[BlueObelisk-discuss] Fwd: CCL: Call for Papers: Free and Open Source Software symposium at ACS Fall 2023 Meeting

Hi all, this seems interesting: -- Forwarded message - From: Susi Lehtola susi.lehtola*_*alumni.helsinki.fi < owner-chemis...@ccl.net> Date: Wed, 22 Mar 2023 at 17:09 Subject: CCL: Call for Papers: Free and Open Source Software symposium at ACS Fall 2023 Meeting Sent to CCL by:

Re: [BlueObelisk-discuss] [Cdk-devel] Registration ending soon for CDK 20th anniversary symposium on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022.

Thanks for the reminder! Egon On Wed, 19 Jan 2022 at 11:30, Christoph Steinbeck < christoph.steinb...@uni-jena.de> wrote: > Dear all, > > as announced last November on this list, the CDK 20th anniversary workshop > will be held on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022. > >

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

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 (

Re: [BlueObelisk-discuss] Euclid/CMLXOM on XOM 1.3.x ?

On Sat, Jan 1, 2022 at 1:10 PM Egon Willighagen wrote: > I intend to push this Euclid 2 and CMLXOM 4, so increasing the major > version. > After Peter's reply, I pushed these to Maven Central. Egon -- BiGCaT received a NWO Open Science grant to support our research into interop

[BlueObelisk-discuss] Euclid/CMLXOM on XOM 1.3.x ?

Hi Peter, all, Most of the dependencies of Euclid/CMLXOM have been updated, with Log4j giving quite some opportunity to pull in updates for other libraries. One update still needs to happen, the update from XOM 1.2 to XOM 1.3. This requires a few API changes:

[BlueObelisk-discuss] log4j 2.17.0

Hi all, I have just pushed a new Euclid and CMLXOM to Maven Central (via Sonatype) based on log4j 2.17.0. Grtz, Egon -- BiGCaT received a NWO Open Science grant to support our research into interoperability of biological data and knowledge:

Re: [BlueObelisk-discuss] Intro + Possible Member

On Thu, Dec 2, 2021 at 6:06 AM Suliman Sharif wrote: > Curious to meet other folk in this group. Is there some sort of cryptic > cheminformatic puzzle I have to solve to join? > The puzzle we're all trying to solve is how we can get chemistry to become a science where knowledge is openly

[BlueObelisk-discuss] CMLXOM 3.2 pushed to Maven Central :)

Hi all, I just pushed CMLXOM 3.2 to Maven Central. After Euclid, this is the second WWMM package now available from Maven Central (via Sonatype). Egon -- This year I am stepping down as co-Editor-in-Chief of the Journal of Cheminformatics, because of a conflict of interest with Springer

Re: [BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

On Sun, Jul 11, 2021 at 8:51 PM Peter Murray-Rust wrote: > As you've probably found the message comes from CMLAtom, and is one of the > hardcoded validation rules for CML (these would be better done with an > XPath-type tool like Schematron, but that's irrelevant). > That's okay. > The error

Re: [BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

On Sun, Jul 11, 2021 at 7:29 PM Peter Murray-Rust wrote: > I imagine I wrote this code but don't have it on my machine at present. > Can you give a pointer to the Github repo and I'll have a look - but I'm > not very optimistic I can help. > https://github.com/BlueObelisk/cmlxom > Would love

[BlueObelisk-discuss] weird cmlxom unit test fail on GitHub (was: Maven Central)

Hi all, On Mon, Jun 28, 2021 at 10:22 PM Egon Willighagen < egon.willigha...@gmail.com> wrote: > Next up is cmlxom :) (And then a PR for the CDK) > I have started working on cmlxom to get it ready for uploading to Maven Central. Today I have done the following things: - update JUn

[BlueObelisk-discuss] Maven Central (was: WWMM & CML -- sunsetting of Mercurial in Bitbucket)

Willighagen wrote: > > > On Fri, Jun 25, 2021 at 4:23 PM Egon Willighagen < > egon.willigha...@gmail.com> wrote: > >> But if you need CMLXOM or other parts to be published in Maven Central, >>> I'd say go ahead. >>> >> >> Okay, g

Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

On Fri, Jun 25, 2021 at 4:23 PM Egon Willighagen wrote: > But if you need CMLXOM or other parts to be published in Maven Central, >> I'd say go ahead. >> > > Okay, going ahead and will use org.blueoblelisk as Maven groupId > GroupId requested: https://issues.sonatyp

Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

Okay, going ahead and will use org.blueoblelisk as Maven groupId Egon > > Cheers, > Oliver > > Oliver Stueker > Research Consultant, ACENET > 709.864.3021 | www.ace-net.ca | @computeatlantic > > A Compute Canada Regional Partner > > > On Fri, Jun 25, 2021 at

[BlueObelisk-discuss] Bacting paper published (Bacting is a follow up of Bioclipse)

Hi all, because I am not good enough to build the Bioclipse UI in Eclipse in a reproducible way, two years ago I decided to move Bioclipse to the command line, Mavenizing things along the way, and this resulted in "Bacting". The paper was just published this week:

Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

Hi Oliver, Mark, all On Fri, Dec 13, 2019 at 9:01 PM Oliver Stueker wrote: > We would like to get your feedback on a number of points: > >- Do you also think that https://github.com/BlueObelisk would be a >good home for the WWMM and CML repositories? The names wwmm and cml are >

[BlueObelisk-discuss] Fwd: [InChI-discuss] NIH Virtual Workshop on InChI, March 22-24, 2021

-- Forwarded message - From: Steve Heller Date: Fri, Feb 26, 2021 at 1:35 AM Subject: [InChI-discuss] NIH Virtual Workshop on InChI, March 22-24,2021 To: inchi-disc...@lists.sourceforge.net Click to Register for the NIH Virtual Workshop on InChI, March 22-24, 2021 Note that a

Re: [BlueObelisk-discuss] Structure database that can be queried by SPARQL?

On Thu, Dec 3, 2020 at 12:08 PM Steve Vestal wrote: > Does anyone know of an open source software package that can convert > SMILES strings into RDF (brass ring) or any sort of attributed graph data > structure? > Oh, that takes me back... yes, I think I wrote an RDF exporter for the CDK at some

Re: [BlueObelisk-discuss] Structure database that can be queried by SPARQL?

Please have a look at: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0282-y On Tue, Dec 1, 2020 at 4:04 PM Steve Vestal wrote: > Does anyone know of a structure database that can be queried using an > RDF query language like SPARQL? PubChemRDF can be accessed in RDF > format,

Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

In related news... XOMCML is now distributed as part of Debian GNU/Linux!!! https://packages.debian.org/sid/libcmlxom-java It was a dependency for CDK 2.3, that's why. Egon On Mon, Dec 30, 2019 at 12:04 PM Peter Murray-Rust wrote: > > > On Sun, Dec 29, 2019 at 10:00 AM Egon Wi

Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

I made a few small edits :) Egon On Sun, Dec 29, 2019 at 4:12 PM Mark Williamson wrote: > > > On 29/12/2019 09:59, Egon Willighagen wrote: > > > Within the BlueObelisk-org, I've also created the teams CML and WWMM > > and assigned the repos to those teams

Re: [BlueObelisk-discuss] WWMM & CML -- sunsetting of Mercurial in Bitbucket

Dear Oliver, On Sat, Dec 28, 2019 at 11:24 PM Oliver Stueker wrote: > Happy Holidays everyone, > Same here. As discussed a couple of weeks ago, I have today imported the 50 > repositories from the WWMM and CML users/teams on Bitbucket into the Blue > Obelisk GitHub-org

[BlueObelisk-discuss] BODR evolution

Hi all, since this year is the Year of the Period Table, it may be nice to make a new Blue Obelisk Data Release (BODR) release, our CC0 release of data on the chemical elements and some simple substances based on them (https://github.com/BlueObelisk/bodr). I had some changes in mind. BODR

Re: [BlueObelisk-discuss] Open Science, not just Open Access

not just complaints. We must fuel the people in cOAlition S that want Open Science. We must show them there is a significant research community that wants that too. Egon On Sun, Feb 3, 2019 at 8:00 PM Egon Willighagen wrote: > > Hi all, > > I guess most people on t

Re: [BlueObelisk-discuss] Open Science, not just Open Access

Thanks, and also for signing! Egon On Mon, Feb 4, 2019 at 2:48 AM Jerome Pansanel wrote: > Hi Egon, > > I forward your message to one of my colleague, in charge of Open Science > at the University of Strasbourg. > > Cheers, > > Jerome > > Le 03/02/2019 à 2

[BlueObelisk-discuss] a Blue Obelisk meet up at the 11th ICCS?

