Re: Open Letter to Lincoln Stein RE: BioMart Renaming

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Re: Open Letter to Lincoln Stein RE: BioMart Renaming

Arek Kasprzyk
Dear Lincoln:

 

As you requested on January 24, 2012, I agreed to have a private discussion with you as I truly believed that you would want to come to an agreement that would be mutually beneficial, while also being beneficial to the entire scientific community (including the ICGC).  I am shocked and disappointed that your proposal did not address my main concerns, which, as discussed are as follows:

 

1) The BioMart code base is being renamed at OICR.

2) You intend to split the BioMart code base, thus creating a separate (yet almost identical) product.

 

I am also shocked and disappointed that when I privately reiterated my concerns and reminded you that there is absolutely no need to rename or split the project since all ICGC-specific customizations can be achieved through project specific configuration (a solution that has worked for all BioMart projects throughout the years, including the ICGC), you refused to engage in any constructive dialogue and plainly stated on February 2, 2012 that you "will not negotiate with me any further on this matter." 

 

Prior to my departure from the institute, I distinctly remember that three of the five OICR values were:

a) Excellence (scientific and ethical)

b) Innovation; and

c) Teamwork

 

In my opinion, your current actions seem to be at odds with these values:


a) By choosing to rename the ICGC data management solution (e.g. "SciMart", "ICGCdb", "franchise"), which has been credited to BioMart (http://database.oxfordjournals.org/content/2011/bar026.full), the result of your colleagues ideas, concepts and algorithms, it raises a number of ethical questions.  None of the other 40+ groups that use BioMart (http://www.biomart.org/community.html) feel it is necessary to rename it in order to support their customizations. OICR should not be any different.   

b) By splitting the BioMart code base, you are duplicating efforts, and simply reinventing the wheel.  As a result, rather than having one highly innovative and unified system (http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1815.html), there will be two almost identical yet incompatible systems, which will impede existing and future collaborations, and create unnecessary confusion and problems for the ICGC and the rest of the scientific community.

c) You have decided to terminate a highly successful collaboration with the BioMart project and rebuffed my many attempts to reinstate a collaboration with me and/or the other BioMart developers.  Expertise the ICGC DCC could certainly benefit from seeing that the last functional software release was in May 2011 - nine months ago.  Had OICR decided to continue to collaborate with the BioMart team, all of the ICGC-specific customizations (e.g. data loading and visualization tools) could have been easily implemented months ago.

 

Based on all of this, I have no doubt that in the end, you will choose to rectify the current situation by:

 

1) No longer attempting to rename BioMart (e.g. "SciMart", "ICGCdb", "franchise", etc)

2) Restoring all BioMart repository names at OICR to "BioMart" (e.g. https://github.com/oicr/icgcdb should be renamed https://github.com/biomart)

3) Ensuring that as long as OICR is using the BioMart code base, all funding applications and publications (current and future), which describe ICGC's data management solution, refer to it as BioMart rather than "SciMart", "ICGCdb", or "franchise", etc.

4) Allowing BioMart experts from outside of OICR to participate in BioMart's development so that they may guide the ICGC DCC through the implementation of ICGC customizations.

 

 

Very truly yours,

 

Arek


PS: since some of the emails were deleted from the latest "public" email thread, I've taken the liberty of reconstructing this thread (below) for the sake of clarity and transparency.

-- 

Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead



On Tue, Jan 24, 2012 at 9:01 AM, Arek Kasprzyk <[hidden email]> wrote:
Dear Lincoln,

That is great news!

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


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,
a

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 Mon, Jan 23, 2012 at 9:47 AM, Arek Kasprzyk <[hidden email]> wrote:
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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Re: Open Letter to Lincoln Stein RE: BioMart Renaming

Arek Kasprzyk
Dear Lincoln,

As discussed over the course of the last few months, I have had two main concerns regarding the use of BioMart at OICR:


1) The BioMart code base was being renamed at OICR (e.g.  "SciMart", "ICGCdb", "franchise").

2) You intended/still intend to split the BioMart code base.


I am pleased that you have taken my first concern seriously by proposing on February 27, 2012 to "rename the github version to BioMart, give me sole admin control of it" and confirming on March 13, 2012 that you "switched the labelling of the code base at GitHub last week and made me its admin".

