Response to Arek Kaspryzk's email

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Response to Arek Kaspryzk's email

Lincoln Stein
Hi Folks,

Just to fill you in a bit on the background of Arek's recent letter, which may rouse concern in the GMOD community. 

Arek was leading the BioMart software development team at OICR until summer 2011, when we were forced to dismiss him for reasons unrelated to the quality of his software development or scientific work. Since then Arek has had little or no independent software development personnel under his supervision, and the circumstances of his departure made it difficult for members of his former software group to continue to work with him effectively. 

Since OICR is dependent on BioMart for several projects, we forked the code base in the fall of 2011 in order to enable us to make bug fixes and feature additions without coming into conflict with Arek over design and user interface decisions. An official repository of the BioMart source code, including all of OICR's changes has been placed on GitHub at https://github.com/biomart/biomart, and we have given Arek sole administrative control over it. OICR maintains a fork of the code base, also on GitHub, and we issue pull requests against the official branch as we make and test changes. This enables Arek to cherry pick the changes he wishes to apply to the main fork.

I am interested in getting the community's input on whether the OICR GitHub fork should be publicly visible or not. We initially made the OICR fork public, but Arek was concerned that this would lead to confusion in the community about which repository was the real one. We've now made it a private fork, and Arek's concern seems to have shifted to OICR developing on a "secret" fork. I emphasize that I have never wanted to work in secret, and am happy to make the OICR fork public once again; however, I am sensitive to the appearance that OICR is taking control of, and credit, for BioMart, which is emphatically not the case.

Finally, in an attempt to bring this ongoing dispute to a conclusion, OICR has made an offer to Arek to let an independent panel adjudicate the issues relating to the use of BioMart in the ICGC data coordinating centre, and I have agreed to be bound by the panel's decisions.

Best regards to all,

Lincoln

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: Response to Arek Kaspryzk's email

Lincoln Stein
Hi Hilmar, et al.,

If folks would like to send your responses to me personally, I will happily collate them and share them in a single post.  Also feel free to post to the list, but please try to be civil. I know that these discussions are sometimes fraught.

Lincoln

On Tue, Mar 20, 2012 at 3:59 PM, Hilmar Lapp <[hidden email]> wrote:
Lincoln - 

Since you are asking for the community's input, I have some opinions on this. I was going to send them to you personally, so that you can collate responses and share them in a single post (or choose not to share them). However, perhaps you wrote this with the intention of creating a thread on the mailing list, in which case I can respond to the list.

Or perhaps do you want responses held until the panel has been put together?

-hilmar

On Mar 20, 2012, at 1:15 PM, Lincoln Stein wrote:

Hi Folks,

Just to fill you in a bit on the background of Arek's recent letter, which may rouse concern in the GMOD community. 

Arek was leading the BioMart software development team at OICR until summer 2011, when we were forced to dismiss him for reasons unrelated to the quality of his software development or scientific work. Since then Arek has had little or no independent software development personnel under his supervision, and the circumstances of his departure made it difficult for members of his former software group to continue to work with him effectively. 

Since OICR is dependent on BioMart for several projects, we forked the code base in the fall of 2011 in order to enable us to make bug fixes and feature additions without coming into conflict with Arek over design and user interface decisions. An official repository of the BioMart source code, including all of OICR's changes has been placed on GitHub at https://github.com/biomart/biomart, and we have given Arek sole administrative control over it. OICR maintains a fork of the code base, also on GitHub, and we issue pull requests against the official branch as we make and test changes. This enables Arek to cherry pick the changes he wishes to apply to the main fork.

I am interested in getting the community's input on whether the OICR GitHub fork should be publicly visible or not. We initially made the OICR fork public, but Arek was concerned that this would lead to confusion in the community about which repository was the real one. We've now made it a private fork, and Arek's concern seems to have shifted to OICR developing on a "secret" fork. I emphasize that I have never wanted to work in secret, and am happy to make the OICR fork public once again; however, I am sensitive to the appearance that OICR is taking control of, and credit, for BioMart, which is emphatically not the case.

Finally, in an attempt to bring this ongoing dispute to a conclusion, OICR has made an offer to Arek to let an independent panel adjudicate the issues relating to the use of BioMart in the ICGC data coordinating centre, and I have agreed to be bound by the panel's decisions.

Best regards to all,

Lincoln

--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>
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===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Try Windows Azure free for 90 days Click Here
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