Re: [BlueObelisk-discuss] Jean-Claude Bradley, Blue Obelisk award winner of 2007

2014-05-14 Thread Peter Murray-Rust 
I echo Egon's sadness.


Jean-Claude was years ahead of his time. He did what he considered right,
not what was expedient or what the world expected.

He and I discussed Open Data and Open Notebook Science. We found that they
were different things and that each was a critically important subject. J-C
set up a webpage on Wikipedia to describe ONS and its practice.

ONS is truly innovative. The research must be available to everyone -
regardless of who they are are or what they had studied. And it must be
fair - "no insider knowledge".

Several groups in chemistry are following J-C's lead - and we honour him in
that.

I have been invited to present a keynote on "Open Data" at Hinxton Genome
Campus tomorrow and shall make J-C's work the focus and inspiration.

I am truly glad we awarded him a Blue Obelisk. As a community we should
think how to take the message further.

P.



On Wed, May 14, 2014 at 2:33 PM, Egon Willighagen <
egon.willigha...@gmail.com> wrote:

> Dear Blue Obelisk community,
>
> with great sadness it is that I heard yesterday that Jean-Claude
> Bradley passed away yesterday. Please read below more information from
> Drexel University below. Jean-Claude received the Blue Obelisk award
> in 2007.
>
> I have know Jean-Claude for some years and did some work together with
> him on Open Data in chemistry. I was looking forward to working with
> him, as member of the SAB of eNanoMapper, on the publisher perspective
> of nanosafety research, in his role of Editor-in-Chief of Chemical
> Central Journal, with the innovative BioMed Central/Chemistry Central
> publisher.
>
> Egon
>
> “Dear Members of the Drexel University Community,
>
> It is with deep sadness that I inform you of the passing of
> Jean-Claude Bradley, PhD, associate professor in the Department of
> Chemistry.
>
> Jean-Claude joined Drexel as an assistant professor in 1996 after
> receiving his PhD in organic chemistry and serving as a postdoctoral
> researcher at Duke University and College de France in Paris. In 2004,
> he was appointed E-Learning Coordinator for Drexel's College of Arts
> and Sciences, helping to spearhead the adoption of novel teaching
> modalities. In that role, he led the University's initiative to buy an
> "island" in the virtual world of Second Life, where students and
> faculty could explore new methods of teaching and learning.
>
> Jean-Claude was most well known for his "Open Notebook Science"(ONS),
> a term he coined to describe his novel approach to making all primary
> research (including both successful and failed experiments) open to
> the public in real time. ONS, he believed—and demonstrated—could
> significantly impact the future of science by reducing financial and
> computational restraints and by granting public access to the raw data
> that shapes scientific conclusions.
>
> "...In the past, trusting people might have been a necessary evil [of
> research]," Bradley said. "Today, it is a choice. Optimally, trust
> should have no place in science."
>
> In June of 2013, Jean-Claude was invited to the White House for an
> "Open Science Poster Session," at which he discussed ONS' role in
> allowing he and his collaborators to confidently determine the melting
> points of over 27,000 substances, including many that were never
> before agreed upon. Currently, his research lab had been working to
> create anti-malarial compounds to aid in the synthesis of drugs to
> fight malaria. His lab's work on this project was made available to
> the public on a wiki called UsefulChem, which Jean-Claude started in
> 2005.
>
> Jean-Claude's philosophy of free, accessible science translated to an
> open approach in the classroom as well. Content from his undergraduate
> chemistry courses was made freely available to the public, and real
> data from the laboratory was used in assignments to practice concepts
> learned in the classroom.
>
> In an article in Chemistry World last April, Bradley said: "It is only
> a matter of time before the internet is saturated with free knowledge
> for all…People will remember those who were first."
>
> Indeed, we will remember Jean-Claude as a pioneer in the open access
> movement, an innovative researcher and colleague, and a kind and
> dedicated educator. His death impacts all who knew him, and especially
> the students, faculty and collaborators who worked with him daily. For
> anyone who may need support in dealing with this loss, we encourage
> you to reach out to the counseling professionals at Drexel's
> Counseling Center at 215-895-1415 (or 215-416-3337 after regular
> business hours).
>
> Our thoughts are with Jean-Claude's family and friends at this difficult
> time.
>
> Sincerely,
>
> Donna M. Murasko, PhD
> Dean of the College of Arts and Sciences”
>
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-

Re: [BlueObelisk-discuss] Jean-Claude Bradley, Blue Obelisk award winner of 2007

2014-05-14 Thread Geoffrey Hutchison 
Ugh. I'm speechless. Very sad news.

