[GMOD-devel] Fwd: UPDATE - RE: Open Letter to Lincoln Stein RE: BioMart Renaming

[Arek K. <are...@gm...>]

Hi everyone,

This email was sent to the GMOD mailing list (along with other recipients)
on December 11th 2012 but it  had never reached its destination. According
to Scott: "It seems that mailman misplaced it since you sent it".

It is very important that we are fully transparent on this issue.


Regards,
a





---------- Forwarded message ----------
From: Arek Kasprzyk <are...@gm...>
Date: Tue, Dec 11, 2012 at 3:11 AM
Subject: Re: Follow-up - RE: Open Letter to Lincoln Stein RE: BioMart
Renaming

Dear All,

As you may recall, following six months of unsuccessful attempts to
establish a constructive dialog with Dr Stein and Dr Hudson regarding Dr
Stein's decision to rename/split/replace BioMart, I was forced to raise my
concerns in an open letter.

 My concerns are outlined below:

*Ethical*

I am concerned that Dr. Stein and/or OICR Scientists reporting to him will
refer to BioMart under a different name ((“SciMart”, “ICGCdb”, “OICR
internal version”, “franchise system”, “forked version of BioMart” etc) to
attract funding despite the fact that BioMart is the result of their former
colleague’s innovative ideas, concepts and algorithms (as documented in
http://database.oxfordjournals.org/content/2011/bar026.full and
http://www.biomart.org/publications.html)

*Public Funding*

I am concerned with Dr. Stein’s decision to “split/fork” the BioMart code
base as this unnecessarily wastes public resources by creating a situation
whereby two almost identical code bases are being developed simultaneously.

I am also concerned with Dr. Stein’s announcement to the ICGC that he plans
on eventually eliminating BioMart altogether and re-creating a new ICGC
data management solution.  Considering OICR has spent millions of dollars
to continue BioMart’s development after I brought it to the institute in
2008 and it has proved to be a highly innovative, successful and publicized
data management solution, it seems absurd to reinvent the wheel, thereby
wasting time and public funding.

*Scientific Community*

In addition to supporting OICR and ICGC scientists, the current BioMart
development model also supports scientific communities in a number of other
organizations around the world without any extra effort or funding.  I am
concerned that Dr. Stein’s decisions have created a number of serious
problems for the scientific community that can be easily avoided by maintaining
a single BioMart code base.

 In March 2012 I requested that my concerns be presented to the funding
bodies that provide support for ICGC DCC. In response, Dr Hudson promptly
suggested that the issue should instead be decided by an independent panel
of experts. In the interest of transparency, I am providing you with an
update which is detailed below.

Please note that I have copied Dr Hudson, Dr Guyer and Professor Chalmers
on this email in order to give them the opportunity, if they so wish, to
confirm the accuracy of the information it contains.



1. Independent panel of experts

On 22nd March 2012, immediately after Dr Hudson's discussion with the ICGC
Executive committee while in Cannes, I received an email informing me: *"Two
ICGC leaders from EXEC and EPC/IDAC offered to take charge of the selection
process."* He also noted that I *"can be involved with the selection of the
panel"* and that he *"will not be involved in that process".* Consequently,
I provided a list of preliminary suggestions directly to the ICGC Exec in
my open letter dated April 19th but received no reply. On 21st May 2012,
almost two months after the initial email from Dr Hudson, I received an
email signed by Professor Chalmers and Dr. Guyer, informing me:  "*The
Executive requested Dr Mark Guyer and me to act as members of a panel*".  I
expressed my surprise that the panel had been chosen without my input,
contrary to the information received from Dr Hudson. In response, Professor
Chalmers and Dr Guyer offered the following explanation in their letter
dated 7th July: *"We are not in a position to understand the basis on which
Dr. Hudson made this factually inaccurate comment"**.** *Although I was
surprised by the fact that according to Professor Chalmers and Dr Guyer I
had been given inaccurate and misleading information by the Chair of the
ICGC Executive Committee and the President and Scientific Director of the
OICR, I agreed that time was of the essence and proceeded to ask Professor
Chalmers and Dr Guyer a number of procedural questions and received their
response in a letter dated 31st August:

*Question*: *Will the panel’s decision be binding?
**Response:* “*our final report and decisions cannot be “binding**””
*
*Question*: *Will the ICGC/OICR (and its representatives) be required to
abide by the panel’s decision?
**Response:* “*We have no appointment from the OICR and do not report to
them**”*.