Hi all, in May there will be 11th International Conference on Chemical Structures [0]. I will go and while the program is normally quite packed, I'm sure there will be an opportunity to come together. Looking forward to hearing who else is going, and looking forward to finally be able to join a

Re: [BlueObelisk-discuss] website / migration to Markdown+git ?

Hi Chris, I think it's time to update the redirect of blueobelisk.org to the new website... Egon On Sun, Oct 1, 2017 at 12:14 PM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > > Hi all, > > On Mon, Sep 11, 2017 at 7:05 PM, Egon Willighagen > <egon.willigha...@g

Re: [BlueObelisk-discuss] Does anyone on this list own the blueobelisk (one word) repository on GitHub?

Geoff, thanks! I've moved the stub index.md to the new "organization" and removed the hyphened one. Egon On Tue, Sep 12, 2017 at 5:44 AM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > So, can you grow the number of admins with people from this list? Then > we ca

Re: [BlueObelisk-discuss] website / migration to Markdown+git ?

On Mon, Sep 11, 2017 at 9:22 PM, Christoph Steinbeck wrote: > Please remind me of the new wiki location and I’ll redirect the domain for > now. My ageing neural network had forgotten about it, otherwise I would have > fixed the problem a while ago.

Re: [BlueObelisk-discuss] Cohen-Ingold-Prelog rules into Jmol

On Sat, Apr 8, 2017 at 1:43 AM, Robert Hanson wrote: > Just thought I would let people know that Jmol/JSmol now can calculate R/S > chirality for any carbon atom. I've been working with Jmol for 10 years and > only yesterday realized it was pretty trivial to write this. Well,

Re: [BlueObelisk-discuss] owner/operator of online web service for CDK?

g 30, 2016 at 8:13 AM, Egon Willighagen > <egon.willigha...@gmail.com> wrote: >> >> >> Rajarshi, Ola, >> >> where is the code base? Then I can look at updating the code. The QSAR >> stack has not changed a lot, neither has the SMILES parsing API.

Re: [BlueObelisk-discuss] owner/operator of online web service for CDK?

s I teach right now, so no course material development time :( Egon > On Tue, Aug 30, 2016 at 7:13 AM, Egon Willighagen > <egon.willigha...@gmail.com> wrote: >> >> >> Rajarshi, Ola, >> >> where is the code base? Then I can look at updating the code. Th

Re: [BlueObelisk-discuss] owner/operator of online web service for CDK?

Rajarshi, Ola, where is the code base? Then I can look at updating the code. The QSAR stack has not changed a lot, neither has the SMILES parsing API. I think I can fix it without much trouble, if there is a git repository and build instructions... Then Ola and I can look at updating the

[BlueObelisk-discuss] soon: BODR 11 release

://github.com/egonw/bodr Grtz, Egon 2016-03-28 Egon Willighagen <egon.willigha...@gmail.com> * elements/symbols.bibxml: added two references for recently confirmed elements 2014-10-09 vaitkus <antanas.vaitku...@gmail.com> * elements/elements.xml: fixed the element symbol for Lv * elements/

Re: [BlueObelisk-discuss] List of chemical names and identifiers

Peter, On Tue, Mar 8, 2016 at 7:43 PM, Peter Murray-Rust wrote: > I am now enhancing contentmine.org to search the daily literature and need > dictionaries to match names. I don't mind false negatives so am simply > matching names, but they should have identifiers. > > The

[BlueObelisk-discuss] Twitter account

Hi all, with all the Open storms around now, which is good, it's important that the Blue Obelisk stays on the radar. It's doing important things and if not well-known it will be easily overlooked. And there remains so much to be done in chemistry... (BTW, anyone among us going to the upcoming