As for my second concern, I am disappointed and surprised that this issue has yet to be rectified. I completely disagree with the plans you noted in your email dated February 27, 2012, to "continue our ICGC development in a private (not publicly visible) BioMart". If, as you mentioned, you intend to continue BioMart development, then it should be done in a single and publicly visible BioMart code base. Any type of secret development is against the open source values of the BioMart project that promote transparency, community building, collaboration and code reuse. 



Request RE: OICR advisory bodies and funding agencies
----------------------------------------------------------------------------------

By working together, both OICR and the BioMart project have enjoyed remarkable success.  As a result of my leadership of BioMart's development and the innovative and flexible architecture I put in place, the challenging ICGC data management goals, were achieved 2 years ahead of schedule (i.e., by the time the 5th ICGC workshop in Kyoto took place).  This success did not go unnoticed as it resulted in a number of high profile publications.

Despite this success, following my departure from OICR, you decided to take over BioMart's development, split the BioMart code base and finally on January 20, 2012 announced your intention to develop a new data management solution for ICGC, although there is no technical justification or benefits to be gained by doing so. On the contrary, as I've noted in a number of previous email exchanges, this plan is problematic for the ICGC as well as the rest of the scientific community as it leads to incompatibilities and thus  impedes collaborations and creates problems for the users. I am yet to comprehend why, given all these problems, it is so critical for you to dismantle perfectly working ICGC data management system that I put in place.

My numerous offers to continue collaborating with you and provide my free cutting edge software and the BioMart group's expertise were rebuffed, although this would substantially reduce the costs that would be necessary if you chose to split the BioMart code or replace BioMart entirely. OICR/ICGC as well as other similar organizations/efforts pledge to use their funding in the best interest of the scientific community. Given this mandate, it seems absurd to reinvent the wheel and replace BioMart, which OICR has already invested years and millions of dollars in and has proven to be a ground-breaking cost-effective solution.    

At the very least I believe that the OICR/ICGC advisory bodies and funding agencies should be informed that there is a much better alternative to your current plan. I am convinced that these organizations will agree with me that if BioMart and OICR continue working together, it is in the best interest of the scientific community. This would prevent the multiple problems your plan creates, make data available to a much wider scientific audience,  deliver all the solutions that you require in a fraction of the time but most importantly would save the funding agencies the millions of dollars that would be required to unnecessarily develop a new ICGC data management system.  

I therefore would like to officially request that OICR's management team enable me to present my arguments to the OICR/ICGC advisory and funding and bodies against your intention to split the BioMart code base and/or eventually replace it.

Very truly yours,

Arek


-- 

Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead



On Mon, Feb 13, 2012 at 1:25 AM, Arek Kasprzyk <[hidden email]> wrote:
Dear Lincoln:

 

As you requested on January 24, 2012, I agreed to have a private discussion with you as I truly believed that you would want to come to an agreement that would be mutually beneficial, while also being beneficial to the entire scientific community (including the ICGC).  I am shocked and disappointed that your proposal did not address my main concerns, which, as discussed are as follows:

 

1) The BioMart code base is being renamed at OICR.

2) You intend to split the BioMart code base, thus creating a separate (yet almost identical) product.

 

I am also shocked and disappointed that when I privately reiterated my concerns and reminded you that there is absolutely no need to rename or split the project since all ICGC-specific customizations can be achieved through project specific configuration (a solution that has worked for all BioMart projects throughout the years, including the ICGC), you refused to engage in any constructive dialogue and plainly stated on February 2, 2012 that you "will not negotiate with me any further on this matter." 

 

Prior to my departure from the institute, I distinctly remember that three of the five OICR values were:

a) Excellence (scientific and ethical)

b) Innovation; and

c) Teamwork

 

In my opinion, your current actions seem to be at odds with these values:


a) By choosing to rename the ICGC data management solution (e.g. "SciMart", "ICGCdb", "franchise"), which has been credited to BioMart (http://database.oxfordjournals.org/content/2011/bar026.full), the result of your colleagues ideas, concepts and algorithms, it raises a number of ethical questions.  None of the other 40+ groups that use BioMart (http://www.biomart.org/community.html) feel it is necessary to rename it in order to support their customizations. OICR should not be any different.   