*Question*: *In order to ensure that both parties, the OICR/ICGC and the
BioMart Project Team, are equally represented, would you be agreeable to
inviting two of my nominees to join the panel? Alternatively, if only one
of my nominees was invited to join the panel, would you be agreeable to
allowing this member to have veto power?
**Response:*   *“legally and procedurally, this is not possible*.”



2. OICR BioMart funding applications

I am deeply concerned by the discrepancy between OICR’s leadership public
declarations and their actions with regards to BioMart funding
applications. In reply to my open letter request made on 23rd January 2012
that among other things, OICR correctly “*Refer to BioMart in funding
applications, which describe their data management system*, Dr Stein stated
“*All these requests are reasonable, and I would not dream of doing
otherwise!*” Contrary to his public pledge, Dr Stein continues to encourage
OICR employees that report to him to seek funding referring to BioMart as
“SciMart” that creates a misleading impression that “SciMart” is a distinct
product from BioMart. At least two such applications have been made so far.
Dr Hudson admitted in his email dated 17th July: "*Both applications
proposed to using SciMart, a forked version of BioMart*". However, in reply
to my request to review the sections of those applications pertaining to
BioMart, Dr Hudson stated in his email dated 18th July: "*I have no
interest in following up"**. *The latest application referring to BioMart
as "SciMart" (Dr Boutros "Systems Biology of Tumour Hypoxia",Terry Fox
Foundation) was submitted by OICR on 5th June 2012 (over two months
after Dr Hudson public initiative to resolve BioMart dispute through the
independent panel of experts).


3. Suggested amendments to the review process

Although I have a deep personal respect for the integrity of Dr Hudson, Dr
Guyer and Professor Chalmers, I am deeply concerned that OICR’s continuing
efforts to attract funding to the BioMart development under a different
name (contrary to public declarations made by Dr Stein) seriously undermine
the credibility of Dr Hudson's initiative. Additionally, a number of
procedural difficulties reported by Professor Chalmers and Dr Guyer in
establishing a fair panel and a transparent review process question the
panel's impartial mandate. Finally, the fact that OICR is not bound by the
panel's decisions renders the panel impotent to resolve the OICR/BioMart
dispute and defeats its very purpose.

However, I have absolutely no doubt that the Chair of the ICGC Executive
Committee and the President and Scientific Director of the OICR is
committed to high academic standards and rigor. Thus, he will be keen to
restore the trust of ICGC and the rest of the scientific community in his
undoubtedly useful initiative to resolve the OICR/BioMart dispute through
an independent panel of experts by kindly agreeing to the proposed
amendments to the review process:


   - Any funding applications and publications submitted or planned that
   refer to BioMart under different names (“SciMart”, “ICGCdb”, “OICR internal
   version”, “franchise system”, “forked version of BioMart” etc) are to be
   corrected without any further delay and the corrections independently
   verified until the panel deliberations are over.


   - Since Dr Stein is yet to reveal to the ICGC and the rest of the
   scientific community what exactly is to be gained from his decision to
   rename/split/replace BioMart, he will kindly disclose the scientific
   rationale behind his decision. I will follow with my arguments in favour of
   the development of BioMart as a single project, after which deliberations
   of the panel may commence. This will keep the process transparent and the
   scientific community engaged.


   - Professor Chalmers and Dr Guyer are provided with a mandate that would
   make it ‘*legally and procedurally’* possible to establish a fair review
   panel; either a representative one where both sides of the dispute are
   represented equally or an independent one, "*consisting of members with
   the necessary expertise and who are free of conflict of interest either
   perceived or real*" as stated in the Tri-Council guidelines. (Since Dr
   Hudson leads the EXEC and Dr Stein is a prominent member/leader of other
   ICGC working groups, I don't think that the EXEC and/or the EPC/IDAC
   members can be considered free of conflict of interest either perceived or
   real. This perception is not removed by the fact that Dr Hudson and Dr
   Stein do not participate in the panel and Professor Chalmers and Dr Guyer
   report to the Exec rather than directly to the chair of the Exec, Dr Hudson)


   - Dr Hudson and all other OICR employees (including Dr Stein) shall be
   bound by the decision of the panel.


