression studies.
This is something of a no-win - those tools that are very easy to
use tend to hide the very complexity that the user has to address,
and so the 'ease of use' / 'ease of thought' tends to weaken an
already iffy analysis.
That said, are there tools (commercial or free) that provide fairly
good tradeoffs between power and ease of use for a non-geek
biologist user. ie runs on Mac & Windows and is mostly GUI? (If
you have experience in introducing such users to R, I'd also be
interested in your experiences).
Due to some aggressive pushing from the local SAS consulting group,
we are in the startup phase of a campus-wide, 1 year trial of
JMP/Genomics. JMP is a fairly cheap, nicely designed,
multiplatform GUI stats package from SAS. The Genomics part tho is
an expensive add-on that runs only on Windows and depends on an
optional, even more expensive Pathways package from InGenuity. The
local research community does not have a problem paying for such
software if it truly does work easily and well. If you have used
it and have an opinion or evaluation, I'd love to hear from you via
email or phone.
Harry
--
Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway,
UC Irvine 92697 949 824-0084(o), 949 285-4487(c)
---
Good judgment comes from experience;
Experience comes from bad judgment. [F. Brooks.]
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