Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

2022-01-20 Thread Andrew Dalke 
On Jan 20, 2022, at 10:05, Peter Murray-Rust via Blueobelisk-discuss 
 wrote:
> 
> I think it's wonderful that we have an un-organization that is still going 
> strong.

What would it look like if the organization were not going strong, but existed 
mostly from inertia and a lack of a better alternative?

>  I highlight the great work done voluntarily by many people, without central 
> management, in tackling the log4j problem. 


Do you highlight how people were not compensated for taking time off during the 
Christmas holidays? Egon writes "It totally messed up my schedule." I wonder 
how many people thanked him for his work.

Do you highlight the urgent need for organizations to set aside budget to 
support these projects, either through direct financial support, or by paying 
people to maintain the software and assure its continued fitness for purpose?

Since Egon took care of the log4j problem for CDK, and Egon is one of the core 
CDK developers, doesn't that make him part of central management of CDK?

Jo Freeman long ago pointed out in "The Tyranny of Structurelessness": "once 
the movement no longer clings tenaciously to the ideology of structurelessness, 
it will be free to develop those forms of organisation best suited to its 
healthy functioning. This does not mean that we should go to the other extreme 
and blindly imitate the traditional forms of organisation. But neither should 
we blindly reject them all. Some traditional techniques will prove useful, 
albeit not perfect; some will give us insights into what we should not do to 
obtain certain ends with minimal costs to the individuals in the movement. 
Mostly, we will have to experiment with different kinds of structuring and 
develop a variety of techniques to use for different situations."

I submit that Blue Obelisk *has a structure*. It's exactly the informal 
structure Freeman described, that happens even when its members assert there is 
no structure.

Here's how I know there's an informal structure - who decides who gets a Blue 
Obelisk award? If I award one to myself, do I get to update the Wikipedia 
entry? For that matter, who gets to decide that Blue Obelisk is an 
un-organization without central management?

I assert that Blue Obelisk as an organization is moribund. Its existence, 
combined with the informal structure which dictates it must have no formal 
centralized authority, prevents more effective organizations from forming. Look 
at our cousin, the Open Bioinformatics Foundation, to see what a more effective 
organization looks like, with yearly meetings on FOSS in bioinformatics and 
acting as a contact point for Google Summer of Code and other projects.

To emphasize by repetition: "This does not mean that we should go to the other 
extreme and blindly imitate the traditional forms of organisation". 

Regards,

Andrew
da...@dalkescientific.com




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Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

2022-01-20 Thread Peter Murray-Rust via Blueobelisk-discuss 
I think it's wonderful that we have an un-organization that is still
going strong. I highlight the great work done voluntarily by many people,
without central management, in tackling the log4j problem.

Some of my colleagues are interested in DAOs (
https://en.wikipedia.org/wiki/Decentralized_autonomous_organization) . Does
this have any role for BO? Do we have algorithms for governance that make
sense for BO?

I am continuing to keep a hand in chemistry, particularly materials. I was
asked to speak at two meetings last year (OMDI2021) and am also invited to
a CECAM meeting next month MADICES2022. (I've also been changing to Python
as it has a better and more integrated set of libraries than Java - which
is increasingly enterprise).  We need new approaches and I'm trying to work
some of these out - particularly a mixture of un-natural language
processing with defined objects rooted in Wikidata. Wikidata is a
gamechanger and Egon is one of the leaders.

I'm also building software to extract data from diagrams. This includes
plots (such as electrochemistry) and biochemical reaction pathways. There
are much better general libraries for images and I think we can make good
progress. I'd be interested in anyone who wants to extract data from
spectra, reaction pathways, plots (scatter, bar, ...) I applaud Christoph
and his group for Decimer ML to identify chemical diagrams and would be
happy to explore. I am particularly keen on extracting knowledge from
preprints (and have been talking with bio/medrxiv people). Being able to
have an immediate preprint reader  - e.g. minutes after the   document was
loaded - would be independent of publishers. Also the PDFs are much more
tractable than the awful 2-column PDFs of the "version of record".

