[BiO BB] gene expression software for mere biologists?

[Alberto Pascual Montano]

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" <veredcc at bgu.ac.il>
To: "'Harry Mangalam'" <harry.mangalam at uci.edu>; "'General Forum at 
Bioinformatics.Org'" <bbb at bioinformatics.org>
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: veredcc at bgu.ac.il
> Tel: 08-6479034 054-7915969
> Fax: 08-6472983
>
> http://bioinfo.bgu.ac.il
> ______________________________________________________________
>
> -----Original Message-----
> From: Harry Mangalam [mailto:harry.mangalam at uci.edu]
> Sent: Wednesday, December 24, 2008 12:23 AM
> To: bbb at bioinformatics.org
> 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: veredcc at bgu.ac.il
>> Tel: 08-6479034 054-7915969
>> Fax: 08-6472983
>>
>> http://bioinfo.bgu.ac.il
>> ______________________________________________________________
>>
>> -----Original Message-----
>> From: bbb-bounces at bioinformatics.org
>> [mailto:bbb-bounces at bioinformatics.org] 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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