b) By splitting the BioMart code base, you are duplicating efforts, and simply reinventing the wheel.  As a result, rather than having one highly innovative and unified system (http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1815.html), there will be two almost identical yet incompatible systems, which will impede existing and future collaborations, and create unnecessary confusion and problems for the ICGC and the rest of the scientific community.

c) You have decided to terminate a highly successful collaboration with the BioMart project and rebuffed my many attempts to reinstate a collaboration with me and/or the other BioMart developers.  Expertise the ICGC DCC could certainly benefit from seeing that the last functional software release was in May 2011 - nine months ago.  Had OICR decided to continue to collaborate with the BioMart team, all of the ICGC-specific customizations (e.g. data loading and visualization tools) could have been easily implemented months ago.

 

Based on all of this, I have no doubt that in the end, you will choose to rectify the current situation by:

 

1) No longer attempting to rename BioMart (e.g. "SciMart", "ICGCdb", "franchise", etc)

2) Restoring all BioMart repository names at OICR to "BioMart" (e.g. https://github.com/oicr/icgcdb should be renamed https://github.com/biomart)

3) Ensuring that as long as OICR is using the BioMart code base, all funding applications and publications (current and future), which describe ICGC's data management solution, refer to it as BioMart rather than "SciMart", "ICGCdb", or "franchise", etc.

4) Allowing BioMart experts from outside of OICR to participate in BioMart's development so that they may guide the ICGC DCC through the implementation of ICGC customizations.

 

 

Very truly yours,

 

Arek


PS: since some of the emails were deleted from the latest "public" email thread, I've taken the liberty of reconstructing this thread (below) for the sake of clarity and transparency.

-- 

Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead



On Tue, Jan 24, 2012 at 9:01 AM, Arek Kasprzyk <[hidden email]> wrote:
Dear Lincoln,

That is great news!

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


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,
a

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 Mon, Jan 23, 2012 at 9:47 AM, Arek Kasprzyk <[hidden email]> wrote:
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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Re: Open Letter to Lincoln Stein RE: BioMart Renaming

Thomas Hudson

Dear all:

 

I would like to apologize for contacting you all in this way.

 

Lincoln and I could choose to send responses to all, but I believe that this would be inappropriate to do it this way.

 

I sent a request to Dr. Kasprzyk suggesting that I will bring his issues forward to the ICGC Exec this Thursday. I will suggest that a three person panel that is independent of OICR be made aware of the complex issues that have arisen over the past year. Dr. Kasprzyk can be involved with the selection of the panel.

 

I am awaiting for Dr. Kasprzyk to agree that he would abide by conclusions of this independent assessment.

 

Lincoln Stein is fine with this.

 

I will not send out additional messages to everyone. The outcome of Arek’s response and next steps (if any) will be reported to attendees of the ICGC workshop after the EXEC meeting on Thursday.

 

There are several OICR people at the ICGC workshop, and I ask that they not be prodded for details.

 

Thank you,

 

Tom

 

 

From: Arek Kasprzyk [mailto:[hidden email]]
Sent: Tuesday, March 20, 2012 10:25 AM
To: Lincoln Stein
Cc: [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; Brett Whitty; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; Francis Ouellette; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; John McPherson; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; Lakshmi Muthuswamy; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; Paul Boutros; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; Thomas Hudson; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; Vincent Ferretti; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; [hidden email]; Abigail Cabunoc; [hidden email]; Amin Zia; Anthony Cros; [hidden email]; Bob Gibson; Brian O'Connor; Brian Ott; Carson Holt; Chenyi Liu; Christina Yung; [hidden email]; [hidden email]; Cindy Yao; Daihai He; Daryl Waggott; David Sutton; David Yim; Denise Mak; Ekaterina Kouzmina; Elena Rivkin; Emilie Chautard; Fouad Yousif; Francis Nguyen; Gavin Wilson; [hidden email]; Hassaan Aamir; Heeyeon Song; Hilary Snider; Irina Kalatskaya; Ivan Borozan; Jack Hsu; Jagadish Rangrej; [hidden email]; Jennifer Liu; Jianxin Wang; Joachim Baran; Joel Weiser; John Watson; Jonathan Guberman; Joseph Yamada; Julie Moon; Junjun Zhang; Kaman Wu; Karen Rothfels; [hidden email]; [hidden email]; Kenneth Chu; Kimberly Begley; Long Yao; Marc Perry; Marie Wong-Erasmus; Marija Orlic-Milacic; Mathieu Lemire; Maud Starmans; Michael Fraser; Michelle Brazas; Michelle Chan-Seng-Yue; Miyuki Fukuma; Monika-Bianca Torio; Morgan Taschuk; Natalie Fox; Natasha Lander; Nicholas Harding; Niloofar Arshadi; Noushin Taghavi; Peter Raboud; Peter Ruzanov; Quang Trinh; [hidden email]; Raffi Melkon; Renata Musa; [hidden email]; Richard De Borja; Rob Denroche; Robin Haw; Rui Yan; Shane Wilson; Shaoming Yin; [hidden email]; [hidden email]; Stephenie Prokopec; Stuart Lawler; Stuart Watt; Sujata Syam; Sylvia Shiah; Tatiana Lomasko; Timothy Beck; Tony DeBat; Wei Jiao; Winston Yeung; Xiaoqi Shi; Xinyi Zhang; [hidden email]; Yonathan Brhane; Yong Liang; Zheng Zha; [hidden email]; Jennifer Jennings; Nicole Baryla; Vanya Peltekova; Brad Wouters; Estrella, Heather; Kan, Zhengyan
Subject: Re: Open Letter to Lincoln Stein RE: BioMart Renaming

