Egon Willighagen | 22 Jul 15:40 2014
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Fwd: [CHMINF-L] Prize for best open source cheminformatic tool, part of the Lausanne Workshop on Chemical Information

Hi all,

I had not seen anything about the below contest... but looks interesting!

Egon

---------- Forwarded message ----------
From: Dietrich Rordorf / MDPI <rordorf <at> mdpi.com>
Date: Tue, Jul 22, 2014 at 3:27 PM
Subject: [CHMINF-L] Prize for best open source cheminformatic tool,
part of the Lausanne Workshop on Chemical Information
To: chminf-l <at> list.indiana.edu

Dear Colleagues,

A short reminder regarding the contest for open source cheminformatic
tools and apps. The competition is still open for participation.

The winner/winning team will be warded a prize of 2’000 CHF (Swiss
Francs), which is about 2'200 USD. The competition is also open to
students/graduates.

The winner of the contest will be invited to present his/her tool at
the Workshop on Chemical Information at the EPFL, Lausanne, Switzerland
on 12 September 2014 [1], where the prize will also be awarded (or if
unable to travel to the workshop as a video lecture or as a paper).

In order to enter the competition, the source code has to be available
in an open source format (for instance on a platform like Github).
A 1 to 2 pages short paper describing the software tool should be
(Continue reading)

Peter Murray-Rust | 9 Jul 08:46 2014
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The last Blue Obelisk manuscript ; TeX help wanted


Dear List,
We are republishing the Blue Obelisk paper as part of a volume published by Open Forum Europe (of which I am a Fellow). [See below]

Unfortunately the manuscript (which came from our DSpace) can't be read by normal TeX readers. It's clearly a TeX document. Could someone [a] reformat it so it works (I guess this is 5 mins max for an expert) and [b] explain what has happened - repositories are meant to preserve things for re-use :-)

On Wed, Jul 9, 2014 at 7:39 AM, Shane Coughlan <shane-Vh7EkPXfeH/j1p73w5sLM0B+6BGkLq7r@public.gmane.org> wrote:
Hi Peter

I can't reformat the document manually including all headings, footnotes etc. within reasonable time constraints. I need a version ready for word processing in ODT, DOC or PAGES format.

I got the Tex document as per your mail in February:

Begin forwarded message:
> From: Peter Murray-Rust <pm286 <at> cam.ac.uk>
> Subject: Re: Your chapter for the OFA book
> Date: February 4, 2014 at 19:10:53 GMT+9
> To: Shane Coughlan <shane-Vh7EkPXfeH/j1p73w5sLM0B+6BGkLq7r@public.gmane.org>
>
> It was written in TeX and we have archived it and the BibTeX at:
> https://www.repository.cam.ac.uk/handle/1810/238393
> Hope that hacks it.
> I will be happy to add commentary if that's useful.

It won't compile on my end for conversion to any word processing document.

