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Open Letter to Lincoln Stein RE: BioMart Renaming

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Arek Kasprzyk

Open Letter to Lincoln Stein RE: BioMart Renaming

Dear Lincoln:

I am concerned about your continued efforts to rename BioMart at OICR. These efforts have far reaching negative consequences for many organizations and projects including the OICR and ICGC and deprive the BioMart project of its well deserved credit. In the last two years, there have been two attempts to disassociate the BioMart brand from the ICGC's data management solution. The first attempt was made in 2009/2010, when you started referring to BioMart in ICGC communications as the "franchise database system", a term that was only dropped after my continued persistence that the BioMart name be rightfully reinstated. Now that I have left the institute, the story is repeating itself and you have decided to continue BioMart development under yet another name. Rebranding BioMart (10 years of your colleague's work), creates the misleading perception that OICR/ICGC is using a different product. As I have noted time and time again, I disagree with these actions.

I am very proud of BioMart's publication record (http://www.biomart.org/publications.html), the size of its community (http://www.biomart.org/community.html), and the fact that it is one of the most successful and innovative technologies in bioinformatics today. I have always been happy to share this success with everyone who have been, are and will be part of this open-source community. It goes without saying that this applies to you as well as everyone else at OICR who have contributed in the past, are presently contributing and/or will contribute in the future. Nevertheless, I expect that those who have benefited from BioMart use it in a way that is ethical and remains beneficial for the entire scientific community. As mentioned before with respect to using and/or developing BioMart, the only options I consider fair and acceptable are as follows:

1. Quit BioMart development at OICR and replace it with an alternative technology (i.e. not a renamed version of BioMart).
2. Quit BioMart development at OICR but remain a BioMart user and let OICR benefit from this free, open source technology just like the other 28 institutes worldwide who are currently using it successfully. You will have my full support.
3. Continue BioMart development at OICR in collaboration with the BioMart project. Your contributions will allow you to prioritize your goals and will be dully acknowledged.

In addition to the issues surrounding the renaming of BioMart at OICR, duplicating BioMart and hence having two almost identical code bases is completely unnecessary. BioMart's data-agnostic development model assumes that the software is generic so that it meets the requirements of a principal organization while fulfilling those of other organizations as well. As long as these other organizations communicate their requirements to the BioMart team (via the mailing list, etc), I include them in my development plans and the additional features benefit everyone. Since the various group requirements often overlap and/or are already included in my vision of BioMart going forward, this has never been a problem to achieve. As you recall, when BioMart was funded by the Wellcome Trust and hosted at EBI, not only did the software meet Ensembl's data management needs but it also benefited other projects including many of your own (e.g. GMOD, Reactome, Wormbase, Gramene and HapMap). More recently, when I began working at OICR, my primary mandate was to ensure that BioMart met the ICGC's data management needs. Not only did it successful meet them, but it also met the needs of other OICR projects such as PopCure, OSIRIS etc, and continued to meet the needs of Ensembl, as well as those of 40 other database projects worldwide. Another benefit of this development model is that it enables projects to utilize existing BioMart databases without having to commit any of its resources. For instance, Ensembl, Reactome, Cosmic, PED, BCTC and Intogen are all available through the ICGC Data Portal. If the the ICGC's data management solution is no longer using the unified BioMart code base, integration of these databases into the ICGC Data Portal will become far more difficult. For those who understand the BioMart development model, it is clear that it is redundant and harmful to create BioMart "duplicates"/"forks"/"copies"/"clones"/"brands" that cause confusion and duplication of efforts. In addition, two different BioMart code bases create incompatibilities that impede existing and future collaborations and destroy the unified system that currently works so well for the scientific community. It is therefore critical that we continue to maintain one BioMart project and one BioMart code base.

For the sake of the BioMart scientific community, which currently includes the ICGC and other OICR initiatives, I have made numerous attempts to come to an agreement with you with regards to maintaining one BioMart code base, however they have consistently been rebuffed or ignored. In our correspondence on this matter, you have neither provided convincing arguments regarding your decision to rename BioMart, nor have you been able to counter any of my arguments against it. Much to my dismay, in reply to my latest initiative, dated December 19th you informed me, and I quote: "with regards to the options that you have proposed in your correspondence of December 12th, 2011, none of them meet with OICR needs for the future development of its projects. Consequently, the only communications OICR is interested in continuing are in connection with the migration of BioMart to an alternative site, separate from OICR". Should you, the GMOD leader not support open dialogue and foster scientific collaborations?