 

Dear Lincoln,

 

As discussed over the course of the last few months, I have had two main concerns regarding the use of BioMart at OICR:

 

1) The BioMart code base was being renamed at OICR (e.g.  "SciMart", "ICGCdb", "franchise").

2) You intended/still intend to split the BioMart code base.

 

I am pleased that you have taken my first concern seriously by proposing on February 27, 2012 to "rename the github version to BioMart, give me sole admin control of it" and confirming on March 13, 2012 that you "switched the labelling of the code base at GitHub last week and made me its admin".

 

As for my second concern, I am disappointed and surprised that this issue has yet to be rectified. I completely disagree with the plans you noted in your email dated February 27, 2012, to "continue our ICGC development in a private (not publicly visible) BioMart". If, as you mentioned, you intend to continue BioMart development, then it should be done in a single and publicly visible BioMart code base. Any type of secret development is against the open source values of the BioMart project that promote transparency, community building, collaboration and code reuse. 

 

 

Request RE: OICR advisory bodies and funding agencies

----------------------------------------------------------------------------------

 

By working together, both OICR and the BioMart project have enjoyed remarkable success.  As a result of my leadership of BioMart's development and the innovative and flexible architecture I put in place, the challenging ICGC data management goals, were achieved 2 years ahead of schedule (i.e., by the time the 5th ICGC workshop in Kyoto took place).  This success did not go unnoticed as it resulted in a number of high profile publications.

 

Despite this success, following my departure from OICR, you decided to take over BioMart's development, split the BioMart code base and finally on January 20, 2012 announced your intention to develop a new data management solution for ICGC, although there is no technical justification or benefits to be gained by doing so. On the contrary, as I've noted in a number of previous email exchanges, this plan is problematic for the ICGC as well as the rest of the scientific community as it leads to incompatibilities and thus  impedes collaborations and creates problems for the users. I am yet to comprehend why, given all these problems, it is so critical for you to dismantle perfectly working ICGC data management system that I put in place.

 

My numerous offers to continue collaborating with you and provide my free cutting edge software and the BioMart group's expertise were rebuffed, although this would substantially reduce the costs that would be necessary if you chose to split the BioMart code or replace BioMart entirely. OICR/ICGC as well as other similar organizations/efforts pledge to use their funding in the best interest of the scientific community. Given this mandate, it seems absurd to reinvent the wheel and replace BioMart, which OICR has already invested years and millions of dollars in and has proven to be a ground-breaking cost-effective solution.    

 

At the very least I believe that the OICR/ICGC advisory bodies and funding agencies should be informed that there is a much better alternative to your current plan. I am convinced that these organizations will agree with me that if BioMart and OICR continue working together, it is in the best interest of the scientific community. This would prevent the multiple problems your plan creates, make data available to a much wider scientific audience,  deliver all the solutions that you require in a fraction of the time but most importantly would save the funding agencies the millions of dollars that would be required to unnecessarily develop a new ICGC data management system.  

