Silicos: Spectrophores ported under OB

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Silicos: Spectrophores ported under OB

Hans De Winter
All,

it is our pleasure to announce that Silicos NV, a Belgian-based company providing services in the field of computational drug discovery and virtual screening, has made a strategic decision to port its own developed software under the open source domain of Open Babel following the GNU GPL.

Porting Silicos' software under Open Babel will be done in three steps. The first of these will involve porting our Spectrophore code. The majority of the work on this has already been done and cross-checked with Tim Vandemeersch; we only need to finalize a standalone application and still have to provide some testing code. We anticipate this to be finalized next week and therefore hope that the Spectrophore code could be incorporated in the next major release of OB. A final issue however concerns an granted patent (WO2009146735) that protects the Spectrophore algorithm. We are aware that having a patent on an algorithm which is at the same time distributed as open source under the GNU GPL might be a difficult combination. Therefore we have decided to not further support this patent so that in the future their will be no issues on this anymore. However, in the meantime and until the time the patent has expired, we would like to guarantee potential users of the Spectrophore code that we will not issue patent infringment claims against individuals and institutions who use the Spectrophore software under the GNU General Public License. We plan to do this by including a modified header in the .h and .cpp files of the Spectrophore code. A proposal for this is given here:

/**********************************************************************
Spectrophore.h - Spectrophore(TM) calculator.
                 Declarations of OBSpectrophore

 

Copyright (C) 2005-2010 by Silicos NV

 

This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>

 

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

The algorithm in this software has been covered by patent WO2009146735.
However, Silicos NV and the inventors of the above mentioned patent assure 
that no patent infringment claims will be issued against individuals or
institutions that use this software under the GNU General Public License.

 

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

Of course, we would like to get feedback from you so that we are sure that this would be sufficient. Please note that the term 'Spectrophore' has also been trademarked. However, we don't think this should be an issue for releasing the code under open source.

In a second phase, planned for mid-summer 2010, we intent to release our pharmacophore-based alignment tool Pharao under the OB environment. Finally, our de-novo design tool, called Cosmos(TM), will be release under OB somewhere near the end of the summer 2010.

The reason why we have made this strategic decision to port all our software to the open source domain is that we, as management of Silicos, strongly believe in an open innovation model, and open source is just one of these factors that make open innovation possible. For Silicos as a company, we believe that by actively participating and supporting the OB community, we could create more business in the form of services than we could otherwise.

Please feel free to comment.
Kind regards,

Hans De Winter
CSO Silicos NV


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Re: Silicos: Spectrophores ported under OB

Noel O'Boyle
Administrator
Thanks Hans,

I'm looking forward to seeing this code in action.

I didn't realise you had some pharmacophore and de novo design
software on the way. I have an interest in (developing) pharmacophore
software myself, and in drug design in general so this looks very
interesting.

- Noel

On 1 July 2010 09:12, Hans De Winter <[hidden email]> wrote:

> All,
> it is our pleasure to announce that Silicos NV, a Belgian-based company
> providing services in the field of computational drug discovery and virtual
> screening, has made a strategic decision to port its own developed software
> under the open source domain of Open Babel following the GNU GPL.
> Porting Silicos' software under Open Babel will be done in three steps. The
> first of these will involve porting our Spectrophore code. The majority of
> the work on this has already been done and cross-checked with Tim
> Vandemeersch; we only need to finalize a standalone application and still
> have to provide some testing code. We anticipate this to be finalized next
> week and therefore hope that the Spectrophore code could be incorporated in
> the next major release of OB. A final issue however concerns an granted
> patent (WO2009146735) that protects the Spectrophore algorithm. We are aware
> that having a patent on an algorithm which is at the same time distributed
> as open source under the GNU GPL might be a difficult combination. Therefore
> we have decided to not further support this patent so that in the future
> their will be no issues on this anymore. However, in the meantime and until
> the time the patent has expired, we would like to guarantee potential users
> of the Spectrophore code that we will not issue patent infringment claims
> against individuals and institutions who use the Spectrophore software under
> the GNU General Public License. We plan to do this by including a modified
> header in the .h and .cpp files of the Spectrophore code. A proposal for
> this is given here:
> /**********************************************************************
> Spectrophore.h - Spectrophore(TM) calculator.
>                  Declarations of OBSpectrophore
>
>
>
> Copyright (C) 2005-2010 by Silicos NV
>
>
>
> This file is part of the Open Babel project.
> For more information, see <http://openbabel.sourceforge.net/>
>
>
>
> This program is free software; you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation version 2 of the License.
> The algorithm in this software has been covered by patent WO2009146735.
> However, Silicos NV and the inventors of the above mentioned patent assure
> that no patent infringment claims will be issued against individuals or
> institutions that use this software under the GNU General Public License.
>
>
>
> This program is distributed in the hope that it will be useful,
> but WITHOUT ANY WARRANTY; without even the implied warranty of
> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> GNU General Public License for more details.
> ***********************************************************************/
> Of course, we would like to get feedback from you so that we are sure that
> this would be sufficient. Please note that the term 'Spectrophore' has also
> been trademarked. However, we don't think this should be an issue for
> releasing the code under open source.
> In a second phase, planned for mid-summer 2010, we intent to release our
> pharmacophore-based alignment tool Pharao under the OB environment. Finally,
> our de-novo design tool, called Cosmos(TM), will be release under OB
> somewhere near the end of the summer 2010.
> The reason why we have made this strategic decision to port all our software
> to the open source domain is that we, as management of Silicos, strongly
> believe in an open innovation model, and open source is just one of these
> factors that make open innovation possible. For Silicos as a company, we
> believe that by actively participating and supporting the OB community, we
> could create more business in the form of services than we could otherwise.
> Please feel free to comment.
> Kind regards,
> Hans De Winter
> CSO Silicos NV
> www.silicos.com
>
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Re: Silicos: Spectrophores ported under OB