Very truly yours,

Arek

Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

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Lincoln Stein-3

Re: Open Letter to Lincoln Stein RE: BioMart Renaming

Dear Arek,

I'm sorry you have so badly misinterpreted my intentions. I remain a strong fan of BioMart and am using it as a data mining engine for several projects, including WormBase, Reactome and a variety of cancer projects. However, as you know, internal changes to the code base were badly needed in order to support the scalability of the ICGC DCC, and OICR's attempts to create a constructive collaboration with you to address these issues were unsuccessful. Therefore we were forced to make a copy of BioMart for internal use by the ICGC DCC so that the needed code development could go forward without impacting the public code base. We have created a temporary, internal name for this version of BioMart in order to avoid confusion, and we have absolutely no intention to compete with BioMart's brand, name recognition or community.

In fact, OICR has offered you financial support, hardware and administrative support in order to continue to support BioMart and its community even though you are no longer employed by us. I am perplexed by the content of your letter, and saddened by its tone. In the future, I hope we can discuss these issues person-to-person, and not in an open forum.

Yours,

Lincoln

On Thu, Jan 19, 2012 at 10:06 AM, Arek Kasprzyk <[hidden email]> wrote:

Dear Lincoln:

I am concerned about your continued efforts to rename BioMart at OICR. These efforts have far reaching negative consequences for many organizations and projects including the OICR and ICGC and deprive the BioMart project of its well deserved credit. In the last two years, there have been two attempts to disassociate the BioMart brand from the ICGC's data management solution. The first attempt was made in 2009/2010, when you started referring to BioMart in ICGC communications as the "franchise database system", a term that was only dropped after my continued persistence that the BioMart name be rightfully reinstated. Now that I have left the institute, the story is repeating itself and you have decided to continue BioMart development under yet another name. Rebranding BioMart (10 years of your colleague's work), creates the misleading perception that OICR/ICGC is using a different product. As I have noted time and time again, I disagree with these actions.

I am very proud of BioMart's publication record (http://www.biomart.org/publications.html), the size of its community (http://www.biomart.org/community.html), and the fact that it is one of the most successful and innovative technologies in bioinformatics today. I have always been happy to share this success with everyone who have been, are and will be part of this open-source community. It goes without saying that this applies to you as well as everyone else at OICR who have contributed in the past, are presently contributing and/or will contribute in the future. Nevertheless, I expect that those who have benefited from BioMart use it in a way that is ethical and remains beneficial for the entire scientific community. As mentioned before with respect to using and/or developing BioMart, the only options I consider fair and acceptable are as follows:

1. Quit BioMart development at OICR and replace it with an alternative technology (i.e. not a renamed version of BioMart).
2. Quit BioMart development at OICR but remain a BioMart user and let OICR benefit from this free, open source technology just like the other 28 institutes worldwide who are currently using it successfully. You will have my full support.
3. Continue BioMart development at OICR in collaboration with the BioMart project. Your contributions will allow you to prioritize your goals and will be dully acknowledged.

In addition to the issues surrounding the renaming of BioMart at OICR, duplicating BioMart and hence having two almost identical code bases is completely unnecessary. BioMart's data-agnostic development model assumes that the software is generic so that it meets the requirements of a principal organization while fulfilling those of other organizations as well. As long as these other organizations communicate their requirements to the BioMart team (via the mailing list, etc), I include them in my development plans and the additional features benefit everyone. Since the various group requirements often overlap and/or are already included in my vision of BioMart going forward, this has never been a problem to achieve. As you recall, when BioMart was funded by the Wellcome Trust and hosted at EBI, not only did the software meet Ensembl's data management needs but it also benefited other projects including many of your own (e.g. GMOD, Reactome, Wormbase, Gramene and HapMap). More recently, when I began working at OICR, my primary mandate was to ensure that BioMart met the ICGC's data management needs. Not only did it successful meet them, but it also met the needs of other OICR projects such as PopCure, OSIRIS etc, and continued to meet the needs of Ensembl, as well as those of 40 other database projects worldwide. Another benefit of this development model is that it enables projects to utilize existing BioMart databases without having to commit any of its resources. For instance, Ensembl, Reactome, Cosmic, PED, BCTC and Intogen are all available through the ICGC Data Portal. If the the ICGC's data management solution is no longer using the unified BioMart code base, integration of these databases into the ICGC Data Portal will become far more difficult. For those who understand the BioMart development model, it is clear that it is redundant and harmful to create BioMart "duplicates"/"forks"/"copies"/"clones"/"brands" that cause confusion and duplication of efforts. In addition, two different BioMart code bases create incompatibilities that impede existing and future collaborations and destroy the unified system that currently works so well for the scientific community. It is therefore critical that we continue to maintain one BioMart project and one BioMart code base.