Regards

Shane

On Jul 9, 2014, at 15:30 , Peter Murray-Rust <pm286-KWPb1pKIrIJaa/9Udqfwiw@public.gmane.org> wrote:
> It opens in a text editor and can be read by humans. It seems to be  copy of our BMC article (which is CC-BY and as such can be reproduced verbatim). My guess is that a small LaTeX tweak might be required. Where did it come from? - was there another person involved?
>
>
> On Wed, Jul 9, 2014 at 5:33 AM, Shane Coughlan <shane-Vh7EkPXfeH/j1p73w5sLM0B+6BGkLq7r@public.gmane.org> wrote:
> Dear all
>
> Please find attached the first PDF draft of the new OpenForum Academy book (reference exports in ODT, DOC and PAGES available).
>
> The chapters already in are:
>         Architecting the Future of Research Communication: Building the Models and Analytics for an Open Access Future
>         By Cameron Neylon
>         Standards and Sustainable Infrastructures:
> Matching Compatibility Strategies with System Flexibility Objectives
>         By Tineke M. Egyedi
>         Four dimensions affecting policy resistance in IT procurement
>         By Mathieu Paapst
>         E-Governance in Public Sector
> ICT Procurement: What is Shaping Practice in Sweden?
>         By Bjorn Lundell
>
> And chapters pledged:
>         Andy Updegrove, Introduction to the book
>         Andrew Adams, The Open vs Closed Debate
>         Andrew Katz, Towards a Functional Licence for Open Hardware
>         Jochen Friedrich, Untitled
> All, please send in your chapters as soon as possible in ODT or DOC format.
>
> Plus I have one problem chapter:
>         Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
>         By Peter Murray-Rust
> Peter, I can't get my LaTex tools to open this document as provided (attached). I get errors when I attempt to do so and this makes conversion impossible. Can you provide it in a ODT, RTF or DOC format?
>
> All authors, please check the draft for errors and necessary corrections.
>
> I would like to try and finish the book by end of July at latest so submissions would need to arrive two weeks before that.
>
> Regards
>
> Shane
>
>
> On Jun 5, 2014, at 20:08 , Shane Coughlan <shane-Vh7EkPXfeH/j1p73w5sLM0B+6BGkLq7r@public.gmane.org> wrote:
> > Dear all
> >
> > I want to reboot our book. It's been pending a while. Some chapters are in, some chapters are pledged as below. Just a reminder: this book will be a collection of previously published research around Open Innovation to complement our book of essays around the topic last year.
> >
> > If you have pledged a chapter, can you give me a timescale for submitting it? I would like to try and wrap up submissions for end of month.
> >
> > Also, I wanted to double-check with Chris Marsden and Jochen Friedrich if you would be interested in providing a chapter consisting of previously published work?
> >
> > Finally, if anyone else wants to submit a chapter of previously published work, now is the moment to speak up.
> >
> > The chapters already in are:
> > Mathieu Paapst, Four dimensions affecting policy resistance in IT procurement
> > Cameron Neylon, 2012: The year it all changed in open access
> > Tineke M. Egyedi, Standards and Sustainable Infrastructures: Matching Compatibility Strategies with System Flexibility Objectives
> > Peter Murray-Rust, Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
> > Andrew Katz, Towards a Functional Licence for Open Hardware
> >
> > And chapters pledged:
> > Andrew Adams, The Open vs Closed Debate
> > Karsten Gerloff, Title pending
> > Andy Updegrove, Introduction to the book
> >
> > Regards
> >
> > Shane
> >
> >
> > <Four Dimensions - OFA EDITION.docx><Egyedi_Standards_Sustain_Infras_Comp_Strategies_Felx_Obj.docx><Nature-Commentary2012.docx>
> > --
> > Shane Coughlan
> > Fellow Coordinator
> > OpenForum Academy
> > e: shane <at> openforumeurope.org
> > p: +81 (0) 80 4035 8083
> > w: www.openforumeurope.org
> >
>
> --
> Shane Coughlan
> Fellow Coordinator
> OpenForum Academy
> e: shane <at> openforumeurope.org
> p: +81 (0) 80 4035 8083
> w: www.openforumeurope.org
>
>
> --
> --
> You received this message because you are subscribed to the "ofafellows" group.
>
> To post to this group, send email to fellows-Vh7EkPXfeH/j1p73w5sLM0B+6BGkLq7r@public.gmane.org
>
>
> To unsubscribe from this group and stop receiving emails from it, send an email to fellows+unsubscribe-Vh7EkPXfeH/j1p73w5sLM0B+6BGkLq7r@public.gmane.org.
>
>
>
>
> --
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069

--
Shane Coughlan
Fellow Coordinator
OpenForum Academy
e: shane-Vh7EkPXfeH/j1p73w5sLM0B+6BGkLq7r@public.gmane.org
p: +81 (0) 80 4035 8083
w: www.openforumeurope.org



--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Karol M. Langner | 24 May 20:02 2014
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Re: Impact

Hi Egon,

Great, i don't think you need to list all the pages. I just provided it for reference.

- Karol

On May 23 2014, Egon Willighagen wrote:
> Hi Karol, all,
> 
> On Thu, May 22, 2014 at 4:36 PM, Karol M. Langner
> <karol.langner@...> wrote:
> > You could also add cclib:
> > paper: http://dx.doi.org/10.1002/jcc.20823
> > repo: https://github.com/cclib/cclib
> 
> I added these two, but not the webpage... I have done that only for
> the main Blue Obelisk website, and Open SMILES because that does not
> other "publication"...
> 
> > docs: http://cclib.github.io/
> 
> Should it also list all project specific web (or documentation) pages?
> 
> 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: 0000-0001-7542-0286

--

-- 
written by Karol M. Langner
Sat May 24 14:01:19 EDT 2014

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Antony Williams | 14 May 15:19 2014

FW: Mourning Jean-Claude Bradley, PhD, Department of Chemistry

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

 

 

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.