-Geoff

---
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Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/


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Re: [BlueObelisk-discuss] Jean-Claude Bradley, Blue Obelisk award winner of 2007

2014-05-14 Thread Saulius Gražulis 
Sad news indeed...

On 2014-05-14 16:33, Egon Willighagen wrote:
> Dear Blue Obelisk community,
> 
> with great sadness it is that I heard yesterday that Jean-Claude
> Bradley passed away yesterday. Please read below more information from
> Drexel University below. Jean-Claude received the Blue Obelisk award
> in 2007.
> 
> I have know Jean-Claude for some years and did some work together with
> him on Open Data in chemistry. I was looking forward to working with
> him, as member of the SAB of eNanoMapper, on the publisher perspective
> of nanosafety research, in his role of Editor-in-Chief of Chemical
> Central Journal, with the innovative BioMed Central/Chemistry Central
> publisher.
> 
> Egon


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Re: [BlueObelisk-discuss] Impact

2014-05-14 Thread Egon Willighagen 
On Wed, May 14, 2014 at 3:43 PM, Craig James  wrote:
> www.opensmiles.org

Yes, checked and website can indeed be listed. Added!

Egon

-- 
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Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: -0001-7542-0286

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Re: [BlueObelisk-discuss] Impact

2014-05-14 Thread Craig James 
I don't know if a web site qualifies as a paper...

www.opensmiles.org

Craig


On Wed, May 14, 2014 at 3:13 AM, Egon Willighagen <
egon.willigha...@gmail.com> wrote:

> Hi all,
>
> some weeks ago I started making an ImpactStory profile for the Blue
> Obelisk. May service as back pocket material if you promote the Blue
> Obelisk. It's hard to say we do not have impact, and I think we
> succeeded in making a change.
>
> I have followed Figure 4 from the second Blue Obelisk paper, and
> listed papers and software hosted on GitHub (no SourceForge support at
> this moment):
>
> https://impactstory.org/BlueObelisk
>
> If you find your project missing (likely), please send me the DOI or
> GitHub URL (please only for top level projects, so I list only
> bioclipse.core).
>
> The ImpactStory page doesn't feature an logo/icon, and this may be a
> good moment to standardize on one, and put that on our project front
> pages (something that keeps coming up now and then but something we
> never all did...)
>
> Egon
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: -0001-7542-0286
>
>
> --
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.
> Get unparalleled scalability from the best Selenium testing platform
> available
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>



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-
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[BlueObelisk-discuss] FW: Mourning Jean-Claude Bradley, PhD, Department of Chemistry

2014-05-14 Thread Antony Williams 
Colleagues,

It is with great sadness that I share this sad news regarding the passing of JC 
Bradley. JC was a friend, collaborator and leader in the domain of Open 
Science. I will miss him. A lot.
Mourning Jean-Claude Bradley, PhD, Department of Chemistry



[http://drexel.edu/%7E/media/Images/coas/email/coas-email-banner.ashx]





Mourning Jean-Claude Bradley, PhD, Department of Chemistry

Dear Members of the Drexel University Community,

It is with deep sadness that I inform you of the passing of Jean-Claude 
Bradley, PhD, associate professor in the Department of Chemistry.

[cid:image001.jpg@01CF6F50.9C215250]Jean-Claude joined Drexel as an assistant 
professor in 1996 after receiving his PhD in organic chemistry and serving as a 
postdoctoral researcher at Duke University and College de France in Paris. In 
2004, he was appointed E-Learning Coordinator for Drexel's College of Arts and 
Sciences, helping to spearhead the adoption of novel teaching modalities. In 
that role, he led the University's initiative to buy an "island" in the virtual 
world of Second Life, where students and faculty could explore new methods of 
teaching and learning.

Jean-Claude was most well known for his "Open Notebook Science"(ONS), a term he 
coined to describe his novel approach to making all primary research (including 
both successful and failed experiments) open to the public in real time. ONS, 
he believed-and demonstrated-could significantly impact the future of science 
by reducing financial and computational restraints and by granting public 
access to the raw data that shapes scientific conclusions.

"...In the past, trusting people might have been a necessary evil [of 
research]," Bradley said. "Today, it is a choice. Optimally, trust should have 
no place in science."

In June of 2013, Jean-Claude was invited to the White House for an "Open 
Science Poster Session," at which he discussed ONS' role in allowing he and his 
collaborators to confidently determine the melting points of over 27,000 
substances, including many that were never before agreed upon. Currently, his 
research lab had been working to create anti-malarial compounds to aid in the 
synthesis of drugs to fight malaria. His lab's work on this project was made 
available to the public on a wiki called UsefulChem, which Jean-Claude started 
in 2005.