 

I therefore would like to officially request that OICR's management team enable me to present my arguments to the OICR/ICGC advisory and funding and bodies against your intention to split the BioMart code base and/or eventually replace it.

 

Very truly yours,


Arek


-- 

Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead

 

On Mon, Feb 13, 2012 at 1:25 AM, Arek Kasprzyk <[hidden email]> wrote:

Dear Lincoln:

 

As you requested on January 24, 2012, I agreed to have a private discussion with you as I truly believed that you would want to come to an agreement that would be mutually beneficial, while also being beneficial to the entire scientific community (including the ICGC).  I am shocked and disappointed that your proposal did not address my main concerns, which, as discussed are as follows:

 

1) The BioMart code base is being renamed at OICR.

2) You intend to split the BioMart code base, thus creating a separate (yet almost identical) product.

 

I am also shocked and disappointed that when I privately reiterated my concerns and reminded you that there is absolutely no need to rename or split the project since all ICGC-specific customizations can be achieved through project specific configuration (a solution that has worked for all BioMart projects throughout the years, including the ICGC), you refused to engage in any constructive dialogue and plainly stated on February 2, 2012 that you "will not negotiate with me any further on this matter." 

 

Prior to my departure from the institute, I distinctly remember that three of the five OICR values were:

a) Excellence (scientific and ethical)

b) Innovation; and

c) Teamwork

 

In my opinion, your current actions seem to be at odds with these values:

 

a) By choosing to rename the ICGC data management solution (e.g. "SciMart", "ICGCdb", "franchise"), which has been credited to BioMart (http://database.oxfordjournals.org/content/2011/bar026.full), the result of your colleagues ideas, concepts and algorithms, it raises a number of ethical questions.  None of the other 40+ groups that use BioMart (http://www.biomart.org/community.html) feel it is necessary to rename it in order to support their customizations. OICR should not be any different.   

b) By splitting the BioMart code base, you are duplicating efforts, and simply reinventing the wheel.  As a result, rather than having one highly innovative and unified system (http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1815.html), there will be two almost identical yet incompatible systems, which will impede existing and future collaborations, and create unnecessary confusion and problems for the ICGC and the rest of the scientific community.

c) You have decided to terminate a highly successful collaboration with the BioMart project and rebuffed my many attempts to reinstate a collaboration with me and/or the other BioMart developers.  Expertise the ICGC DCC could certainly benefit from seeing that the last functional software release was in May 2011 - nine months ago.  Had OICR decided to continue to collaborate with the BioMart team, all of the ICGC-specific customizations (e.g. data loading and visualization tools) could have been easily implemented months ago.

 

Based on all of this, I have no doubt that in the end, you will choose to rectify the current situation by:

 

1) No longer attempting to rename BioMart (e.g. "SciMart", "ICGCdb", "franchise", etc)

2) Restoring all BioMart repository names at OICR to "BioMart" (e.g. https://github.com/oicr/icgcdb should be renamed https://github.com/biomart)

3) Ensuring that as long as OICR is using the BioMart code base, all funding applications and publications (current and future), which describe ICGC's data management solution, refer to it as BioMart rather than "SciMart", "ICGCdb", or "franchise", etc.

4) Allowing BioMart experts from outside of OICR to participate in BioMart's development so that they may guide the ICGC DCC through the implementation of ICGC customizations.

 

 

Very truly yours,

 

Arek

 

PS: since some of the emails were deleted from the latest "public" email thread, I've taken the liberty of reconstructing this thread (below) for the sake of clarity and transparency.

-- 

Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead

 

 

On Tue, Jan 24, 2012 at 9:01 AM, Arek Kasprzyk <[hidden email]> wrote:

Dear Lincoln,

 

That is great news!

 

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

 

 

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,

a

 

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 Mon, Jan 23, 2012 at 9:47 AM, Arek Kasprzyk <[hidden email]> wrote:

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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Re: Open Letter to Lincoln Stein RE: BioMart Renaming

Arek Kasprzyk
In reply to this post by Arek Kasprzyk
Dear Tom and Lincoln

I appreciate the rapid replies I received yesterday following my latest email.  I've replied to your most salient points below.


Re: Suggestion to bring my issue forward to the ICGC Exec this week. 
I am pleased that you believe (as I do) that there is a need to independently assess whether the decision to split the BioMart code base is taken in the best interest of the scientific community, which includes the OICR/ICGC.  

