[BioC] Re: offer from I Neuhaus to create a BMS response; keep incore, please

[Park, Richard]

Hi Everyone, 
I was just talking with my PI the other day and he told me that he had an interesting conversation with one of the lead developers at affymetrix. I know there have been discussions about affy's move toward a binary format and how this will affect open source environments such as bioconductor. 

The developer at affymetrix said that they are moving toward open source analysis of chips. He said one of the purposes of the conference in August at Berkeley (http://eci-events.com/AffyGeneChip/) was to discuss the best way to proceed with this approach. 

I am not sure how the move towards a binary format will affect the bioconductor community, but I am optimistic that it will not stop the developments within bioconductor. I am going to go to the conference and see what they have to say for myself. 

HTH, 
Richard Park 
Computational Data Analyzer
Joslin Diabetes Center


-----Original Message-----
From: Isaac Neuhaus [mailto:isaac.neuhaus at bms.com]
Sent: Tuesday, July 01, 2003 10:3 AM
To: Todd Richmond
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Re: offer from I Neuhaus to create a BMS response;
keep incore, please


Todd Richmond wrote:

>>-----Original Message-----
>>From: bioconductor-bounces at stat.math.ethz.ch
>>[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Rafael A.
>>Irizarry
>>Sent: Tuesday, July 01, 2003 8:14 AM
>>To: bioconductor at stat.math.ethz.ch
>>
>>On Tue, 1 Jul 2003, Robert Gentleman wrote:
>>
>><SNIP>
>>    
>>
>>>Vis a vis the phone call, it was about 1 hour long, it was slightly
>>>focussed on marketing hype on their side and some substantial,
>>>although peculiar concerns came out. One of the major concerns that
>>>they have is that if they make their formats public then anyone can
>>>create a "CEL" file of the right format and make it look very much
>>>like one that they generated. They believe that this would lead to
>>>substantial confusion.
>>>      
>>>
>
>That doesn't make a lot of sense. If they are concerned about the
>authenticity of "CEL" files can't they just use a digital signature, or some
>sort of checksum scheme for verification? 
>
Am I missing something? Do they want to patent their own CEL format? 
(sorry just being facetious)

>I can't imagine that a binary
>format is going to make life easier for anyone. If they are concerned about
>size, there are standard compression libraries that you can use to
>compress/uncompress your data files on-the-fly as you save/load.
>
I disagree. A binary file could facilitate getting chunks of data using 
random access without having to go through the whole file. For example, 
you can imagine at some point creating you own 'probe sets' with 
features that are different than those mapped by Affy. However the 
structure of the file MUST be publicly available.

I

>
>Todd
>
>--
>Todd Richmond
>Manager of Research Informatics
>NimbleGen Systems, Inc
>One Science Court
>Madison, WI 53711
>Ph: 1-608-218-7651
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
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>  
>

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