Re: [BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

that students can see the ideas too! Egon On Tue, Mar 1, 2016 at 7:06 PM, Greg Landrum <greg.land...@gmail.com> wrote: > I can probably help with that Egon, at least as far as the RDKit bit is > concerned. > > > On Tuesday, 1 March 2016, Egon Willighagen <egon.willig

[BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

Hi all, the NRNB is an USA-based organization around Cytoscape and WikiPathways, the latter involving PathVisio. You may know that Cytoscape has a plugin that used the CDK (by Scooter Morris et al., UCSF) and here in Maastricht we have been working on PathVisio plugins for metabolites also using

[BlueObelisk-discuss] 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 rord...@mdpi.com Date: Tue, Jul 22, 2014 at 3:27 PM Subject: [CHMINF-L] Prize for best open source cheminformatic tool, part of the

Re: [BlueObelisk-discuss] The last Blue Obelisk manuscript ; TeX help wanted

On Thu, Jul 10, 2014 at 9:43 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: . I plan to try pandoc. Egon, does it REQUIRE the BMC stylesheet? Or can I take the style sheet out of the TeX and just convert it anyhow? Yes, but I would indeed take the approach you suggest, and remove the templates,

Re: [BlueObelisk-discuss] Impact

Hi Karol, all, On Thu, May 22, 2014 at 4:36 PM, Karol M. Langner karol.lang...@gmail.com 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

[BlueObelisk-discuss] 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

Re: [BlueObelisk-discuss] Impact

On Wed, May 14, 2014 at 12:26 PM, Rzepa, Henry S h.rz...@imperial.ac.uk 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:

Re: [BlueObelisk-discuss] Impact

On Wed, May 14, 2014 at 1:29 PM, Peter Murray-Rust pm...@cam.ac.uk 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:

[BlueObelisk-discuss] 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

Re: [BlueObelisk-discuss] Impact

On Wed, May 14, 2014 at 3:43 PM, Craig James cja...@emolecules.com wrote: www.opensmiles.org Yes, checked and website can indeed be listed. Added! Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage:

Re: [BlueObelisk-discuss] Google Summer of Code 2014 options?

Dear Peter, On Sun, Mar 2, 2014 at 11:09 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: Is this still possible (I was invited to a phylogenetic project but told that it wasn't funded). So has the deadline passed? The deadline for mentoring organizations has passed. I did not have time to try and

[BlueObelisk-discuss] 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

Re: [BlueObelisk-discuss] BODR covalent radii patch (all elements)

On Thu, Feb 20, 2014 at 8:07 AM, Wibe de Jong wadej...@lbl.gov wrote: Please peer review, comment, and apply. Can you check my comment? https://github.com/wadejong/bodr/commit/c7917225cad829507bdd4c8c2fe7ebd3d795c021#commitcomment-5447272 Thanks, Egon -- E.L. Willighagen Department of

[BlueObelisk-discuss] vacancies in our group (for doing Open stuff in a EU setting)

Hi all, our group has three vacancies open. Our group does a lot of open chem- and bioinformatics, and includes the Open Source projects WikiPathways, PathVisio, BridgeDb, the CDK, etc. Two of the three positions (a postdoc and PhD position) are for a EU FP7 project that I will start early next

[BlueObelisk-discuss] BODR/CDK-based app in the F-Droid app store

Hi all, with a lot of pleasure I can tell you that my very basic, one afternoon Android hacky app has made it into the F-Droid app store: https://f-droid.org/repository/browse/?fdid=com.github.egonw.isotopes It uses the Blue Obelisk Data Repository and the Chemistry Development Kit. It's GPLv3

[BlueObelisk-discuss] Fwd: [open-science] European Commision Science 2.0 survey

Hi all Blue Obelisk-ers, this just came by on the open-science mailing list of the OKFN... Interesting questions... crappy survey (not particularly hard to see what they like as answers; which is Open for a change), I'd say, but good for the cause... In fact, it makes me suspicions this is