For the sake of the BioMart scientific community, which currently includes the ICGC and other OICR initiatives, I have made numerous attempts to come to an agreement with you with regards to maintaining one BioMart code base, however they have consistently been rebuffed or ignored. In our correspondence on this matter, you have neither provided convincing arguments regarding your decision to rename BioMart, nor have you been able to counter any of my arguments against it. Much to my dismay, in reply to my latest initiative, dated December 19th you informed me, and I quote: "with regards to the options that you have proposed in your correspondence of December 12th, 2011, none of them meet with OICR needs for the future development of its projects. Consequently, the only communications OICR is interested in continuing are in connection with the migration of BioMart to an alternative site, separate from OICR". Should you, the GMOD leader not support open dialogue and foster scientific collaborations?

Very truly yours,

Arek

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

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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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Arek Kasprzyk

Re: Open Letter to Lincoln Stein RE: BioMart Renaming

Dear Lincoln,

The BioMart software that I released in May 2011 and it still in use today is fully functional and perfectly scalable as a result of the the parallel query engine, which was implemented some time ago. I believe you may be referring to changes to the peripheral package of MLoader tools that I scheduled for implementation and integration with the configuration tool prior to my departure. Since a) I fully support these changes; b) this does not contradict any of my plans; and c) this issue was never discussed with me, I don't see how this could possibly be a reason to split the development.

In any case, the OICR is not the first group that has made modifications to their local BioMart code base. However, none of these groups felt it was necessary to rename their local copy of BioMart to give the impression they are using a different product. In fact, they:

1. Keep the BioMart name and logo clearly displayed on their websites;

2. Acknowledge BioMart in their publications;

3. Refer to BioMart in funding applications, which describe their data management system; and

4. Offer their local modifications to the code base as their contributions to the BioMart project.

I expect that you will do the same with the "internal version" of BioMart, which will be used to support the ICGC data portal and other OICR initiatives.

Thank you,

Arek

On Thu, Jan 19, 2012 at 2:07 PM, Lincoln Stein <[hidden email]> wrote:

Dear Arek,

I'm sorry you have so badly misinterpreted my intentions. I remain a strong fan of BioMart and am using it as a data mining engine for several projects, including WormBase, Reactome and a variety of cancer projects. However, as you know, internal changes to the code base were badly needed in order to support the scalability of the ICGC DCC, and OICR's attempts to create a constructive collaboration with you to address these issues were unsuccessful. Therefore we were forced to make a copy of BioMart for internal use by the ICGC DCC so that the needed code development could go forward without impacting the public code base. We have created a temporary, internal name for this version of BioMart in order to avoid confusion, and we have absolutely no intention to compete with BioMart's brand, name recognition or community.

In fact, OICR has offered you financial support, hardware and administrative support in order to continue to support BioMart and its community even though you are no longer employed by us. I am perplexed by the content of your letter, and saddened by its tone. In the future, I hope we can discuss these issues person-to-person, and not in an open forum.

Yours,

Lincoln

On Thu, Jan 19, 2012 at 10:06 AM, Arek Kasprzyk <[hidden email]> wrote:

Dear Lincoln:

I am concerned about your continued efforts to rename BioMart at OICR. These efforts have far reaching negative consequences for many organizations and projects including the OICR and ICGC and deprive the BioMart project of its well deserved credit. In the last two years, there have been two attempts to disassociate the BioMart brand from the ICGC's data management solution. The first attempt was made in 2009/2010, when you started referring to BioMart in ICGC communications as the "franchise database system", a term that was only dropped after my continued persistence that the BioMart name be rightfully reinstated. Now that I have left the institute, the story is repeating itself and you have decided to continue BioMart development under yet another name. Rebranding BioMart (10 years of your colleague's work), creates the misleading perception that OICR/ICGC is using a different product. As I have noted time and time again, I disagree with these actions.