Jean-Claude's philosophy of free, accessible science translated to an open 
approach in the classroom as well. Content from his undergraduate chemistry 
courses was made freely available to the public, and real data from the 
laboratory was used in assignments to practice concepts learned in the 
classroom.

In an article in Chemistry World last April, Bradley said: "It is only a matter 
of time before the internet is saturated with free knowledge for all...People 
will remember those who were first."

Indeed, we will remember Jean-Claude as a pioneer in the open access movement, 
an innovative researcher and colleague, and a kind and dedicated educator. His 
death impacts all who knew him, and especially the students, faculty and 
collaborators who worked with him daily. For anyone who may need support in 
dealing with this loss, we encourage you to reach out to the counseling 
professionals at Drexel's Counseling Center at 215-895-1415 (or 215-416-3337 
after regular business hours).

Our thoughts are with Jean-Claude's family and friends at this difficult time.

Sincerely,

Donna M. Murasko, PhD
Dean of the College of Arts and Sciences





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[BlueObelisk-discuss] Jean-Claude Bradley, Blue Obelisk award winner of 2007

2014-05-14 Thread Egon Willighagen 
Dear Blue Obelisk community,

with great sadness it is that I heard yesterday that Jean-Claude
Bradley passed away yesterday. Please read below more information from
Drexel University below. Jean-Claude received the Blue Obelisk award
in 2007.

I have know Jean-Claude for some years and did some work together with
him on Open Data in chemistry. I was looking forward to working with
him, as member of the SAB of eNanoMapper, on the publisher perspective
of nanosafety research, in his role of Editor-in-Chief of Chemical
Central Journal, with the innovative BioMed Central/Chemistry Central
publisher.

Egon

“Dear Members of the Drexel University Community,

It is with deep sadness that I inform you of the passing of
Jean-Claude Bradley, PhD, associate professor in the Department of
Chemistry.

Jean-Claude joined Drexel as an assistant professor in 1996 after
receiving his PhD in organic chemistry and serving as a postdoctoral
researcher at Duke University and College de France in Paris. In 2004,
he was appointed E-Learning Coordinator for Drexel's College of Arts
and Sciences, helping to spearhead the adoption of novel teaching
modalities. In that role, he led the University's initiative to buy an
"island" in the virtual world of Second Life, where students and
faculty could explore new methods of teaching and learning.

Jean-Claude was most well known for his "Open Notebook Science"(ONS),
a term he coined to describe his novel approach to making all primary
research (including both successful and failed experiments) open to
the public in real time. ONS, he believed—and demonstrated—could
significantly impact the future of science by reducing financial and
computational restraints and by granting public access to the raw data
that shapes scientific conclusions.

"...In the past, trusting people might have been a necessary evil [of
research]," Bradley said. "Today, it is a choice. Optimally, trust
should have no place in science."

In June of 2013, Jean-Claude was invited to the White House for an
"Open Science Poster Session," at which he discussed ONS' role in
allowing he and his collaborators to confidently determine the melting
points of over 27,000 substances, including many that were never
before agreed upon. Currently, his research lab had been working to
create anti-malarial compounds to aid in the synthesis of drugs to
fight malaria. His lab's work on this project was made available to
the public on a wiki called UsefulChem, which Jean-Claude started in
2005.

Jean-Claude's philosophy of free, accessible science translated to an
open approach in the classroom as well. Content from his undergraduate
chemistry courses was made freely available to the public, and real
data from the laboratory was used in assignments to practice concepts
learned in the classroom.

In an article in Chemistry World last April, Bradley said: "It is only
a matter of time before the internet is saturated with free knowledge
for all…People will remember those who were first."

Indeed, we will remember Jean-Claude as a pioneer in the open access
movement, an innovative researcher and colleague, and a kind and
dedicated educator. His death impacts all who knew him, and especially
the students, faculty and collaborators who worked with him daily. For
anyone who may need support in dealing with this loss, we encourage
you to reach out to the counseling professionals at Drexel's
Counseling Center at 215-895-1415 (or 215-416-3337 after regular
business hours).

Our thoughts are with Jean-Claude's family and friends at this difficult time.

Sincerely,

Donna M. Murasko, PhD
Dean of the College of Arts and Sciences”


-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: -0001-7542-0286

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Re: [BlueObelisk-discuss] Impact

2014-05-14 Thread Egon Willighagen 
On Wed, May 14, 2014 at 1:29 PM, Peter Murray-Rust  wrote:
> I am giving a keynote on Open Data at the Hinxton Genome Campus tomorrow and
> will highlight this.