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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Egon Willighagen | 14 May 15:33 2014
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Jean-Claude Bradley, Blue Obelisk award winner of 2007

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: 0000-0001-7542-0286

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Egon Willighagen | 14 May 12:13 2014
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Impact

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: 0000-0001-7542-0286

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Egon Willighagen | 24 Mar 09:04 2014
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CML Schema maintenance

Hi all,

because there were some things I like to update with respect to the
CML Schema, I have asked Peter and Henry if I could pick up
maintenance of the XML Schema. The result is this:

https://github.com/egonw/cml-schema

I have already applied two patches to add four recent new element symbols [0].

If you have additional points, you can file those here:

https://github.com/egonw/cml-schema/issues

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: 0000-0001-7542-0286

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Peter Murray-Rust | 2 Mar 11:09 2014
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Re: Google Summer of Code 2014 options?

Is this still possible (I was invited to a phylogenetic project but told that it wasn't funded). So has the deadline passed?


On Sat, Mar 1, 2014 at 11:41 PM, Egon Willighagen <egon.willighagen-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi all,

another year, another Google Summer of Code. And again it is possible
to work on Open Source tools in the area of chemistry.

Below are a few things that I have spotted. What else is out there?

* NRNB mentoring organization [0]
 - Cytoscape has a chemical structure viz plugin based on the CDK that
needs updating
 - PathVisio has a chemical structure viz plugin based on the CDK that
needs updating
 - There is a project idea to integrate Cytoscape into Bioclipse
 - There is a project idea to integrate PathVisio into Bioclipse
* VTK mentoring organization [1]
 - various chemistry related ideas
* ScaffoldHunter (GPLv3) [2]
 - no specific ideas, but based on the CDK, and could use updating to CDK 1.5

Anything else?

Egon

0.http://nrnb.org/gsoc/index.html#ideas-tab
1.http://www.vtk.org/Wiki/VTK/GSoC
2.http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=project_ideas

--
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: 0000-0001-7542-0286

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Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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Egon Willighagen | 1 Mar 13:41 2014
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Google Summer of Code 2014 options?

Hi all,

another year, another Google Summer of Code. And again it is possible
to work on Open Source tools in the area of chemistry.

Below are a few things that I have spotted. What else is out there?

* NRNB mentoring organization [0]
 - Cytoscape has a chemical structure viz plugin based on the CDK that
needs updating
 - PathVisio has a chemical structure viz plugin based on the CDK that
needs updating
 - There is a project idea to integrate Cytoscape into Bioclipse
 - There is a project idea to integrate PathVisio into Bioclipse
* VTK mentoring organization [1]
 - various chemistry related ideas
* ScaffoldHunter (GPLv3) [2]
 - no specific ideas, but based on the CDK, and could use updating to CDK 1.5

Anything else?

Egon

0.http://nrnb.org/gsoc/index.html#ideas-tab
1.http://www.vtk.org/Wiki/VTK/GSoC
2.http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=project_ideas

--

-- 
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: 0000-0001-7542-0286

------------------------------------------------------------------------------
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Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
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Robert Hanson | 23 Feb 19:08 2014

referencing of data

Can someone explain to me the general schema for referencing data in the BODR? I'm not seeing it. For example, at

https://github.com/wadejong/bodr/tree/c7917225cad829507bdd4c8c2fe7ebd3d795c021/bodr/elements

I see xml and bibxml files, but I see nothing that connects those. Just randomly named files. Is there something in, for example, elements.xml, that points one to the specific bibxml for a specific entry?

Bob


--
Robert M. Hanson
Larson-Anderson 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

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Wibe de Jong | 20 Feb 08:07 2014

BODR covalent radii patch (all elements)

Hi,

I have updated the covalent radii for all 118 elements following the definition of one consistent set of radii published Pyykko and Atsumi in Chem. Eur. J. published in 2009. This addresses all elements for which the radii were not given (mainly heavy elements), and updates others. 

The git pull request can be found at https://github.com/egonw/bodr 

Please peer review, comment, and apply. 

Thanks,

Bert
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Gmane