I am very proud of BioMart's publication record (http://www.biomart.org/publications.html), the size of its community (http://www.biomart.org/community.html), and the fact that it is one of the most successful and innovative technologies in bioinformatics today. I have always been happy to share this success with everyone who have been, are and will be part of this open-source community. It goes without saying that this applies to you as well as everyone else at OICR who have contributed in the past, are presently contributing and/or will contribute in the future. Nevertheless, I expect that those who have benefited from BioMart use it in a way that is ethical and remains beneficial for the entire scientific community. As mentioned before with respect to using and/or developing BioMart, the only options I consider fair and acceptable are as follows:

1. Quit BioMart development at OICR and replace it with an alternative technology (i.e. not a renamed version of BioMart).
2. Quit BioMart development at OICR but remain a BioMart user and let OICR benefit from this free, open source technology just like the other 28 institutes worldwide who are currently using it successfully. You will have my full support.
3. Continue BioMart development at OICR in collaboration with the BioMart project. Your contributions will allow you to prioritize your goals and will be dully acknowledged.

In addition to the issues surrounding the renaming of BioMart at OICR, duplicating BioMart and hence having two almost identical code bases is completely unnecessary. BioMart's data-agnostic development model assumes that the software is generic so that it meets the requirements of a principal organization while fulfilling those of other organizations as well. As long as these other organizations communicate their requirements to the BioMart team (via the mailing list, etc), I include them in my development plans and the additional features benefit everyone. Since the various group requirements often overlap and/or are already included in my vision of BioMart going forward, this has never been a problem to achieve. As you recall, when BioMart was funded by the Wellcome Trust and hosted at EBI, not only did the software meet Ensembl's data management needs but it also benefited other projects including many of your own (e.g. GMOD, Reactome, Wormbase, Gramene and HapMap). More recently, when I began working at OICR, my primary mandate was to ensure that BioMart met the ICGC's data management needs. Not only did it successful meet them, but it also met the needs of other OICR projects such as PopCure, OSIRIS etc, and continued to meet the needs of Ensembl, as well as those of 40 other database projects worldwide. Another benefit of this development model is that it enables projects to utilize existing BioMart databases without having to commit any of its resources. For instance, Ensembl, Reactome, Cosmic, PED, BCTC and Intogen are all available through the ICGC Data Portal. If the the ICGC's data management solution is no longer using the unified BioMart code base, integration of these databases into the ICGC Data Portal will become far more difficult. For those who understand the BioMart development model, it is clear that it is redundant and harmful to create BioMart "duplicates"/"forks"/"copies"/"clones"/"brands" that cause confusion and duplication of efforts. In addition, two different BioMart code bases create incompatibilities that impede existing and future collaborations and destroy the unified system that currently works so well for the scientific community. It is therefore critical that we continue to maintain one BioMart project and one BioMart code base.

For the sake of the BioMart scientific community, which currently includes the ICGC and other OICR initiatives, I have made numerous attempts to come to an agreement with you with regards to maintaining one BioMart code base, however they have consistently been rebuffed or ignored. In our correspondence on this matter, you have neither provided convincing arguments regarding your decision to rename BioMart, nor have you been able to counter any of my arguments against it. Much to my dismay, in reply to my latest initiative, dated December 19th you informed me, and I quote: "with regards to the options that you have proposed in your correspondence of December 12th, 2011, none of them meet with OICR needs for the future development of its projects. Consequently, the only communications OICR is interested in continuing are in connection with the migration of BioMart to an alternative site, separate from OICR". I must say that this type of communication projects an image of OICR that I find very disturbing. Should you, a representative of OICR and ICGC not support open dialogue and foster scientific collaborations?

Very truly yours,

Arek

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

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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
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>

Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

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Lincoln Stein

Re: Open Letter to Lincoln Stein RE: BioMart Renaming

All these requests are reasonable, and I would not dream of doing otherwise!

Lincoln

1. Keep the BioMart name and logo clearly displayed on their websites;
2. Acknowledge BioMart in their publications;
3. Refer to BioMart in funding applications, which describe their data management system; and

4. Offer their local modifications to the code base as their contributions to the BioMart project.

I expect that you will do the same with the "internal version" of BioMart, which will be used to support the ICGC data portal and other OICR initiatives.