[BlueObelisk-discuss] Predicting Chemical Liabilities with Bioclipse and OpenTox workshop in Mainz, 30 Sept 2013

to take advantage of that: http://www.opentox.org/meet/opentoxeu2013/opentox-euro-2013-hotels-1 Please also ping me if you are interested in a Blue Obelisk meeting or dinner. Looking forward to meet up again with the Open Science chemistry community! With kind regards, Egon Willighagen 0.http

Re: [BlueObelisk-discuss] BODR updates

On Sun, Aug 4, 2013 at 10:21 PM, Egon Willighagen egon.willigha...@gmail.com wrote: I will try to make a BODR 10 release due in a week or two. BODR 10 is now available from SourceForge for download: https://sourceforge.net/projects/bodr/files/bodr/10/ Thanks to all that contributed

[BlueObelisk-discuss] Fwd: OpenTox Euro 2013 conference, announcement update

: Barry Hardy (Douglas Connect), Andreas Karwath, Stefan Kramer (Johannes Gutenberg University of Mainz), Nina Jeliazkova (Ideaconsult), Egon Willighagen (Maastricht University), and Juergen Borlak (Hannover Medical School) Abstract Submission: https://www.easychair.org/conferences/?conf

[BlueObelisk-discuss] BODR updates

Hi all, just a quick ping that I have been working on updating BODR, addressing outstanding issues, updates for recent element namings, and going through CDK and Kalzium bug reports to see what is relevant for the next release. Please note the following: 1. if your project uses BODR data,

[BlueObelisk-discuss] BODR 10 release upcoming

Hi all, I am preparing a BODR 10 release. Please check the ChangeLog for the changes: https://sourceforge.net/p/bodr/code/74/tree/trunk/bodr/ChangeLog I guess the biggest change is the license change (discussed some 1.5 yrs ago) from MIT to CCZero. For the rest, several bug fixes and updates

Re: [BlueObelisk-discuss] dinner at ACS meeting in New Orleans?

On Wed, Apr 3, 2013 at 10:35 AM, Noel O'Boyle baoille...@gmail.com wrote: Sunday after CINF reception? Yeah, that should work for me too, I think. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/)

Re: [BlueObelisk-discuss] dinner at ACS meeting in New Orleans?

On Tue, Apr 2, 2013 at 1:41 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote: Any suggestions on where and when to meet? My vote is 7:45pm, at the Convention Center I think I am expected to show up at the Sci-Mix meeting that night with two posters... I would join around 10pm for a drink. Egon

[BlueObelisk-discuss] dinner at ACS meeting in New Orleans?

Hi all, who else is going to the ACS meeting in New Orleans in April and like to join a Blue Obelisk dinner/drink? Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/

[BlueObelisk-discuss] Fwd: [Jmol-users] PDB - OK, who's the wise guy?

Anyone knows? -- Forwarded message -- From: Robert Hanson hans...@stolaf.edu Date: Fri, Jan 18, 2013 at 11:26 PM Subject: [Jmol-users] PDB - OK, who's the wise guy? To: jmol-us...@lists.sourceforge.net jmol-us...@lists.sourceforge.net Where does THIS come from? Hex code in a PDB

[BlueObelisk-discuss] who likes to join a Blue Obelisk pub drink tonight at 20:00 ?

Hi all, I know some of you are festing in Helsinki, but I'm in Cambridge and up for a pub drink tonight. Feel free to join! Of course, discussions will be about the Blue Obelisk and Blue Obelisk projects... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics -

Re: [BlueObelisk-discuss] who likes to join a Blue Obelisk pub drink tonight at 20:00 ?

On Tue, Sep 18, 2012 at 2:15 PM, Noel O'Boyle baoille...@gmail.com wrote: Excellent. Count me in in spirit. Unfortunately, actually getting there will involve working around other things which I don't know the details of right now. Can you email me a phone number off-list and I can text closer

Re: [BlueObelisk-discuss] ODOSOS text

On Thu, Aug 30, 2012 at 9:36 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Thu, Aug 30, 2012 at 2:08 AM, Andrew Dalke da...@dalkescientific.com wrote: On Aug 29, 2012, at 4:02 PM, Peter Murray-Rust wrote: [Please note that I personally do not have write access to the BO pages]. So, umm,