Since you have kindly invited me to be involved in the selection of the panel I request that:
1) The panel consist of top experts in the fields of bioinformatics, data management and open source so that a meaningful assessment can be made.  
2) The assessment process be completely transparent.

I am sure this is your intent as well, however I want ensure we are on the same page prior to beginning this process.

Re: the circumstances of my departure
I would have preferred to keep our discussions on a technical and professional level.  I am therefore disappointed that you felt the need to allude to the "circumstances" surrounding my "dismissal", despite admitting yourself that this is "unrelated to the quality of my software development or scientific work".  Since it is my understanding that as of late, OICR has chosen to undergo an independent investigation related to those very circumstances and those allegedly involved, I would think that it is in OICR's best interest, to avoid discussing these issues on a public forum such as GMOD.


Re: Reasons for a BioMart Split 
Since we've begun our debate regarding the BioMart split, there have been a number of statements made, which were both blatantly untrue and misleading for those without technical knowledge of the current BioMart software.  For instance:

On January 19, 2012, you stated that: "internal changes to the code base were badly needed in order to support the scalability of the ICGC DCC".  As previously noted, the current version of the BioMart software is fully functional and perfectly scalable as a result of the parallel query engine, which was implemented months prior to my departure from OICR. 

More recently, on March 20, 2012, you stated that "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." I have always encouraged you and the ICGC DCC to continue development in the single, publicly visible BioMart code base; I do not comprehend why you are so reluctant to do so.

You have yet to provide valid and logical reasons for this intended split. 

Regards,
a



On Tue, Mar 20, 2012 at 10:25 AM, Arek Kasprzyk <[hidden email]> wrote:
Dear Lincoln,

As discussed over the course of the last few months, I have had two main concerns regarding the use of BioMart at OICR:


1) The BioMart code base was being renamed at OICR (e.g.  "SciMart", "ICGCdb", "franchise").

2) You intended/still intend to split the BioMart code base.


I am pleased that you have taken my first concern seriously by proposing on February 27, 2012 to "rename the github version to BioMart, give me sole admin control of it" and confirming on March 13, 2012 that you "switched the labelling of the code base at GitHub last week and made me its admin".

As for my second concern, I am disappointed and surprised that this issue has yet to be rectified. I completely disagree with the plans you noted in your email dated February 27, 2012, to "continue our ICGC development in a private (not publicly visible) BioMart". If, as you mentioned, you intend to continue BioMart development, then it should be done in a single and publicly visible BioMart code base. Any type of secret development is against the open source values of the BioMart project that promote transparency, community building, collaboration and code reuse. 



Request RE: OICR advisory bodies and funding agencies
----------------------------------------------------------------------------------

By working together, both OICR and the BioMart project have enjoyed remarkable success.  As a result of my leadership of BioMart's development and the innovative and flexible architecture I put in place, the challenging ICGC data management goals, were achieved 2 years ahead of schedule (i.e., by the time the 5th ICGC workshop in Kyoto took place).  This success did not go unnoticed as it resulted in a number of high profile publications.

Despite this success, following my departure from OICR, you decided to take over BioMart's development, split the BioMart code base and finally on January 20, 2012 announced your intention to develop a new data management solution for ICGC, although there is no technical justification or benefits to be gained by doing so. On the contrary, as I've noted in a number of previous email exchanges, this plan is problematic for the ICGC as well as the rest of the scientific community as it leads to incompatibilities and thus  impedes collaborations and creates problems for the users. I am yet to comprehend why, given all these problems, it is so critical for you to dismantle perfectly working ICGC data management system that I put in place.

My numerous offers to continue collaborating with you and provide my free cutting edge software and the BioMart group's expertise were rebuffed, although this would substantially reduce the costs that would be necessary if you chose to split the BioMart code or replace BioMart entirely. OICR/ICGC as well as other similar organizations/efforts pledge to use their funding in the best interest of the scientific community. Given this mandate, it seems absurd to reinvent the wheel and replace BioMart, which OICR has already invested years and millions of dollars in and has proven to be a ground-breaking cost-effective solution.    