Thank you,

Arek

On Thu, Jan 19, 2012 at 2:07 PM, Lincoln Stein <[hidden email]> wrote:

Dear Arek,

I'm sorry you have so badly misinterpreted my intentions. I remain a strong fan of BioMart and am using it as a data mining engine for several projects, including WormBase, Reactome and a variety of cancer projects. However, as you know, internal changes to the code base were badly needed in order to support the scalability of the ICGC DCC, and OICR's attempts to create a constructive collaboration with you to address these issues were unsuccessful. Therefore we were forced to make a copy of BioMart for internal use by the ICGC DCC so that the needed code development could go forward without impacting the public code base. We have created a temporary, internal name for this version of BioMart in order to avoid confusion, and we have absolutely no intention to compete with BioMart's brand, name recognition or community.

In fact, OICR has offered you financial support, hardware and administrative support in order to continue to support BioMart and its community even though you are no longer employed by us. I am perplexed by the content of your letter, and saddened by its tone. In the future, I hope we can discuss these issues person-to-person, and not in an open forum.

Yours,

Lincoln

On Thu, Jan 19, 2012 at 10:06 AM, Arek Kasprzyk <[hidden email]> wrote:

Dear Lincoln:

I am concerned about your continued efforts to rename BioMart at OICR. These efforts have far reaching negative consequences for many organizations and projects including the OICR and ICGC and deprive the BioMart project of its well deserved credit. In the last two years, there have been two attempts to disassociate the BioMart brand from the ICGC's data management solution. The first attempt was made in 2009/2010, when you started referring to BioMart in ICGC communications as the "franchise database system", a term that was only dropped after my continued persistence that the BioMart name be rightfully reinstated. Now that I have left the institute, the story is repeating itself and you have decided to continue BioMart development under yet another name. Rebranding BioMart (10 years of your colleague's work), creates the misleading perception that OICR/ICGC is using a different product. As I have noted time and time again, I disagree with these actions.

I am very proud of BioMart's publication record (http://www.biomart.org/publications.html), the size of its community (http://www.biomart.org/community.html), and the fact that it is one of the most successful and innovative technologies in bioinformatics today. I have always been happy to share this success with everyone who have been, are and will be part of this open-source community. It goes without saying that this applies to you as well as everyone else at OICR who have contributed in the past, are presently contributing and/or will contribute in the future. Nevertheless, I expect that those who have benefited from BioMart use it in a way that is ethical and remains beneficial for the entire scientific community. As mentioned before with respect to using and/or developing BioMart, the only options I consider fair and acceptable are as follows:

1. Quit BioMart development at OICR and replace it with an alternative technology (i.e. not a renamed version of BioMart).
2. Quit BioMart development at OICR but remain a BioMart user and let OICR benefit from this free, open source technology just like the other 28 institutes worldwide who are currently using it successfully. You will have my full support.
3. Continue BioMart development at OICR in collaboration with the BioMart project. Your contributions will allow you to prioritize your goals and will be dully acknowledged.

In addition to the issues surrounding the renaming of BioMart at OICR, duplicating BioMart and hence having two almost identical code bases is completely unnecessary. BioMart's data-agnostic development model assumes that the software is generic so that it meets the requirements of a principal organization while fulfilling those of other organizations as well. As long as these other organizations communicate their requirements to the BioMart team (via the mailing list, etc), I include them in my development plans and the additional features benefit everyone. Since the various group requirements often overlap and/or are already included in my vision of BioMart going forward, this has never been a problem to achieve. As you recall, when BioMart was funded by the Wellcome Trust and hosted at EBI, not only did the software meet Ensembl's data management needs but it also benefited other projects including many of your own (e.g. GMOD, Reactome, Wormbase, Gramene and HapMap). More recently, when I began working at OICR, my primary mandate was to ensure that BioMart met the ICGC's data management needs. Not only did it successful meet them, but it also met the needs of other OICR projects such as PopCure, OSIRIS etc, and continued to meet the needs of Ensembl, as well as those of 40 other database projects worldwide. Another benefit of this development model is that it enables projects to utilize existing BioMart databases without having to commit any of its resources. For instance, Ensembl, Reactome, Cosmic, PED, BCTC and Intogen are all available through the ICGC Data Portal. If the the ICGC's data management solution is no longer using the unified BioMart code base, integration of these databases into the ICGC Data Portal will become far more difficult. For those who understand the BioMart development model, it is clear that it is redundant and harmful to create BioMart "duplicates"/"forks"/"copies"/"clones"/"brands" that cause confusion and duplication of efforts. In addition, two different BioMart code bases create incompatibilities that impede existing and future collaborations and destroy the unified system that currently works so well for the scientific community. It is therefore critical that we continue to maintain one BioMart project and one BioMart code base.