Ah, that reminds me I still had to upload BODR 10 to FigShare... now done:

http://figshare.com/articles/Blue_Obelisk_Data_Repository_10/1025775

Egon

-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
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Re: [BlueObelisk-discuss] Impact

2014-05-14 Thread Peter Murray-Rust 
Thanks Egon,

I am giving a keynote on Open Data at the Hinxton Genome Campus tomorrow
and will highlight this.


On Wed, May 14, 2014 at 11:13 AM, Egon Willighagen <
egon.willigha...@gmail.com> wrote:

> Hi all,
>
> some weeks ago I started making an ImpactStory profile for the Blue
> Obelisk. May service as back pocket material if you promote the Blue
> Obelisk. It's hard to say we do not have impact, and I think we
> succeeded in making a change.
>
> I have followed Figure 4 from the second Blue Obelisk paper, and
> listed papers and software hosted on GitHub (no SourceForge support at
> this moment):
>
> https://impactstory.org/BlueObelisk
>
> If you find your project missing (likely), please send me the DOI or
> GitHub URL (please only for top level projects, so I list only
> bioclipse.core).
>
> The ImpactStory page doesn't feature an logo/icon, and this may be a
> good moment to standardize on one, and put that on our project front
> pages (something that keeps coming up now and then but something we
> never all did...)
>
> Egon
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: -0001-7542-0286
>
>
> --
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.
> Get unparalleled scalability from the best Selenium testing platform
> available
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> ___
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> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>



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Re: [BlueObelisk-discuss] Impact

2014-05-14 Thread Egon Willighagen 
On Wed, May 14, 2014 at 12:26 PM, Rzepa, Henry S  wrote:
> I wonder how that might be useful for collaborative applications such as eg  
> CDK, JSmol and the like?  Would all the contributor’s ORCIDs bee needed?

Interesting idea! Passed along to @ImpactStory:
https://twitter.com/egonwillighagen/status/466525714376712192

Egon


-- 
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Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: -0001-7542-0286

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Re: [BlueObelisk-discuss] Impact

2014-05-14 Thread Rzepa, Henry S 
I had not imagined that  Impact story would apply to groups as well as 
individuals, but it makes great sense.

ImpactStory also operates against an individual’s  ORCiD identifier, and  I am 
not aware that a group can also acquire a  ORCiD? 

Also, we  have been using the  ORCID public  API to authenticate ORCID 
identifies into applications  (such as eg an  ELN or a digital repository), so 
that the trust is firm and complete. I wonder how that might be useful for 
collaborative applications such as eg  CDK, JSmol and the like?  Would all the 
contributor’s ORCIDs bee needed?

On 14 May 2014, at 11:13, Egon Willighagen  wrote:

> Hi all,
> 
> some weeks ago I started making an ImpactStory profile for the Blue
> Obelisk. May service as back pocket material if you promote the Blue
> Obelisk. It's hard to say we do not have impact, and I think we
> succeeded in making a change.
> 
> I have followed Figure 4 from the second Blue Obelisk paper, and
> listed papers and software hosted on GitHub (no SourceForge support at
> this moment):
> 
> https://impactstory.org/BlueObelisk
> 
> If you find your project missing (likely), please send me the DOI or
> GitHub URL (please only for top level projects, so I list only
> bioclipse.core).
> 
> The ImpactStory page doesn't feature an logo/icon, and this may be a
> good moment to standardize on one, and put that on our project front
> pages (something that keeps coming up now and then but something we
> never all did…)
> 



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[BlueObelisk-discuss] Impact

2014-05-14 Thread Egon Willighagen 
Hi all,

some weeks ago I started making an ImpactStory profile for the Blue
Obelisk. May service as back pocket material if you promote the Blue
Obelisk. It's hard to say we do not have impact, and I think we
succeeded in making a change.

I have followed Figure 4 from the second Blue Obelisk paper, and
listed papers and software hosted on GitHub (no SourceForge support at
this moment):

https://impactstory.org/BlueObelisk

If you find your project missing (likely), please send me the DOI or
GitHub URL (please only for top level projects, so I list only
bioclipse.core).

The ImpactStory page doesn't feature an logo/icon, and this may be a
good moment to standardize on one, and put that on our project front
pages (something that keeps coming up now and then but something we
never all did...)

Egon

-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: -0001-7542-0286

--
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