In short I think there are huge opportunities for modern tools to innovate
in chemistry again and take semantic control.

P.


>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
> *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
> honor with gratitude the people who have stewarded the land throughout the
> generations and their ongoing contributions to this region. We acknowledge
> the ongoing injustices that we have committed against the Dakota Nation,
> and we wish to interrupt this legacy, beginning with acts of healing and
> honest storytelling about this place.*
>


-- 
Peter Murray-Rust
Founder ContentMine.org
and
Reader Emeritus in Molecular Informatics
Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK
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Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

2022-01-19 Thread Robert Hanson via Blueobelisk-discuss 
yeah -- well, Happy New Year 2022!  Seems I picked up and replied to a
message from 2015!!! NO idea how that happened.


On Mon, Jan 17, 2022 at 11:58 PM Egon Willighagen <
egon.willigha...@gmail.com> wrote:

>
>
> On Tue, 18 Jan 2022 at 06:53, Robert Hanson via Blueobelisk-discuss <
> blueobelisk-discuss@lists.sourceforge.net> wrote:
>
>> Great idea!
>>
>
> Okay, no idea where this message is coming from :)
>
> It was indeed a great idea (imho). The first Blue Obelisk paper (
> https://pubs.acs.org/doi/10.1021/ci050400b) has had a CC-BY license for
> almost 7 years now:
> https://sourceforge.net/p/blueobelisk/mailman/message/33816652/ (thx to
> funding by Chris).
>
> Egon
>
> --
> 
> BiGCaT received a NWO Open Science grant to support our research into
> interoperability of biological data and knowledge:
> https://www.nature.com/articles/d41586-021-03418-1 and
> https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants
>
> -
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Twitter/Mastodon: @egonwillighagen 
>  / @egonw 
> Homepage: http://egonw.github.io/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: -0001-7542-0286 
> ImpactStory: https://impactstory.org/u/egonwillighagen
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

*We stand on the homelands of the Wahpekute Band of the Dakota Nation. We
honor with gratitude the people who have stewarded the land throughout the
generations and their ongoing contributions to this region. We acknowledge
the ongoing injustices that we have committed against the Dakota Nation,
and we wish to interrupt this legacy, beginning with acts of healing and
honest storytelling about this place.*
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Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

2022-01-17 Thread Egon Willighagen 
On Tue, 18 Jan 2022 at 06:53, Robert Hanson via Blueobelisk-discuss <
blueobelisk-discuss@lists.sourceforge.net> wrote:

> Great idea!
>

Okay, no idea where this message is coming from :)

It was indeed a great idea (imho). The first Blue Obelisk paper (
https://pubs.acs.org/doi/10.1021/ci050400b) has had a CC-BY license for
almost 7 years now:
https://sourceforge.net/p/blueobelisk/mailman/message/33816652/ (thx to
funding by Chris).

Egon

-- 

BiGCaT received a NWO Open Science grant to support our research into
interoperability of biological data and knowledge:
https://www.nature.com/articles/d41586-021-03418-1 and
https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Twitter/Mastodon: @egonwillighagen  /
@egonw 
Homepage: http://egonw.github.io/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
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Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

2022-01-17 Thread Robert Hanson via Blueobelisk-discuss 
Great idea!
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Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

2015-04-14 Thread Noel O'Boyle 
*applause*

On 14 April 2015 at 16:47, Christoph Steinbeck
christoph.steinb...@gmail.com wrote:
 Dear friends,

 with great pleasure I announce that we have liberated the foundational 
 BlueObelisk article published in 2006:
 J. Chem. Inf. Model., 2006, 46 (3), pp 991–998
 DOI: 10.1021/ci050400b

 The article is now published under a Creative Commons Attribution (CC-BY) 
 License, which permits unrestricted use, distribution and reproduction in any 
 medium, provided the author and source are cited.