For the sake of the BioMart scientific community, which currently includes the ICGC and other OICR initiatives, I have made numerous attempts to come to an agreement with you with regards to maintaining one BioMart code base, however they have consistently been rebuffed or ignored. In our correspondence on this matter, you have neither provided convincing arguments regarding your decision to rename BioMart, nor have you been able to counter any of my arguments against it. Much to my dismay, in reply to my latest initiative, dated December 19th you informed me, and I quote: "with regards to the options that you have proposed in your correspondence of December 12th, 2011, none of them meet with OICR needs for the future development of its projects. Consequently, the only communications OICR is interested in continuing are in connection with the migration of BioMart to an alternative site, separate from OICR". I must say that this type of communication projects an image of OICR that I find very disturbing. Should you, a representative of OICR and ICGC not support open dialogue and foster scientific collaborations?

Very truly yours,

Arek

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

------------------------------------------------------------------------------
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_______________________________________________
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[hidden email]
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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
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

--
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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Arek Kasprzyk

Re: Open Letter to Lincoln Stein RE: BioMart Renaming

Dear Lincoln,

That is great news!

On a related note, one of the BioMart programmers has come across repository for OICR's SciMart:

https://github.com/oicr/SciMart/blob/master/README.md

After having looked at it briefly, the BioMart group and I have a few questions:

1. Below the surface (https://github.com/oicr/SciMart/commit/10b3f3c8c55eb56a9129bb299ff6dfd9584f7619#src/org/scimart/queryEngine), it appears to be a renamed BioMart. Can we expect the BioMart name to be re-instated?

2. The code does not seem to be entirely functional but has acquired ~1GB of dependencies? Are we looking in the right place?

3. Can BioMart programmers outside of OICR review this code to help take it forward?

cheers,

PS. There were some difficulties with my email getting through to the GMOD mailing list yesterday

On Mon, Jan 23, 2012 at 12:05 PM, Lincoln Stein <[hidden email]> wrote:

All these requests are reasonable, and I would not dream of doing otherwise!

Lincoln

1. Keep the BioMart name and logo clearly displayed on their websites;
2. Acknowledge BioMart in their publications;
3. Refer to BioMart in funding applications, which describe their data management system; and

4. Offer their local modifications to the code base as their contributions to the BioMart project.

I expect that you will do the same with the "internal version" of BioMart, which will be used to support the ICGC data portal and other OICR initiatives.

Thank you,

Arek

On Thu, Jan 19, 2012 at 2:07 PM, Lincoln Stein <[hidden email]> wrote:

Dear Arek,

I'm sorry you have so badly misinterpreted my intentions. I remain a strong fan of BioMart and am using it as a data mining engine for several projects, including WormBase, Reactome and a variety of cancer projects. However, as you know, internal changes to the code base were badly needed in order to support the scalability of the ICGC DCC, and OICR's attempts to create a constructive collaboration with you to address these issues were unsuccessful. Therefore we were forced to make a copy of BioMart for internal use by the ICGC DCC so that the needed code development could go forward without impacting the public code base. We have created a temporary, internal name for this version of BioMart in order to avoid confusion, and we have absolutely no intention to compete with BioMart's brand, name recognition or community.

In fact, OICR has offered you financial support, hardware and administrative support in order to continue to support BioMart and its community even though you are no longer employed by us. I am perplexed by the content of your letter, and saddened by its tone. In the future, I hope we can discuss these issues person-to-person, and not in an open forum.