At the very least I believe that the OICR/ICGC advisory bodies and funding agencies should be informed that there is a much better alternative to your current plan. I am convinced that these organizations will agree with me that if BioMart and OICR continue working together, it is in the best interest of the scientific community. This would prevent the multiple problems your plan creates, make data available to a much wider scientific audience,  deliver all the solutions that you require in a fraction of the time but most importantly would save the funding agencies the millions of dollars that would be required to unnecessarily develop a new ICGC data management system.  

I therefore would like to officially request that OICR's management team enable me to present my arguments to the OICR/ICGC advisory and funding and bodies against your intention to split the BioMart code base and/or eventually replace it.

Very truly yours,

Arek


-- 

Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead



On Mon, Feb 13, 2012 at 1:25 AM, Arek Kasprzyk <[hidden email]> wrote:
Dear Lincoln:

 

As you requested on January 24, 2012, I agreed to have a private discussion with you as I truly believed that you would want to come to an agreement that would be mutually beneficial, while also being beneficial to the entire scientific community (including the ICGC).  I am shocked and disappointed that your proposal did not address my main concerns, which, as discussed are as follows:

 

1) The BioMart code base is being renamed at OICR.

2) You intend to split the BioMart code base, thus creating a separate (yet almost identical) product.

 

I am also shocked and disappointed that when I privately reiterated my concerns and reminded you that there is absolutely no need to rename or split the project since all ICGC-specific customizations can be achieved through project specific configuration (a solution that has worked for all BioMart projects throughout the years, including the ICGC), you refused to engage in any constructive dialogue and plainly stated on February 2, 2012 that you "will not negotiate with me any further on this matter." 

 

Prior to my departure from the institute, I distinctly remember that three of the five OICR values were:

a) Excellence (scientific and ethical)

b) Innovation; and

c) Teamwork

 

In my opinion, your current actions seem to be at odds with these values:


a) By choosing to rename the ICGC data management solution (e.g. "SciMart", "ICGCdb", "franchise"), which has been credited to BioMart (http://database.oxfordjournals.org/content/2011/bar026.full), the result of your colleagues ideas, concepts and algorithms, it raises a number of ethical questions.  None of the other 40+ groups that use BioMart (http://www.biomart.org/community.html) feel it is necessary to rename it in order to support their customizations. OICR should not be any different.   

b) By splitting the BioMart code base, you are duplicating efforts, and simply reinventing the wheel.  As a result, rather than having one highly innovative and unified system (http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1815.html), there will be two almost identical yet incompatible systems, which will impede existing and future collaborations, and create unnecessary confusion and problems for the ICGC and the rest of the scientific community.

c) You have decided to terminate a highly successful collaboration with the BioMart project and rebuffed my many attempts to reinstate a collaboration with me and/or the other BioMart developers.  Expertise the ICGC DCC could certainly benefit from seeing that the last functional software release was in May 2011 - nine months ago.  Had OICR decided to continue to collaborate with the BioMart team, all of the ICGC-specific customizations (e.g. data loading and visualization tools) could have been easily implemented months ago.

 

Based on all of this, I have no doubt that in the end, you will choose to rectify the current situation by:

 

1) No longer attempting to rename BioMart (e.g. "SciMart", "ICGCdb", "franchise", etc)

2) Restoring all BioMart repository names at OICR to "BioMart" (e.g. https://github.com/oicr/icgcdb should be renamed https://github.com/biomart)

3) Ensuring that as long as OICR is using the BioMart code base, all funding applications and publications (current and future), which describe ICGC's data management solution, refer to it as BioMart rather than "SciMart", "ICGCdb", or "franchise", etc.

4) Allowing BioMart experts from outside of OICR to participate in BioMart's development so that they may guide the ICGC DCC through the implementation of ICGC customizations.

 

 

Very truly yours,

 

Arek


PS: since some of the emails were deleted from the latest "public" email thread, I've taken the liberty of reconstructing this thread (below) for the sake of clarity and transparency.

-- 

Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead



On Tue, Jan 24, 2012 at 9:01 AM, Arek Kasprzyk <[hidden email]> wrote:
Dear Lincoln,

That is great news!

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


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,
a

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 Mon, Jan 23, 2012 at 9:47 AM, Arek Kasprzyk <[hidden email]> wrote:
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







--

Arek Kasprzyk, MD, MSc, PhD 
BioMart Project Lead



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