 Among other things, this means that we can now attach the article to this 
 email, which we do :)

 Kind regards,

 Christoph Steinbeck and Egon Willighagen




 --
 Dr. Christoph Steinbeck, Head of Cheminformatics and Metabolism
 European Bioinformatics Institute (EMBL-EBI), European Molecular Biology 
 Laboratory
 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
 Phone +44 1223 49 2640, Email: steinb...@ebi.ac.uk, Admin: khol...@ebi.ac.uk
 https://www.ebi.ac.uk/about/people/christoph-steinbeck

 What is man but that lofty spirit - that sense of enterprise.
 ... Kirk, I, Mudd, stardate 4513.3..


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Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

2015-04-14 Thread Peter Murray Rust 
Brilliant , how did you do it?

Sent from my iPhone

On 14 Apr 2015, at 20:10, Noel O'Boyle baoille...@gmail.com wrote:

 *applause*
 
 On 14 April 2015 at 16:47, Christoph Steinbeck
 christoph.steinb...@gmail.com wrote:
 Dear friends,
 
 with great pleasure I announce that we have liberated the foundational 
 BlueObelisk article published in 2006:
 J. Chem. Inf. Model., 2006, 46 (3), pp 991–998
 DOI: 10.1021/ci050400b
 
 The article is now published under a Creative Commons Attribution (CC-BY) 
 License, which permits unrestricted use, distribution and reproduction in 
 any medium, provided the author and source are cited.
 
 Among other things, this means that we can now attach the article to this 
 email, which we do :)
 
 Kind regards,
 
 Christoph Steinbeck and Egon Willighagen
 
 
 
 
 --
 Dr. Christoph Steinbeck, Head of Cheminformatics and Metabolism
 European Bioinformatics Institute (EMBL-EBI), European Molecular Biology 
 Laboratory
 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
 Phone +44 1223 49 2640, Email: steinb...@ebi.ac.uk, Admin: khol...@ebi.ac.uk
 https://www.ebi.ac.uk/about/people/christoph-steinbeck
 
 What is man but that lofty spirit - that sense of enterprise.
 ... Kirk, I, Mudd, stardate 4513.3..
 
 
 --
 BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
 Develop your own process in accordance with the BPMN 2 standard
 Learn Process modeling best practices with Bonita BPM through live exercises
 http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
 source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF
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Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

2015-04-14 Thread Marcus D. Hanwell 
Great news, applause for all who made this happen :-)

On Tue, Apr 14, 2015 at 3:10 PM, Noel O'Boyle baoille...@gmail.com wrote:
 *applause*

 On 14 April 2015 at 16:47, Christoph Steinbeck
 christoph.steinb...@gmail.com wrote:
 Dear friends,

 with great pleasure I announce that we have liberated the foundational 
 BlueObelisk article published in 2006:
 J. Chem. Inf. Model., 2006, 46 (3), pp 991–998
 DOI: 10.1021/ci050400b

 The article is now published under a Creative Commons Attribution (CC-BY) 
 License, which permits unrestricted use, distribution and reproduction in 
 any medium, provided the author and source are cited.

 Among other things, this means that we can now attach the article to this 
 email, which we do :)

 Kind regards,

 Christoph Steinbeck and Egon Willighagen




 --
 Dr. Christoph Steinbeck, Head of Cheminformatics and Metabolism
 European Bioinformatics Institute (EMBL-EBI), European Molecular Biology 
 Laboratory
 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
 Phone +44 1223 49 2640, Email: steinb...@ebi.ac.uk, Admin: khol...@ebi.ac.uk
 https://www.ebi.ac.uk/about/people/christoph-steinbeck

 What is man but that lofty spirit - that sense of enterprise.
 ... Kirk, I, Mudd, stardate 4513.3..


 --
 BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
 Develop your own process in accordance with the BPMN 2 standard
 Learn Process modeling best practices with Bonita BPM through live exercises
 http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
 source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF
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 Learn Process modeling best practices with Bonita BPM through live exercises
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