Re: [BlueObelisk-discuss] legal rights concerning SMILES and SMARTS collections

Dear Andrew, On Mon, Aug 27, 2012 at 12:14 PM, Andrew Dalke da...@dalkescientific.com wrote: 3) SMARTS from Ehrlich and Rarey's recent J. Cheminformatics paper Ehrlich and Rarey published a list of 1235 SMARTS in Systematic benchmark of substructure search in molecular graphs - From

[BlueObelisk-discuss] Chemical blogspace cited

Hi all, thanx to Peter Maas, Chemical blogspace is still up and running: http://cb.openmolecules.net/ While I was looking for citations of OpenMolecule RDF (http://rdf.openmolecules.net/) I noted that Cb was cited a few months ago in this paper: Buchanan, Robert A. (2011) Beyond the Chemistry

Re: [BlueObelisk-discuss] Request for Information about Code libraries for CML

On Thu, Mar 29, 2012 at 11:11 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: If you write a section on your code then this will generally mean that you are listed as an author. We only want descriptions of the CML interface/API/coverage - not the greater functionality of the program/library I

Re: [BlueObelisk-discuss] Article in The Guardian

On Sun, Jan 22, 2012 at 4:37 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Sun, Jan 22, 2012 at 2:25 PM, Karol M. Langner karol.lang...@gmail.com They sure are independent, if that's what you mean by orthogonal, but many people would claim they are correlated (at least statistically). Yes -

Re: [BlueObelisk-discuss] Current status of JCAMP parsers

On Sun, Jan 8, 2012 at 12:05 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: Does anyone know what the current state of the Open Source JCAMP parsing library at http://sourceforge.net/projects/jcamp-dx is? Peter, since you are one of the three project leaders of that project, I guess the most

Re: [BlueObelisk-discuss] Paper for special issue of J.Cheminformatics

On Tue, Jun 14, 2011 at 1:39 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: The original paper 5 years ago is still being cited and I expect this new one will also be highly read and act as a reference for those interested in Open chemistry. 119 times now, according to Web of Science, with 19

Re: [BlueObelisk-discuss] [quixote-qcdb] Questions and answers for compchem problems (?Shapado)

Hi all, On Sun, Jun 5, 2011 at 12:24 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: Action = We need to know what is involved in setting up such a site and running it. I know that Egon has been heavily involved - who else. I'm guessing that there would be Quixotans who can get started.

Re: [BlueObelisk-discuss] Fwd: CCL: OpenTox Online Tutorial: Predict the toxicity of a molecule using ToxPredict. (Wed, 20 April, 15:00 CEST)

On Sat, Apr 16, 2011 at 9:54 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Sat, Apr 16, 2011 at 7:03 AM, Egon Willighagen egon.willigha...@gmail.com wrote: I was just wondering... how (un)common are tutorials like this in the Blue Obelisk community? Does like this mean

[BlueObelisk-discuss] Fwd: CCL: OpenTox Online Tutorial: Predict the toxicity of a molecule using ToxPredict. (Wed, 20 April, 15:00 CEST)

Hi all, I was just wondering... how (un)common are tutorials like this in the Blue Obelisk community? Egon -- Forwarded message -- From: Roman Affentranger roman#%#douglasconnect.com owner-chemis...@ccl.net Date: Thu, Apr 14, 2011 at 9:38 AM Subject: CCL: OpenTox Online

[BlueObelisk-discuss] unanswered hot questions on the Blue Obelisk eXchange

Hi all, I know I need to this more frequently, but here's again a shortlist of hot questions (most upvoted) that have not received any answer yet: - Which (open) electronic lab notebook (ELN) tools do you use? -

[BlueObelisk-discuss] DataONE

Hi all, just wanted to make you aware of this: https://www.dataone.org/content/2011-summer-internship-program M.Sc. students, PhD, and even post-docs seem eligible... tough competition, or very well funded. #opendata #science Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för

Re: [BlueObelisk-discuss] Wiki

On Tue, Feb 15, 2011 at 12:03 PM, Noel O'Boyle baoille...@gmail.com wrote: The wiki is now back up at http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Main_Page. There's still a bit more work to do fixing the redirects, and sorting out images, and so forth. Thanx! To make

Re: [BlueObelisk-discuss] Open data platform beta testers.

Hi Mark, On Mon, Feb 14, 2011 at 2:20 PM, Hahnel, Mark m.hahne...@imperial.ac.uk wrote: All figures are licensed under a Creative Commons Attribution 3.0 Unported License. - with the CC-BY logo. Perhaps this isnt prominent enough. I personally would prefer CC0 but I know that 'normal

Re: [BlueObelisk-discuss] Wiki

On Thu, Feb 10, 2011 at 9:14 AM, Noel O'Boyle baoille...@gmail.com wrote: SourceForge have just changed everything on their server, so the wiki is down. I'll sort it out by and by... :( SourceForge-- (for not giving a warning...) Noel++ (for looking into getting it fixed...) Egon -- Dr

Re: [BlueObelisk-discuss] Wiki

Hi Greg, On Thu, Feb 10, 2011 at 9:46 AM, Greg Landrum greg.land...@gmail.com wrote: On Thu, Feb 10, 2011 at 10:21 AM, Egon Willighagen SourceForge-- (for not giving a warning...) This criticism is unjustified. After the attacks on the site, the folks at sf.net did send around an email

[BlueObelisk-discuss] what the CDK really needs...

are the CDK could really need help with, and also hope to have clear that anyone is most welcome to help out, and shape the future of the project! With kind regards from a sunny Uppsala, Egon Willighagen -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska

[BlueObelisk-discuss] Fwd: [Jmol-users] Jmol integrated with chemCanvas

Looks really interesting! -- Forwarded message -- From: Dimitris Dimitropoulos ddimit...@gmail.com Date: Sat, Jan 22, 2011 at 12:26 AM Subject: [Jmol-users] Jmol integrated with chemCanvas To: jmol-us...@lists.sourceforge.net Hi, I though that some people may find interesting

Re: [BlueObelisk-discuss] [FYI] Java API for PubChem

Hi Jun, On Fri, Jan 14, 2011 at 11:58 AM, Jun Zhao jun.z...@zoo.ox.ac.uk wrote: This might be of interest to someone! Sure is! A Java API for working with PubChem data-sets. Mark Southern and Patrick Griffin Bioinformatics 2011 published 6 January 2011, 10.1093/bioinformatics/btq715 Thanx

Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml

On Fri, Dec 31, 2010 at 2:57 AM, Neumann, Steffen steffen.neum...@ipb-halle.de wrote: but is it bodr's job to take care of implementation details about indexing ? What if someone is coding in pascal (where arrays start from 1 ...) Dummy atoms are at the level of atom types, and do not really

[BlueObelisk-discuss] CC0 RDF hosting service

Hi all, Mark Hahnel has extended his Science 3.0 website with a CC0 RDF hosting service. The purpose is small data sets, like results from experiments. http://www.science3point0.com/opendata/ It is still new, and most certainly not in its final form. Yet, this should be of such interested to

Re: [BlueObelisk-discuss] [Kalzium] Re: [Bug 255854] Element 117 (UUs) has wrong discovery date

On Wed, Nov 3, 2010 at 12:09 AM, Rebetez Etienne etienne.rebe...@oberwallis.ch wrote: Am Dienstag, 2. November 2010, 20:19:46 schrieb Carsten Niehaus: Have you already contacted BO? It is important to fix those things upstream. I used to sync the dataset every few month. It is just a matter of

Re: [BlueObelisk-discuss] Chemical MIME types

Hi Martin, On Thu, Oct 28, 2010 at 8:20 PM, Martin Peeks martin...@googlemail.com wrote: On 28 October 2010 16:36, Peter Murray-Rust pm...@cam.ac.uk wrote: From looking at the update-desktop-database package's website http://www.freedesktop.org/wiki/Software/desktop-file-utils, it appears

Re: [BlueObelisk-discuss] Chemical MIME types

On Thu, Oct 28, 2010 at 11:23 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: If KDE and Debian are treating chemical/ as an upperlevel type then it may well be worth trying IETF/IANA  again. I am trying to collect real world adoption on the Blue Obelisk eXchange... Ubuntu supports it too, and