Geoffrey Hutchison-3
In reply to this post by Hans De Winter
Dear Hans,

I want to thank you for your contribution -- I think it's a brave step forward, and I welcome you to the OB community. I think the Spectrophore code looks very interesting for a range of new fingerprint/descriptor techniques, and we definitely look forward to Pharao and Cosmos as well. It will probably be easier to add these as closely aligned "related projects":
http://openbabel.org/wiki/Related_Projects

As some of you know, the Spectrophore code was ported by Silicos with help from Tim Vandermeersch and is now in the SVN trunk. This is an even better reason to finish up the 2.3 release process and get these features in the hands of end-users.

> Of course, we would like to get feedback from you so that we are sure that this would be sufficient. Please note that the term 'Spectrophore' has also been trademarked. However, we don't think this should be an issue for releasing the code under open source.

You are likely aware that several open source projects protect code using trademarks. Mozilla Firefox is probably the most notable example -- if third parties modify the code beyond recognition, it can no longer be called Firefox anymore. In the chemistry field, there is a trademark on CML for the chemical markup language and has similar protective aims.

> The reason why we have made this strategic decision to port all our software to the open source domain is that we, as management of Silicos, strongly believe in an open innovation model, and open source is just one of these factors that make open innovation possible. For Silicos as a company, we believe that by actively participating and supporting the OB community, we could create more business in the form of services than we could otherwise.

Again, we look forward to you joining and pushing the OB development community.

Welcome and thanks!
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: [hidden email]
web: http://hutchison.chem.pitt.edu/


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Re: Silicos: Spectrophores ported under OB

Andrew Dalke
In reply to this post by Hans De Winter
Hello, and thanks for your contribution to OpenBabel and to free software in general.

On Jul 1, 2010, at 3:12 AM, Hans De Winter wrote:

> We plan to do this by including a modified header in the .h and .cpp files of the Spectrophore code. A proposal for this is given here:
  ...
> This program is free software; you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation version 2 of the License.

If the software is based on work done by Silicos and is not directly
derived from OpenBabel then I urge you to use the following phrase from
the GPLv2:


   This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
   as published by the Free Software Foundation; either version 2
   of the License, or (at your option) any later version.


OpenBabel is based on OpenEye's OELib, and OpenEye specified version 2 only,
without the option to use later versions of the GPL.

When OpenEye released under that license, it wasn't a problem as there was
no later license. But GPLv3 was released several years ago, and I expect
problems in the future as more and more people start using the v3 license
over the v2.

It expect it will take about a decade to be a serious problem, but there's
no reason that new contributions can't using a "or any later version",
which would help reduce the severity of future problems.

It also means that someone could take your contribution and make it work
with, under Indigo, which is a relatively recent cheminformatics code
released under GPLv3.

Best regards,

                                Andrew Dalke
                                [hidden email]



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Re: Silicos: Spectrophores ported under OB

Geoffrey Hutchison

On Jul 6, 2010, at 12:26 AM, Andrew Dalke wrote:

> It expect it will take about a decade to be a serious problem, but there's
> no reason that new contributions can't using a "or any later version",
> which would help reduce the severity of future problems.

I have some general concerns about using GPLv2 "or later" with the Silicos code right now, since it is currently covered by an expiring patent. I suspect this would be an easy change once the patent expires next year.

Incidentally, I will be relicensing *my* contributions to Open Babel under BSD shortly.

-Geoff
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Re: Silicos: Spectrophores ported under OB

Andrew Dalke
On Jul 6, 2010, at 11:58 AM, Geoffrey Hutchison wrote:
> I have some general concerns about using GPLv2 "or later" with the Silicos code right now, since it is currently covered by an expiring patent. I suspect this would be an easy change once the patent expires next year.

I see your point. I think the right interpretation is to say that if there's a conflict between the patent grant from Silicos and the choice to use GPLv3 then that part of the code cannot be used under the v3 license.

Here's the GNU FAQ on that topic:

http://www.gnu.org/licenses/gpl-faq.html#v2OrLaterPatentLicense

Q: My company owns a lot of patents. Over the years we've contributed code to
Q: projects under “GPL version 2 or any later version”, and the project itself
Q: has been distributed under the same terms. If a user decides to take the
Q: project's code (incorporating my contributions) under GPLv3, does that mean
Q: I've automatically granted GPLv3's explicit patent license to that user?

  No. When you convey GPLed software, you must follow the terms and conditions
  of one particular version of the license. When you do so, that version
  defines the obligations you have. If users may also elect to use later
  versions of the GPL, that's merely an additional permission they have—it does
  not require you to fulfill the terms of the later version of the GPL as well.

  Do not take this to mean that you can threaten the community with your
  patents. In many countries, distributing software under GPLv2 provides
  recipients with an implicit patent license to exercise their rights under
  the GPL. Even if it didn't, anyone considering enforcing their patents
  aggressively is an enemy of the community, and we will defend ourselves
  against such an attack.


> Incidentally, I will be relicensing *my* contributions to Open Babel under BSD shortly.

I'm pleased to hear that. Or in internet-speak ... "yay!"

                                Andrew
                                [hidden email]



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