Kind regards,

Arek
-- 
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org






On Thu, Apr 19, 2012 at 3:11 PM, Arek Kasprzyk <are...@gm...>wrote:

> Dear members of the ICGC Executive Committee:
>
>
>
> Following my email to Lincoln Stein and Tom Hudson dated March 22, 2012
> (below) I've been informed that the ICGC EXEC suggested that one member
> from the EXEC and one member from the Ethics and Policy Committee or
> International Data Access Committee would be assigned to establish a panel
> to discuss the ICGC/BioMart matter.  Since Tom informed me that I "can be
> involved with the selection of the panel", i subsequently, provided him
> with a list of preliminary suggestions.  However, since he noted that he
> "will not be involved in that process", I've decided to present my concerns
> and suggestions to you directly.
>
>
>
>
>
> *Concerns RE: BioMart Splitting/Renaming/Replacing Decision:*
>
> *
> *
>
> It is important that this decision undergoes a thorough scientific review
> and that this review is genuinely independent, meaningful
> and completely transparent since:
>
>
> 1. OICR has spent millions of dollars to continue BioMart development
> after I brought it to the institute in 2008.  It has proved to be a highly
> innovative, successful and publicized data management solution.  It
> therefore seems absurd to reinvent the wheel, thereby wasting time and
> public funding to simply remove the BioMart brand from the ICGC.
>
>
>
> 2. The current BioMart development model supports OICR and ICGC
> scientists as well as scientific communities in 27 other organizations
> around the world without any extra effort or funding.  Therefore, Lincoln's
> decision to split/rename/replace BioMart negatively affects a number of
> scientific organizations outside of OICR/ICGC and therefore it transcends
> the boundaries of OICR/ICGC and cannot be considered an internal issue.
>
>
>
> 3. The circumstances surrounding my departure from OICR are very complex.
>  In fact, they have resulted in an independent investigation into the
> alleged actions of an OICR leader.  I am concerned that despite this
> ongoing investigation, and the seriousness of these allegations, the
> circumstances of my departure are being publicly alluded to by Lincoln in
> order to justify the argument to split/rename/replace BioMart.
>
>
>
>
>
> *Concerns RE: Suggested Panel Selection Process:*
>
> While I greatly appreciate that the EXEC is taking a number of measures to
> ensure that an ethical and non-biased decision is made, for the following
> reasons, I am not certain that the suggestion that has been proposed is
> ideal:
>
>
>
> 1. Since Tom Hudson leads the EXEC and Lincoln Stein is a prominent
> member/leader of other ICGC working groups, I don't think that the EXEC
> and/or the EPC/IDAC members can be considered truly unbiased.
>
>
>
> 2. It is critical that the panel consists of individuals with sufficient
> expertise to deal with this matter. I am not sure if the EXEC and EPC/IDAC
> members who offered to take part in the selection process have significant
> knowledge in the matter and are in a position to make the appropriate
> decision.
>
>
>
>
>
> *Suggestions RE: Panel Selection Process:*
>
> 1. I will propose a three person panel with appropriate expertise (who may
> or may not be ICGC members). Needless to say, these will be outstanding
> scientists with unquestionable integrity and relevant expertise.
>
>
>
> 2. Tom, Lincoln, the EXEC, the EPC/IDAC, etc. are free to accept or reject
> my selection.
>
>
>
> 3. If a panel cannot be agreed upon, or proposed panel members are
> unwilling to participate, I suggest that the SAB established to guide the
> ICGC's funding (including the DCC) be the default panel as it is an
> established and independent body of experts.
>
>
>
> 4. Once the panel has been established, Lincoln and I will both submit our
> respective rationals, which explain why our option is better for the
> scientific community than our counterpart's.
>
>
>
> 5. The panel will provide the ruling and its justification based on our
> submissions along with any further necessary information and comments.
>
>
>
> 6. In the interest of transparency, the names of the panel members, our
> submissions and the panel ruling/comments are to be made public and
> submitted to the SAB (unless of course the panel is the SAB).
>
>
>
> 7. Lincoln is to stop any further development and/or renaming of BioMart
> until a decision is reached. (Please rest assured that this will absolutely
> not impact ICGC services as the ICGC portal is still supported by the
> BioMart software that I released a year ago).
>
>
>
> 8. All funding applications that refer to the BioMart code base as
> 'SciMart', 'franchise database', 'ICGCdb', etc. should be revised or put on
> hold until the matter is resolved.
>
>
>
>
>
> Kind regards,
>
>
>
> Arek
>
>
>
> --
>
> Arek Kasprzyk, MD, MSc, PhD
> BioMart Project Lead
>
> www.biomart.org
>
>
>
>
> On Thu, Mar 22, 2012 at 1:57 AM, Arek Kasprzyk <are...@gm...>wrote:
>
>> 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 <are...@gm...>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 <are...@gm...>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 <https://github.com/oicr/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 <are...@gm...
>>>> > wrote:
>>>>
>>>>> 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,
>>>>> 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 <
>>>> lin...@gm...> 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 <are...@gm...
>>>> > 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 <
>>>> Lin...@oi...> 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 <
>>>> are...@gm...> 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
>>
>>
>


-- 
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org