Re: [BlueObelisk-discuss] Chemical MIME types

On Fri, Oct 29, 2010 at 12:22 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: Things have changed a lot in the last hours (including some private correspondence) and I am now quite optimistic so I would certainly support it. We can make a very good case including - I suspect:  * many 100s of

[BlueObelisk-discuss] Fwd: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties

FYI -- Forwarded message -- From: P.Canepa pc...@kent.ac.uk Date: Mon, Oct 25, 2010 at 10:09 AM Subject: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties To: jmol-us...@lists.sourceforge.net jmol-us...@lists.sourceforge.net,

Re: [BlueObelisk-discuss] [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk

On Sun, Oct 24, 2010 at 10:13 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Perhaps we can collaborate with reusing/extending existing OpenTox REST services with similar functionality and sharing experience with development of  web services based on RDF . Perhaps as a start the data can

Re: [BlueObelisk-discuss] [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk

On Mon, Oct 25, 2010 at 11:13 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Perhaps as a start the data can just be pulled and put in one of the current OpenTox servers? No problem with this - do you have in mind particular piece of data to start with ? Check here...

Re: [BlueObelisk-discuss] [quixote-qcdb] Re: [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk

Nina, On Mon, Oct 25, 2010 at 12:28 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Mon, Oct 25, 2010 at 10:33 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: For gaussian files it should be feasible as well, does CDK reads gaussian files ? JUMBO does and the transofrmation is

[BlueObelisk-discuss] CDK 10 year anniversary

Hi all, tomorrow, September 27-29, it is exactly 10 years ago that Dan Gezelter (the Jmol inventor) hosted a meeting at Notre Dame (South Bend) where he, Christoph Steinbeck (the CompChem and JChemPaint inventor), and me founded the Chemistry Development Kit, loosely named after the 'Java

[BlueObelisk-discuss] making video's and podcasts more semantic

Hi all, I just ran into this interesting video: http://www.drumbeat.org/content/popcorn-js-semantic-video-demo Should be able to make video's and podcasts less hamburger-like... Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse

[BlueObelisk-discuss] Nina Jeliazkova awarded a Blue Obelisk Award

Hi all, on behalf of Peter, Christoph awarded Nina Jeliazkova the Blue Obelisk Award for her contributions to ODOSOS cheminformatics at the Blue Obelisk dinner tonight at the ACS meeting in Boston. Egon PS. the award is not for any particular achievement, but I do like to mention some of Nina's

[BlueObelisk-discuss] Open Standards: Resource Description Framework

Cheminformatics should have special interest in these three sessions, and I am very much looking forward to seeing you all next Sunday and/or Monday! The full program can be found at: http://egonw.github.com/acsrdf2010/ (please retweet and share with friends otherwise) with kind regards, Egon

[BlueObelisk-discuss] PDF 2 text parsing?

Hi all (and Peter's team in particular), Converting PDF back into text is a somewhat tricky exercise, as words can actually be characters rendered in approximately word format... Strigi [0] does a decent but not perfect recovery of text... is there someone here who has experience with PDF 2 text

Re: [BlueObelisk-discuss] PDF 2 text parsing?

On Sat, Aug 14, 2010 at 4:26 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Sat, Aug 14, 2010 at 11:41 AM, Egon Willighagen Converting PDF back into text is a somewhat tricky exercise, as words can actually be characters rendered in approximately word format... This understates the problem

Re: [BlueObelisk-discuss] Distributing Blue Obelisk Propaganda at ACS

On Fri, Jul 30, 2010 at 4:38 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: Maybe we can come up with something for CDK, and maybe an overview sheet with a list of open source chemistry packages (courtesy of the Blue Obelisk)? Then we'd have three little piles of sheets to compete

Re: [BlueObelisk-discuss] Silicos NV releases Sieve v3 under GNU GPL version 2

Dear Gert, On Wed, Aug 4, 2010 at 10:00 AM, Gert Thijs gert.th...@silicos.com wrote: Silicos is pleased to announce the release of version 3 of its molecular filtering software Sieve. Thank you for another contribution to the community! • Selection criteria by means of smarts patterns;

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