Yours,

Lincoln

On Thu, Jan 19, 2012 at 10:06 AM, Arek Kasprzyk <[hidden email]> wrote:

Dear Lincoln:

I am concerned about your continued efforts to rename BioMart at OICR. These efforts have far reaching negative consequences for many organizations and projects including the OICR and ICGC and deprive the BioMart project of its well deserved credit. In the last two years, there have been two attempts to disassociate the BioMart brand from the ICGC's data management solution. The first attempt was made in 2009/2010, when you started referring to BioMart in ICGC communications as the "franchise database system", a term that was only dropped after my continued persistence that the BioMart name be rightfully reinstated. Now that I have left the institute, the story is repeating itself and you have decided to continue BioMart development under yet another name. Rebranding BioMart (10 years of your colleague's work), creates the misleading perception that OICR/ICGC is using a different product. As I have noted time and time again, I disagree with these actions.

I am very proud of BioMart's publication record (http://www.biomart.org/publications.html), the size of its community (http://www.biomart.org/community.html), and the fact that it is one of the most successful and innovative technologies in bioinformatics today. I have always been happy to share this success with everyone who have been, are and will be part of this open-source community. It goes without saying that this applies to you as well as everyone else at OICR who have contributed in the past, are presently contributing and/or will contribute in the future. Nevertheless, I expect that those who have benefited from BioMart use it in a way that is ethical and remains beneficial for the entire scientific community. As mentioned before with respect to using and/or developing BioMart, the only options I consider fair and acceptable are as follows:

1. Quit BioMart development at OICR and replace it with an alternative technology (i.e. not a renamed version of BioMart).
2. Quit BioMart development at OICR but remain a BioMart user and let OICR benefit from this free, open source technology just like the other 28 institutes worldwide who are currently using it successfully. You will have my full support.
3. Continue BioMart development at OICR in collaboration with the BioMart project. Your contributions will allow you to prioritize your goals and will be dully acknowledged.

In addition to the issues surrounding the renaming of BioMart at OICR, duplicating BioMart and hence having two almost identical code bases is completely unnecessary. BioMart's data-agnostic development model assumes that the software is generic so that it meets the requirements of a principal organization while fulfilling those of other organizations as well. As long as these other organizations communicate their requirements to the BioMart team (via the mailing list, etc), I include them in my development plans and the additional features benefit everyone. Since the various group requirements often overlap and/or are already included in my vision of BioMart going forward, this has never been a problem to achieve. As you recall, when BioMart was funded by the Wellcome Trust and hosted at EBI, not only did the software meet Ensembl's data management needs but it also benefited other projects including many of your own (e.g. GMOD, Reactome, Wormbase, Gramene and HapMap). More recently, when I began working at OICR, my primary mandate was to ensure that BioMart met the ICGC's data management needs. Not only did it successful meet them, but it also met the needs of other OICR projects such as PopCure, OSIRIS etc, and continued to meet the needs of Ensembl, as well as those of 40 other database projects worldwide. Another benefit of this development model is that it enables projects to utilize existing BioMart databases without having to commit any of its resources. For instance, Ensembl, Reactome, Cosmic, PED, BCTC and Intogen are all available through the ICGC Data Portal. If the the ICGC's data management solution is no longer using the unified BioMart code base, integration of these databases into the ICGC Data Portal will become far more difficult. For those who understand the BioMart development model, it is clear that it is redundant and harmful to create BioMart "duplicates"/"forks"/"copies"/"clones"/"brands" that cause confusion and duplication of efforts. In addition, two different BioMart code bases create incompatibilities that impede existing and future collaborations and destroy the unified system that currently works so well for the scientific community. It is therefore critical that we continue to maintain one BioMart project and one BioMart code base.

For the sake of the BioMart scientific community, which currently includes the ICGC and other OICR initiatives, I have made numerous attempts to come to an agreement with you with regards to maintaining one BioMart code base, however they have consistently been rebuffed or ignored. In our correspondence on this matter, you have neither provided convincing arguments regarding your decision to rename BioMart, nor have you been able to counter any of my arguments against it. Much to my dismay, in reply to my latest initiative, dated December 19th you informed me, and I quote: "with regards to the options that you have proposed in your correspondence of December 12th, 2011, none of them meet with OICR needs for the future development of its projects. Consequently, the only communications OICR is interested in continuing are in connection with the migration of BioMart to an alternative site, separate from OICR". I must say that this type of communication projects an image of OICR that I find very disturbing. Should you, a representative of OICR and ICGC not support open dialogue and foster scientific collaborations?

Very truly yours,

Arek

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

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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
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>

--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead

--
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]>

Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead