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

[Noel O'Boyle]

Just to note that importing from Bitbucket is handled by GitHub. Also that
GitHub pages can serve HTML by turning off Jekyll (a process which I'd
recommend).

- Noel

On Fri, 25 Jun 2021, 16:19 Peter Murray-Rust,  wrote:

> Oliver and colleagues did a really great job in porting CML code.
>
> It is valuable and will continue to be. Wikidata+CML adds a lot of
> potential to semantic chemistry.
>
> We are still continuing to work on (a) plant science and (b) battery
> materials , both of which will need a semantic framework.
>
> I have moved from Java to Python and it would be relatively easy to
> migrate CML to Python. XML has a considerable overhead in Java which can be
> bypassed in Python. So we have an XML paper-reader (AMI) and it would be
> fun to add chemistry. But it needs users to help drive it. A circular
> problem but one which gets continually easier to solve.
>
> P.
>
>
>
> On Fri, Jun 25, 2021 at 3:23 PM Egon Willighagen <
> egon.willigha...@gmail.com> wrote:
>
>>
>> On Fri, Jun 25, 2021 at 3:25 PM Oliver Stueker 
>> wrote:
>>
>>> Back between Christmas 2019 and the early days of 2020, Mark and I made
>>> good progress in enabling CI (Travis) on many of the projects.
>>> At some point I had to stop because I needed to get access to publish
>>> modules on Maven Central, which took a few days. Then 2020 happened.
>>>
>>
>> Indeed.
>>
>> I haven't touched those repos in 18 months now
>>>
>>
>> Yes, I saw that... time has passed by quickly... it's all such a blur
>>
>>
>>> and I don't know when I'll take the time to continue working on them.
>>>
>>
>> This is what we have the Dr. Who model for :)
>>
>>
>>> I still have the plan to get the jumbo-converters and all their
>>> dependencies set-up for CI and published to Maven Central, but I don't have
>>> a timeline, as for me this is just a hobby-project.
>>>
>>
>> Understood! (same here)
>>
>>
>>> At some point I'd even like to work on porting the www.xml-cml.org
>>> website to use Jekyll and be hosted from a GitHub-repo, so that we can
>>> expand the dictionaries with Pull-requests.
>>>
>>
>> Yes, that sounds good.
>>
>>
>>> 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
>>
>> 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 3:46 AM Egon Willighagen <
>>> egon.willigha...@gmail.com> wrote:
>>>

 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
>already taken on GitHub.com.
>
> I think it worked out quite well.

>
>- What are your thoughts?
>
> What are people's current plans to make modules available on Maven
 Central? For example, I just discovered the CMLXOM needs updates and needs
 to be uploaded to Maven Central.

- Has anyone already started this?
- Should we use io.github.blueobelisk as (new) group ID?

 I have a Sonatype account and can set something up, but want to make
 sure no one else is already planning this.

 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 Nature.
 See https://twitter.com/egonwillighagen/status/1403299501947899907

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

>>>
>>
>> --
>> This year I am stepping down as co-Editor-in-Chief of the Journal of
>> Cheminformatics, because of a conflict of interest with Springer Nature.
>> See https://twitter.com/egonwillighagen/status/1403299501947899907
>>
>> -
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Twitter/Mastodon: @egonwillighagen 
>>  / @egonw 
>> Homepage: http://egonw.github.com/
>> Blog: http://chem-bla-ics.blogspot.com/
>> PubList: https://www.zotero.org/egonw
>> ORCID: -0001-7542-0286 
>> ImpactStory: 

Re: [BlueObelisk-discuss] Retirement

[Noel O'Boyle]

Wishing you all the best, Craig.

It was great to finally meet you in person in San Diego. You've been a very
positive force in open source and commercial cheminformatics over many
years. For the new here, Craig was a developer at Daylight, co-founded
eMolecules (chmoogle as was), made major contributions to Open Babel, and
was the principal contributor to Open Smiles. And that's just what I can
think of off the top of my head.

Here's to your next bestseller,
Noel

On Tue, 12 Jan 2021, 21:43 Craig James,  wrote:

> Dear colleagues and friends,
>
> I am officially retired from eMolecules as of December 31st.
>
> I would like to say thank you to everyone involved with the BlueObelisk
> project, and particularly the OpenSMILES and IUPAC SMILES projects. It has
> been a fun and rewarding collaboration. I really enjoy the theory and
> practice of cheminformatics, molecular modeling, and computer science, but
> I have decided to move on to new adventures .
>
> Best wishes to all of you!
> Craig
>
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[Noel O'Boyle]

Your understanding is correct, though this is not widely appreciated. There
are many more papers that discuss improving the fingerprint filtering, but
whether they filter out 30% or 20% is kind of irrelevant, given the orders
of magnitude differences in speed for algorithms for subgraph matching.

Most cheminformatics tools represent molecules as graphs internally. It
should not be difficult to add a new output format to Open Babel for
example, or write a Python script to do this, that generates whatever graph
format you require. You just need a "for" loop over the bonds.

On Thu, 3 Dec 2020 at 11:09, Steve Vestal 
wrote:

> Thanks, this was an interesting paper.  I am in fact curious about the
> substructure search problem.
>
> I would appreciate a sanity-check on my understanding of this paper.  My
> impression was that partially ordered fingerprints are used in an initial
> relational database comparison query to obtain a modestly sized set of
> candidate structures, after which a subgraph matching algorithm (e.g., a
> VF2 variant) is applied sequentially to each element of that set to get an
> exact answer.  Is that the general approach?  I got the vague impression
> the sequential subgraph matching, not the fingerprint comparison query, is
> the performance bottleneck -- is that generally true in this approach?
>
> To answer the earlier question, I am interested in seeing if graph
> database and description logic technologies can be applied to structure
> queries.  To play around with that, I would want a true graph database
> representation of structure.  I looked at ChEBI, like PubChem also
> available in RDF format, and like PubChemRDF also encodes structure using
> SMILES strings rather than RDF graphs.
>
> Does anyone know of any structure database that uses an attributed graph
> rather than string representation?
>
> 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?  What about open source tools to generate graphical
> visualizations from SMILES strings?  I assume those would have this
> capability buried inside them.  The CDK page cites a few export formats,
> SMILES, SDF, InChI, Mol2, CML, *and others*.   Are any of the formats
> attributed graph data structures?
>
>
> On 12/2/2020 12:09 PM, Egon Willighagen wrote:
>
>
> 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 <
> steve.ves...@adventiumlabs.com> 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, but it encodes structures as SMILES strings, which cannot be
>> queried in this way.
>>
>> If not, can anyone suggest open source software that might be used to
>> construct a modest RDF dataset from an existing structure database for
>> the purpose of experimenting?  For example, software that can translate
>> SMILES strings into an annotated graph data structure of some sort?
>>
>> Thanks in advance for any suggestions.
>>
>>
>>
>>
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>
>
> --
> Have you heard about Wikidata already? "Use Scholia and Wikidata to find
> scientific literature" is a new tutorial from my colleague Lauren Dupuis.
> https://laurendupuis.github.io/Scholia_tutorial/
>
> -
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: -0001-7542-0286 
> ImpactStory: https://impactstory.org/u/egonwillighagen
>
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[Noel O'Boyle]

GitHub has an import button that will import directly from a mercurial
repository on BitBucket. I've already done this for some of my projects. It
maintains history.

- Noel

On Tue, 17 Dec 2019 at 08:05, Mark Williamson  wrote:

>
>
> On 17/12/2019 02:06, Oliver Stueker wrote:
> > Dear All (especially Egon and Henry),
> >
> > I'd really like to hear your opinion (in favor or against) adding these
> > WWMM and CML source-code repositories to https://github.com/BlueObelisk.
>
> Hello Oliver,
>
> Sounds fine to me; just make sure that it is clear that the old repos
> are deprecated and that there is some kind of forwarding message to the
> new repos. Also, try to maintain history with something like hg-git in
> migration. I'll try and help in any way, time permitting; my github id
> is mjw99.
>
> Thanks,
>
> Mark
>
>
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[Noel O'Boyle]

Sounds good to me. I'll add your account when at my computer.

On Tue, 17 Dec 2019, 06:48 Rzepa, Henry S,  wrote:

> I am happy for you to go ahead!
>
> Thanks.
>
> Henry Rzepa
>
> On 17 Dec 2019, at 02:04, Oliver Stueker  wrote:
>
> 
>
> This email from oliver.stue...@mun.ca originates from outside Imperial.
> Do not click on links and attachments unless you recognise the sender. If
> you trust the sender, add them to your safe senders list
>  to disable email
> stamping for this address.
>
>
> Dear All (especially Egon and Henry),
>
> I'd really like to hear your opinion (in favor or against) adding these
> WWMM and CML source-code repositories to  https://github.com/BlueObelisk.
>
> If you agree that BlueObelisk is a suitable destination, someone (Egon?)
> would need to add my GitHub account (ostueker) to that GH-organization, so
> that I can create the repos.
> If you have concerns about adding this to BlueObelisk, please let me know
> and I'll simply create a new GH-organization (how about WWMolecularMatrix
> or ChemicalMarkupLanguage ?).
>
>
> Cheers,
> Oliver
>
>
>
> On Sat, Dec 14, 2019 at 2:40 AM Peter Murray-Rust  wrote:
>
>> Many thanks Oliver,
>> Copying Mark Williamson
>>
>>
>> On Fri, Dec 13, 2019 at 8:01 PM Oliver Stueker 
>> wrote:
>>
>>> Dear Henry, Egon and Blue Obelisk team,
>>>
>>>
>> I'd first like to thank Oliver for the several years that he has forked
>> and maintained JUMBO-converters software in the context of
>> https://retrievium.com/ . Oliver was on this project which develops
>> computational chemistry tools and has a CML component. I has used
>> JUMBO-converters in the past and may do again.
>>
>> Oliver is now in Newfoundland, Canada and no longer in chemistry but has
>> generously offered to help this migration. He knows more about the details
>> of this than I.
>>
>> His JUMBO fork has taken place since my last commits (which will have
>> been  about 2013 - with minor additional features in 2017 (Scala).
>>
>>
>>> Today Peter (Murray-Rust) and I had a conversation about the future of
>>> the source-code repositories of the WWMM and CML (XML-CML.org) projects.
>>>
>> ...
>>
>> Makes complete sense. I use only Github at present.
>>
>>>
>>> Peter and I have agreed that we want to transfer all of the repositories
>>> (which include projects like oscar4, JUMBO, the JUMBO-converters, the CML
>>> schema and dictionaries) over into a new "Organization" on GitHub which
>>> would then allow to grant merge privileges or even transfer ownership in
>>> case a new "Doctor Who" wants to take on development.
>>>
>>
>> Absolutely. I am very happy to hand over to a new Doctor Who - including
>> Oliver if he wishes - and also to take his current forks if there are no
>> other developments in the last few years that conflict with Oliver's fork.
>>
>>>
>>> Peter suggested that the "Blue Obelisk" might be a good place for the
>>> repositories and I see that https://github.com/BlueObelisk already
>>> exists and contain the code for the Blue Obelisk website and  Blue Obelisk
>>> Data Repository.
>>>
>>>
>> Makes sense - we have suffered from having to migrate at verious times
>> and keep services running and Github looks like a one-stop shop.
>>
>> 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
>>>already taken on GitHub.com.
>>>
>>>
>>> I think the names may belong to me and I may have forgotten passwords .
>>
>>>
>>>-
>>>- With https://github.com/BlueObelisk already containing data,
>>>should we create "Teams" within the "BlueObelisk-org" to  keep things 
>>> tidy
>>>and manage access?
>>>
>>> I don't think I ised teamns on BB. What is the virtue if the numbers are
>> small?
>>
>>>
>>>-
>>>- Should we at some point migrate the xml-cml.org website to be
>>>hosted directly out of the Git-repository?
>>>This would allow publishing updates simply by merging Pull Requests.
>>>Who runs the current website (and manages the xml-cml.org domain)?
>>>Henry?
>>>
>>> I'd be happy to work on migrating the repositories from Bitbucket (hg)
>>> to GitHub (git) over the holidays and even try using GitHub Actions or
>>> Travis-CI for building for some select repositories.
>>>
>>> What are your thoughts?
>>>
>>> Cheers,
>>> Peter and Oliver
>>>
>>> 

>>>
>>
>>>

 From 2014 to 2016, our team at Memorial University has expanded the
 JUMBO-converters as well as a few CML-CompChem dictionaries, however so far
 we fell short at contributing our changes back to the original projects.

>>>
>> Ideally dictionaries shiudl be centrally maintained but I suspect this
>> has been patchy.
>>
>>>
 Now with the risk of all the work being lost when Bitbucket pulls the
 

Re: [BlueObelisk-discuss] Compiling a List of Seminal Papers in Cheminformatics

[Noel O'Boyle]

Apologies - I see you have the correct reference and my memory betrays me.

On Thu, 5 Sep 2019, 06:55 Noel O'Boyle,  wrote:

> Regarding Tanimoto, credit should be given to the original source,
> whatever language it's written in. From memory, la distribution des flores
> dans la zone alpine, I believe.
>
> On Wed, 4 Sep 2019, 20:21 Andrew Dalke,  wrote:
>
>> Here's another example of how it's important to know the clear goal of
>> collecting such a list.
>>
>> One of the entries someone added to the spreadsheet is:
>>   Tanimoto, Taffee T. (17 Nov 1958).
>>   "An Elementary Mathematical theory of Classification and Prediction".
>>   Internal IBM Technical Report. 1957 (8?).
>>
>> I'm going to argue that it's not useful.
>>
>>
>> This is likely present because it's the reason why we call Tanimoto
>> "Tanimoto".
>>
>> However, I don't think it's worthwhile to point to that citation. Here's
>> the history as I know it:
>>
>> The first paper to really use the Tanimoto for similarity search was:
>>
>> Willett, P.; Winterman, V.; Bawden, D. Implementation of Nearest-Neighbor
>> Searching in an Online Chemical Structure Search System. Journal of
>> Chemical Information and Computer Sciences 1986, 26 (1), 36–41.
>> https://doi.org/10.1021/ci00049a008.
>>
>> Others quickly picked up on it, because 1) it was easy to do - Willett
>> told me that one of the first external implementation took an afternoon to
>> implement, and 2) bitstrings were already present because everyone already
>> had pre-computed MACCS keys.
>>
>> The choice of Tanimoto was based on a comparison of several different
>> schemes, in:
>>
>> Willett, P.; Winterman, V. A Comparison of Some Measures for the
>> Determination of Inter-Molecular Structural Similarity Measures of
>> Inter-Molecular Structural Similarity. Quant. Struct.-Act. Relat. 1986, 5
>> (1), 18–25. https://doi.org/10.1002/qsar.19860050105.
>>
>> (That's the one which should property be quoted as demonstrating that the
>> Tanimoto was at least as effective as the others, and easiest to implement,
>> so was chosen. The two papers were jointly published, and reference each
>> other "in press".)
>>
>> However, you'll notice that neither paper cites Tanimoto. Instead, they
>> cite earlier work by Adamson and Bush. These are:
>>
>> Adamson, G. W.; Bush, J. A. A Method for the Automatic Classification of
>> Chemical Structures. Information Storage and Retrieval 1973, 9 (10),
>> 561–568. https://doi.org/10.1016/0020-0271(73)90059-4.
>>
>> Adamson, G. W.; Bush, J. A. A Comparison of the Performance of Some
>> Similarity and Dissimilarity Measures in the Automatic Classification of
>> Chemical Structures. Journal of Chemical Information and Computer Sciences
>> 1975, 15 (1), 55–58. https://doi.org/10.1021/ci60001a016.
>>
>> The 1975 paper cites David J. Rogers, Taffee T. Tanimoto, A Computer
>> Program for Classifying Plants, Science, 21 Oct 1960 1115-1118.
>> https://science.sciencemag.org/content/132/3434/1115
>>
>> More specifically, it's on p56 of the paper, starting on the last
>> sentence of the first column, going to the top of the second column:
>>
>>Several coefficients have been proposed based on this criterion,
>> [8-10,14-16] and some of these were used in the classification of the
>> anesthetics."
>>
>> The 1973 paper neither cites Tanimoto nor uses a Tanimoto similarity.
>>
>> So it appears that Adamson et al. investigated bitstrings using other
>> comparison methods, while Willett et al. were the first to investigate the
>> Tanimoto.
>>
>> For several years after Willett et al. there is few/no citations to
>> Tanimoto (1958) or to Rogers and Tanimoto (1960). As an example of one of
>> the indirect citations, see:
>>
>> Grethe, G.; Moock, T. E. Similarity Searching in REACCS. A New Tool for
>> the Synthetic Chemist. J. Chem. Inf. Comput. Sci. 1990, 30 (4), 511–520.
>> https://doi.org/10.1021/ci00068a025.
>>
>> where the Tanimoto is citation (9): "Ref 1; p54", where reference 1 from
>> the same paper is: Willett, P. Similarity and Clustering in Chemical
>> Information Systems; Reseach Studies Press: Letchworth, Herfordshire,
>> England, 1987
>>
>>
>> Now, go back to the citation that's currently in the spreadsheet:
>>   Tanimoto, Taffee T. (17 Nov 1958).
>>   "An Elementary Mathematical theory of Classification and Prediction".
>>   Internal IBM Technical Report. 1957 (8?).
>

Re: [BlueObelisk-discuss] Compiling a List of Seminal Papers in Cheminformatics

[Noel O'Boyle]

Regarding Tanimoto, credit should be given to the original source, whatever
language it's written in. From memory, la distribution des flores dans la
zone alpine, I believe.

On Wed, 4 Sep 2019, 20:21 Andrew Dalke,  wrote:

> Here's another example of how it's important to know the clear goal of
> collecting such a list.
>
> One of the entries someone added to the spreadsheet is:
>   Tanimoto, Taffee T. (17 Nov 1958).
>   "An Elementary Mathematical theory of Classification and Prediction".
>   Internal IBM Technical Report. 1957 (8?).
>
> I'm going to argue that it's not useful.
>
>
> This is likely present because it's the reason why we call Tanimoto
> "Tanimoto".
>
> However, I don't think it's worthwhile to point to that citation. Here's
> the history as I know it:
>
> The first paper to really use the Tanimoto for similarity search was:
>
> Willett, P.; Winterman, V.; Bawden, D. Implementation of Nearest-Neighbor
> Searching in an Online Chemical Structure Search System. Journal of
> Chemical Information and Computer Sciences 1986, 26 (1), 36–41.
> https://doi.org/10.1021/ci00049a008.
>
> Others quickly picked up on it, because 1) it was easy to do - Willett
> told me that one of the first external implementation took an afternoon to
> implement, and 2) bitstrings were already present because everyone already
> had pre-computed MACCS keys.
>
> The choice of Tanimoto was based on a comparison of several different
> schemes, in:
>
> Willett, P.; Winterman, V. A Comparison of Some Measures for the
> Determination of Inter-Molecular Structural Similarity Measures of
> Inter-Molecular Structural Similarity. Quant. Struct.-Act. Relat. 1986, 5
> (1), 18–25. https://doi.org/10.1002/qsar.19860050105.
>
> (That's the one which should property be quoted as demonstrating that the
> Tanimoto was at least as effective as the others, and easiest to implement,
> so was chosen. The two papers were jointly published, and reference each
> other "in press".)
>
> However, you'll notice that neither paper cites Tanimoto. Instead, they
> cite earlier work by Adamson and Bush. These are:
>
> Adamson, G. W.; Bush, J. A. A Method for the Automatic Classification of
> Chemical Structures. Information Storage and Retrieval 1973, 9 (10),
> 561–568. https://doi.org/10.1016/0020-0271(73)90059-4.
>
> Adamson, G. W.; Bush, J. A. A Comparison of the Performance of Some
> Similarity and Dissimilarity Measures in the Automatic Classification of
> Chemical Structures. Journal of Chemical Information and Computer Sciences
> 1975, 15 (1), 55–58. https://doi.org/10.1021/ci60001a016.
>
> The 1975 paper cites David J. Rogers, Taffee T. Tanimoto, A Computer
> Program for Classifying Plants, Science, 21 Oct 1960 1115-1118.
> https://science.sciencemag.org/content/132/3434/1115
>
> More specifically, it's on p56 of the paper, starting on the last sentence
> of the first column, going to the top of the second column:
>
>Several coefficients have been proposed based on this criterion,
> [8-10,14-16] and some of these were used in the classification of the
> anesthetics."
>
> The 1973 paper neither cites Tanimoto nor uses a Tanimoto similarity.
>
> So it appears that Adamson et al. investigated bitstrings using other
> comparison methods, while Willett et al. were the first to investigate the
> Tanimoto.
>
> For several years after Willett et al. there is few/no citations to
> Tanimoto (1958) or to Rogers and Tanimoto (1960). As an example of one of
> the indirect citations, see:
>
> Grethe, G.; Moock, T. E. Similarity Searching in REACCS. A New Tool for
> the Synthetic Chemist. J. Chem. Inf. Comput. Sci. 1990, 30 (4), 511–520.
> https://doi.org/10.1021/ci00068a025.
>
> where the Tanimoto is citation (9): "Ref 1; p54", where reference 1 from
> the same paper is: Willett, P. Similarity and Clustering in Chemical
> Information Systems; Reseach Studies Press: Letchworth, Herfordshire,
> England, 1987
>
>
> Now, go back to the citation that's currently in the spreadsheet:
>   Tanimoto, Taffee T. (17 Nov 1958).
>   "An Elementary Mathematical theory of Classification and Prediction".
>   Internal IBM Technical Report. 1957 (8?).
>
> What does "*Internal* IBM Technical Report" mean?!
>
> Wikipedia used to describe this as "unavailable". I pointed out that it is
> available through worldcat, and I got a copy from SUB Göttingen :
>
> https://en.wikipedia.org/w/index.php?title=Jaccard_index=704793261=688763411
>
> It's at http://dalkescientific.com/tanimoto.pdf for the really curious.
>
> I can't figure out why anyone would refer a student to 1) an internal
> publication, where 2) it's so hard to get, especially given 3) the actual
> cheminformatics literature references a 1960 Science publication which is a
> further refinement of the internal report.
>
> My guess is that it's one of those citations that everyone passes around,
> but which no one has actually read.
>
> (If Tanimoto's 1958 internal report is a good citation, then I have a copy
> of the 

Re: [BlueObelisk-discuss] ACS Dinner on Monday at 6

[Noel O'Boyle]

How about meet in lobby of Omni at 5.30? Craig James should also be joining
us.

On Thu, 22 Aug 2019, 07:49 Noel O'Boyle,  wrote:

> Absolutely.
>
> On Wed, 21 Aug 2019 at 16:39, David Koes  wrote:
>
>> I'm up for it as long as I can bring group members with me.
>>
>> David Koes
>>
>> Assistant Professor
>> Computational & Systems Biology
>> University of Pittsburgh
>>
>> On 8/21/19 7:42 AM, Noel O'Boyle wrote:
>> > Hi all,
>> >
>> > Any interested in joining me + Rich Apodaca for dinner on Monday at 6?
>> I need to be back for Sci-Mix at 8. Suggestions
>> > for venues v. welcome.
>> >
>> > Regards,
>> > - Noel
>> >
>> >
>> > ___
>> > Blueobelisk-discuss mailing list
>> > Blueobelisk-discuss@lists.sourceforge.net
>> >
>> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fblueobelisk-discussdata=02%7C01%7Cdkoes%40pitt.edu%7C6b454ce3bd2f4dffe68908d7262ca3f7%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637019845478712469sdata=9W2KEKU%2Bm5hbIjQ%2FTqzOWq%2F8%2BwUK7yE%2BXGQ4BYxlHl4%3Dreserved=0
>> >
>>
>>
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] ACS Dinner on Monday at 6

[Noel O'Boyle]

Hi all,

Any interested in joining me + Rich Apodaca for dinner on Monday at 6? I
need to be back for Sci-Mix at 8. Suggestions for venues v. welcome.

Regards,
- Noel
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Doodle Poll for Blue Obelisk Dinner at ACS Meeting Washington August 2017

[Noel O'Boyle]

And the winner is...? Christoph we need you to give the casting vote as
there are three equal options.

On 1 August 2017 at 13:40, Chalk, Stuart  wrote:

> Quick reminder that the ACS CINF Division Reception and Poster Session is
> Sunday 6.30 - 8.30 pm.
>
> Stuart
>
>
> > On Aug 1, 2017, at 8:02 AM, Christoph Steinbeck <
> christoph.steinb...@uni-jena.de> wrote:
> >
> > Dear all,
> >
> > there seems to be some interest in a BO dinner, so here is the poll.
> > Please note, that you can also vote for your favorite starting time
> (6pm, 7pm, 8pm). The later, the tougher for us Europeans :)
> >
> > https://doodle.com/poll/c3ehh6kh7tpzf43s
> >
> > Kind regards,
> >
> > Chris
> >
> > —
> > Prof. Dr. Christoph Steinbeck
> > Analytical Chemistry - Cheminformatics and Chemometrics
> > Friedrich-Schiller-University Jena, Germany
> > Phone Secretariat: +49-3641-948171
> > http://orcid.org/-0001-6966-0814
> >
> > What is man but that lofty spirit - that sense of enterprise.
> > ... Kirk, "I, Mudd," stardate 4513.3..
> >
> >
> > 
> --
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > ___
> > Blueobelisk-discuss mailing list
> > Blueobelisk-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Doodle Poll for Blue Obelisk Dinner at ACS Meeting Washington August 2017

[Noel O'Boyle]

Ah OK - got it. I need to set the time zone to EST.

On 1 August 2017 at 13:21, Noel O'Boyle <baoille...@gmail.com> wrote:
> Doodle is being clever and changing the times from Berlin time to
> London time for me. So everything is an hour off. Is there any way to
> turn this off?
>
> On 1 August 2017 at 13:02, Christoph Steinbeck
> <christoph.steinb...@uni-jena.de> wrote:
>> Dear all,
>>
>> there seems to be some interest in a BO dinner, so here is the poll.
>> Please note, that you can also vote for your favorite starting time (6pm, 
>> 7pm, 8pm). The later, the tougher for us Europeans :)
>>
>> https://doodle.com/poll/c3ehh6kh7tpzf43s
>>
>> Kind regards,
>>
>> Chris
>>
>> —
>> Prof. Dr. Christoph Steinbeck
>> Analytical Chemistry - Cheminformatics and Chemometrics
>> Friedrich-Schiller-University Jena, Germany
>> Phone Secretariat: +49-3641-948171
>> http://orcid.org/-0001-6966-0814
>>
>> What is man but that lofty spirit - that sense of enterprise.
>> ... Kirk, "I, Mudd," stardate 4513.3..
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[Noel O'Boyle]

We need libRS. Everyone reimplementing these rules is some type of madness.

On 9 Apr 2017 7:05 p.m., "Robert Hanson"  wrote:

> OK, I don't get the logic of this:
>
>
> Rule 1 (a) Higher atomic number precedes lower;
> (b) A duplicated atom, with its predecessor node having the same label
> closer
> to the root, ranks higher than a duplicated atom, with its predecessor node
> having the same label farther from the root, which ranks higher than any
> nonduplicated-atom-node (proposed by Custer, ref. 36)
>
> Rule 2 Higher atomic mass number precedes lower;
>
>
> Seriously? root distance is checked before isotope. Sure seems odd to me.
> Why would that distance check not be after atomic number and mass??
>
> Whatever...
>
> Bob
>
>
>
>
> On Sun, Apr 9, 2017 at 12:11 PM, Robert Hanson  wrote:
>
>> OK, so I am reading Chapter 9 now to see the gory details. I didn't know
>> about the root-distance check, and so now
>>
>> 1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-cyclop
>> ropylethyl)-pentan-3-yl]methan-1-ol.mol
>>
>> is working. So all of this is easy enough. That's probably it for
>> independent stereochemistry.  Where there is a dependency  of one
>> stereochemical determination from another -- R/S after E/Z; E/Z after R/S,
>> E/Z after E/Z, R/S after R/S -- obviously that takes some sort of more
>> general iteration.
>>
>> I think I will have to tackle that another day.
>>
>> Bob
>>
>>
>>
>>
>>
>> On Sun, Apr 9, 2017 at 11:03 AM, John Mayfield <
>> john.wilkinson...@gmail.com> wrote:
>>
>>> Good good,
>>>
>>> Fake news before fake news - a paper published in the CCG journal by the
>>> CCG.
>>>
>>> John
>>>
>>> On 9 April 2017 at 16:51, Robert Hanson  wrote:
>>>
 No, John. Don't worry.  I just happened to look at that page prior to
 designing my own.

 On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield <
 john.wilkinson...@gmail.com> wrote:

> Hi Bob,
>
> On 9 April 2017 at 13:42, Robert Hanson  wrote:
>
>> [I actually do know it is Cahn; pulled "Cohen" without thinking from
>> https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
>>
>
> Was that the algorithm you implemented because it's not correct - it
> doesn't (and can't) handle ghost atoms. Trying to track down the example
> but Daniel Lowe constructed a small reproducible example to demonstrate 
> why
> this can never work.
>
> John
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>


 --
 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


>>>
>>
>>
>> --
>> 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
>>
>>
>
>
> --
> 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
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] great InChI JavaScript library

[Noel O'Boyle]

I'm happy to take credit for all chemistry emscripten projects from
here on in, but Rich is to blame for this one.

On 9 March 2016 at 02:33, Robert Hanson  wrote:
> inchi.js is great fun. It is now part of JSmol. See the demo at:
>
> http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm
>
> and http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.3_2016.03.08.zip
>
> Whom do we have to thank for this? Noel?
>
> Bob
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department 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
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>

--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111=/4140
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Blue Obelisk at ACS Boston

[Noel O'Boyle]

Anyone up for dinner before Sci-Mix?

On 17 August 2015 at 15:13, Marcus D. Hanwell mar...@cryos.org wrote:
 Will there be? Too much travel, but I would love to join if there is one.

 On May 27, 2015 5:29 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:

 There could be :)

 On Wed, May 27, 2015 at 5:26 PM, Andrew Lang asidl...@gmail.com wrote:

 Hi Guys:

 Is there going to be a Blue Obelisk dinner at ACS Boston? I'll be there
 Sunday and Monday nights.

 Andy Lang



 --

 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss




 --
 Rajarshi Guha | http://blog.rguha.net
 NIH Center for Advancing Translational Science


 --

 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


 --

 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Blue Obelisk at ACS Boston

[Noel O'Boyle]

Just spoke to Marcus - other plans. I'm over near the CINF rooms if
you want to meet up.

On 17 August 2015 at 18:07, Rajarshi Guha rajarshi.g...@gmail.com wrote:
 Yes, I'm hungry

 On Mon, Aug 17, 2015 at 5:44 PM, Noel O'Boyle baoille...@gmail.com wrote:

 Anyone up for dinner before Sci-Mix?

 On 17 August 2015 at 15:13, Marcus D. Hanwell mar...@cryos.org wrote:
  Will there be? Too much travel, but I would love to join if there is
  one.
 
  On May 27, 2015 5:29 PM, Rajarshi Guha rajarshi.g...@gmail.com
  wrote:
 
  There could be :)
 
  On Wed, May 27, 2015 at 5:26 PM, Andrew Lang asidl...@gmail.com
  wrote:
 
  Hi Guys:
 
  Is there going to be a Blue Obelisk dinner at ACS Boston? I'll be
  there
  Sunday and Monday nights.
 
  Andy Lang
 
 
 
 
  --
 
  ___
  Blueobelisk-discuss mailing list
  Blueobelisk-discuss@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
 
 
 
 
  --
  Rajarshi Guha | http://blog.rguha.net
  NIH Center for Advancing Translational Science
 
 
 
  --
 
  ___
  Blueobelisk-discuss mailing list
  Blueobelisk-discuss@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
 
 
 
  --
 
  ___
  Blueobelisk-discuss mailing list
  Blueobelisk-discuss@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
 




 --
 Rajarshi Guha | http://blog.rguha.net
 NIH Center for Advancing Translational Science

--
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[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..


 --
 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
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
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
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Fwd: [CHMINF-L] Prize for best open source cheminformatic tool, part of the Lausanne Workshop on Chemical Information

[Noel O'Boyle]

Nice, but note the casual redefinition of open source.

- Noel


On 22 July 2014 14:40, Egon Willighagen egon.willigha...@gmail.com wrote:

 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 Lausanne Workshop on Chemical Information
 To: chmin...@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
 submitted to the special issue in the journal Challenges [2] before the
 15 August 2014 and will be published in the journal Challenges after
 editorial review.

 [1] http://cheminformatics.epfl.ch/workshop/index.shtml
 [2]
 http://www.mdpi.com/journal/challenges/special_issues/cheminformatic_tool_contest

 If you have question about this contest, please e-mail
 luc.pat...@epfl.ch.

 On behalf of Dr. Luc Patiny,
 Organizer of the Workshop

 Kind regards,
 Dietrich Rordorf

 *MDPI AG* - Multidisciplinary Digital Publishing Institute
 Klybeckstrassse 64
 CH-4057 Basel, Switzerland
 Tel. +41 61 683 77 34 (office)
 Tel. +41 76 561 41 83 (mobile)
 E-mail: rord...@mdpi.com mailto:rord...@mdpi.com
 http://www.mdpi.com/


 --
 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


 --
 Want fast and easy access to all the code in your enterprise? Index and
 search up to 200,000 lines of code with a free copy of Black Duck
 Code Sight - the same software that powers the world's largest code
 search on Ohloh, the Black Duck Open Hub! Try it now.
 http://p.sf.net/sfu/bds
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

--
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[Noel O'Boyle]

Actually, Monday is looking less attractive now for me too. How
about...any day except Monday? :-)

Sunday after CINF reception?

- Noel

On 3 April 2013 02:37, Egon Willighagen egon.willigha...@gmail.com wrote:
 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

 --
 Dr E.L. Willighagen
 Postdoctoral Researcher
 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

 --
 Minimize network downtime and maximize team effectiveness.
 Reduce network management and security costs.Learn how to hire
 the most talented Cisco Certified professionals. Visit the
 Employer Resources Portal
 http://www.cisco.com/web/learning/employer_resources/index.html
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

--
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire 
the most talented Cisco Certified professionals. Visit the 
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[Noel O'Boyle]

Is that Monday? Either way. Sounds good.

On 2 April 2013 12:41, Rajarshi Guha rajarshi.g...@gmail.com wrote:
 Any suggestions on where and when to meet? My vote is

 7:45pm, at the Convention Center

 As for places to sit, chat, eat and drink, I'm not a local, so not
 very familiar. Some interesting ones, all a few blocks from the
 convention center:

 http://rootnola.com/
 http://www.riomarseafood.com/
 http://www.cochonrestaurant.com/

 for a bar style stting theres a Gordon Biersch close by, or for more
 local flavor http://www.districtnola.com/


 On Wed, Mar 6, 2013 at 10:52 AM, Egon Willighagen
 egon.willigha...@gmail.com wrote:
 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/
 LinkedIn: http://se.linkedin.com/in/egonw
 Blog: http://chem-bla-ics.blogspot.com/
 PubList: http://www.citeulike.org/user/egonw/tag/papers

 --
 Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
 Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the
 endpoint security space. For insight on selecting the right partner to
 tackle endpoint security challenges, access the full report.
 http://p.sf.net/sfu/symantec-dev2dev
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss



 --
 Rajarshi Guha | http://blog.rguha.net
 NIH Center for Advancing Translational Science

 --
 Own the Future-Intel(R) Level Up Game Demo Contest 2013
 Rise to greatness in Intel's independent game demo contest. Compete
 for recognition, cash, and the chance to get your game on Steam.
 $5K grand prize plus 10 genre and skill prizes. Submit your demo
 by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

--
Own the Future-Intel(R) Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest. Compete 
for recognition, cash, and the chance to get your game on Steam. 
$5K grand prize plus 10 genre and skill prizes. Submit your demo 
by 6/6/13. http://altfarm.mediaplex.com/ad/ck/12124-176961-30367-2
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[Noel O'Boyle]

Me too.

On 6 March 2013 15:55, Rajarshi Guha rajarshi.g...@gmail.com wrote:
 I'll be there


 On Wed, Mar 6, 2013 at 10:52 AM, Egon Willighagen
 egon.willigha...@gmail.com wrote:

 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/
 LinkedIn: http://se.linkedin.com/in/egonw
 Blog: http://chem-bla-ics.blogspot.com/
 PubList: http://www.citeulike.org/user/egonw/tag/papers


 --
 Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
 Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the
 endpoint security space. For insight on selecting the right partner to
 tackle endpoint security challenges, access the full report.
 http://p.sf.net/sfu/symantec-dev2dev
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss




 --
 Rajarshi Guha | http://blog.rguha.net
 NIH Center for Advancing Translational Science

 --
 Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
 Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the
 endpoint security space. For insight on selecting the right partner to
 tackle endpoint security challenges, access the full report.
 http://p.sf.net/sfu/symantec-dev2dev
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the  
endpoint security space. For insight on selecting the right partner to 
tackle endpoint security challenges, access the full report. 
http://p.sf.net/sfu/symantec-dev2dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

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

[Noel O'Boyle]

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 to the time?

- Noel

On 18 September 2012 11:15, Egon Willighagen egon.willigha...@gmail.com wrote:
 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 - 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

 --
 Live Security Virtual Conference
 Exclusive live event will cover all the ways today's security and
 threat landscape has changed and how IT managers can respond. Discussions
 will include endpoint security, mobile security and the latest in malware
 threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Wiki editing reminder

[Noel O'Boyle]

As a reminder, wiki editing is open to anyone with a SourceForge
account. Just log in to your SF account and try to edit the wiki. If
it doesn't work, email this list to be whitelisted by an admin.

- Noel

--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Wikis will need to be migrated *back* to local hosting

[Noel O'Boyle]

On 14 August 2012 08:02, Peter Murray-Rust pm...@cam.ac.uk wrote:


 On Mon, Aug 13, 2012 at 9:25 PM, Noel O'Boyle baoille...@gmail.com wrote:

 Hey there everyone,

 FYI, great news. All of the SF mediawikis will need to be migrated
 back to local hosting on SF's web space.


 What does this mean for BO members in practce?

The current wikis will disappear unless they are migrated. The
instructions for migration will be provided by SF but are not yet
available...



 See http://sourceforge.net/blog/hosted-apps-retirement/ and
 https://sourceforge.net/p/forge/community-docs/Hosted%20Apps%20Retirement/

 The timeframe was originally Sept 1st but that has been pushed back to
 later in Q4 2012.

 - Noel


 --
 Live Security Virtual Conference
 Exclusive live event will cover all the ways today's security and
 threat landscape has changed and how IT managers can respond. Discussions
 will include endpoint security, mobile security and the latest in malware
 threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss




 --
 Peter Murray-Rust
 Reader in Molecular Informatics
 Unilever Centre, Dep. Of Chemistry
 University of Cambridge
 CB2 1EW, UK
 +44-1223-763069

--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Wikis will need to be migrated *back* to local hosting

[Noel O'Boyle]

Hey there everyone,

FYI, great news. All of the SF mediawikis will need to be migrated
back to local hosting on SF's web space.

See http://sourceforge.net/blog/hosted-apps-retirement/ and
https://sourceforge.net/p/forge/community-docs/Hosted%20Apps%20Retirement/

The timeframe was originally Sept 1st but that has been pushed back to
later in Q4 2012.

- Noel

--
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Interested in testing out a web conferencing system?

[Noel O'Boyle]

Hello all,

I'm looking for a couple of people interested in trying out the open source
web conferencing system BigBlueButton (designed for distance learning).
This software, started in 2009, appears to work very well and combines
voice, video, slides, chat and desktop sharing. Given that the commercial
alternatives are out of reach for open source projects like Open Babel
etc., this system opens up the possibility of online conferences, tutorials
and meetings. The system allows recording, so that people who miss the
meeting or want to look at the tutorial afterwards can easily do so.

The only catch is that you need your own server (the hosting companies are
too expensive for occasional use). I've set up a server on EC2 and I need 5
or so people (no more) as volunteers to test it out, stress test it and
give some feedback. Hopefully, some of you will be interested in using it
yourselves and may even have the resources to provide a permanent server
for Blue Obelisk projects (hint hint).

So, get in touch on or off list and let me know. I note in advance that the
client requires Flash but is otherwise crossplatform, and a headset or just
a pair of ear phones will help avoid echo.

- Noel
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] How to distribute models

[Noel O'Boyle]

Hi Andy,

If a web service would be acceptable, you should check out http://ochem.eu/.

- Noel

On 2 December 2011 15:15, Andrew Lang gameshon...@hotmail.com wrote:

 There are plenty of ways I now know to create CDK descriptors and build
 models but I'm looking for the best way to distribute them as a desktop
 application.

 My dream program would be one where you would input a SMILES (GUI), it would
 generate the CDK descriptors and then report back (user selected) predicted
 properties based upon Open models (linear, random forest, etc) with the
 ability to download and add new models (like you can add new functionality
 with R). A command line option that does batches would be important too.

 Does this program exist?

 Thanks,

 Andy


 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Mini Blue Obelisk meeting at 5th Meeting on U.S. Government Chemical Databases and Open Chemistry?

[Noel O'Boyle]

Hi all,

I'll be attending the database meeting organising by the NCI on Aug
25-26, and arriving on the afternoon of the 24th. Anyone interested in
meeting up for dinner?

(Unfortunately, unable to make the ACS)

- Noel

--
Get a FREE DOWNLOAD! and learn more about uberSVN rich system, 
user administration capabilities and model configuration. Take 
the hassle out of deploying and managing Subversion and the 
tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] BO dinner at the Fall ACS in Denver

[Noel O'Boyle]

Can't make it, but if you try to make an edit on the wiki, then one of
the admins can give you access

On 15 August 2011 16:57, Rajarshi Guha rajarshi.g...@gmail.com wrote:
 Hi, with the Fall ACS coming up in two weeks, are there any BO'ers (or
 BO'ers to be) who'd like to meet up for dinner?

 If so, could somebody with edit permissions set up a page on the BO
 wiki to list interested people. Also, suggestions for a dinner venue
 in Denver would be welcome

 --
 Rajarshi Guha
 NIH Chemical Genomics Center

 --
 uberSVN's rich system and user administration capabilities and model
 configuration take the hassle out of deploying and managing Subversion and
 the tools developers use with it. Learn more about uberSVN and get a free
 download at:  http://p.sf.net/sfu/wandisco-dev2dev
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
uberSVN's rich system and user administration capabilities and model 
configuration take the hassle out of deploying and managing Subversion and 
the tools developers use with it. Learn more about uberSVN and get a free 
download at:  http://p.sf.net/sfu/wandisco-dev2dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Fwd: Announcing 2nd Open Babble - Pre-registration now open

[Noel O'Boyle]

(Cross-posted as may be of interest, further announcements will not be
posted here)

-- Forwarded message --
From: Noel O'Boyle baoille...@gmail.com
Date: 24 March 2011 12:36
Subject: Announcing 2nd Open Babble - Pre-registration now open
To: Openbabel-DEV openbabel-de...@lists.sourceforge.net,
openbabel-disc...@lists.sourceforge.net


Hello all,

Pre-registration is now open for the 2nd Open Babble, a hands-on Open
Babel workshop presented by Open Babel developers. This will take
place on July 5-6 2011 at the Unilever Centre in the Dept of
Chemistry, University of Cambridge, UK.

The workshop will start on the afternoon of the 5th July, and finish
on the evening of the 6th. The precise topics to be covered will
depend on the attendees’ interests but we anticipate covering topics
such as how to get the most from the Open Babel command line
applications and the GUI, to writing Python scripts and developing
software based on the Open Babel library.

Since only 20 places are available, we are running a pre-registration
process to select a diverse range of attendees, from novices to expert
users, and from both academia and industry. The registration fee will
be €70 for academics, and €220 for industry attendees. This includes
one lunch and dinner, but does not include accommodation.

We also note that sponsorship opportunities are available.

To register your interest in attending, please email
openbab...@gmail.com before April 22nd with the following information:

Name: ___
Position: __ (e.g. PhD student)
Address: ___
Email: _
Registration fee: €70/€220
Reason that you should be selected to attend (max three sentences):
___
___
___
Topics you would like covered: 
___
___


Regards,
  Noel O'Boyle
  (On behalf of the Open Babble organisers)

--
Enable your software for Intel(R) Active Management Technology to meet the
growing manageability and security demands of your customers. Businesses
are taking advantage of Intel(R) vPro (TM) technology - will your software 
be a part of the solution? Download the Intel(R) Manageability Checker 
today! http://p.sf.net/sfu/intel-dev2devmar
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Branding (Was Re: Wiki)

[Noel O'Boyle]

As a first step towards branding, please find attached an Inkscape SVG
version of the blue obelisk logo. (I'll put a link on the wiki
eventually, but consider this a backup in the cloud.)

I'm using this to generate a little blue obelisk for the cover of the
OB user guide (to be published this side of Christmas).

- Noel

On 15 February 2011 13:06, Peter Murray-Rust pm...@cam.ac.uk wrote:
 Thanks to those who helped. This is boring unrewarding work and also done as
 a reaction to emergency.

 We now need to continue to work on branding our outputs... If there are any
 volunteers who would like to help edit a Blue Obelisk theme into the various
 docs for the programs and data, and perhaps create a list of current BO
 tools that would be much appreciated.

 Our group are working hard on http://www.xml-cml.org, especially on
 Dictionaries which are a key resource.

 P.
attachment: blueobelisk.svg--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Wiki

[Noel O'Boyle]

On 14 February 2011 13:55, Noel O'Boyle baoille...@gmail.com wrote:
 I have to think there's a way to script this if the database can't be 
 migrated.

 I've successfully migrated cclib's mediawiki to SF's wiki. It was a
 frustrating experience figuring it out, but having done it once I
 should be able to sort it out for the BO wiki. I have a script to make
 things easy for the export of wiki pages...

 (Come back static web pages, all is forgiven...)

 - Noel

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.

To make things easier for me, I didn't bother retaining the history
(would have to do several uploads as there is a max upload limit).

The main problem, apart from trivial path updates, was that our
mediawiki install was too old to work with PHP 5.3. Going forward, I
think moving to SF's mediawiki makes more sense, as they will keep
mediawiki updated and apply security patches etc.

- Noel

--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Wiki

[Noel O'Boyle]

On 10 February 2011 15:16, Geoffrey Hutchison geo...@pitt.edu wrote:

 On Feb 10, 2011, at 5:22 AM, Egon Willighagen wrote:

 Agreed. I think at the time SF did not offer a MW install yet...

 That's right. They woke up and realized they had a few thousand MW installs, 
 all of which needed patching, and many of which wanted integration into the 
 SF login system.

 What's the number of pages we are talking about? Can we migrate the
 database, or do we need to copy the content manually? (which we did
 for the CDK at least three times...)


 I have to think there's a way to script this if the database can't be 
 migrated.

I've successfully migrated cclib's mediawiki to SF's wiki. It was a
frustrating experience figuring it out, but having done it once I
should be able to sort it out for the BO wiki. I have a script to make
things easy for the export of wiki pages...

(Come back static web pages, all is forgiven...)

- Noel

--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Wiki

[Noel O'Boyle]

Hi all,

SourceForge have just changed everything on their server, so the wiki
is down. I'll sort it out by and by...

- Noel

--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Wiki

[Noel O'Boyle]

On 10 February 2011 09:54, Egon Willighagen egon.willigha...@gmail.com wrote:
 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 announcing that there were
 problems and that things would be changed. There have been regular
 updates provided on progress.

 Indeed they did say things would change. It is true that it is hard to
 predict what will get broken in the process. I do not remember those
 emails saying that existing MediaWiki installs would likely go down.

 But I should indeed have compensated the -- with the many ++'s
 SourceForge deserves for the free service they do provide. They are
 not perfect, but at the same time they provide an infinite value for
 money (literally)!

 Greg, thanx for correcting me!

I think we should consider moving to using the SourceForge provided
mediawiki, as does http://cdk.sf.net. That one is still up, and it's
not much fun fixing the Mediawiki installation every year or so.

- Noel

--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Wiki

[Noel O'Boyle]

On 10 February 2011 10:22, Egon Willighagen egon.willigha...@gmail.com wrote:
 On Thu, Feb 10, 2011 at 10:14 AM, Noel O'Boyle baoille...@gmail.com wrote:
 I think we should consider moving to using the SourceForge provided
 mediawiki, as does http://cdk.sf.net. That one is still up, and it's
 not much fun fixing the Mediawiki installation every year or so.

 Agreed. I think at the time SF did not offer a MW install yet...

 What's the number of pages we are talking about? Can we migrate the
 database, or do we need to copy the content manually? (which we did
 for the CDK at least three times...)

I'll try the high-tech route. If that doesn't work, we can split up
the work and do the low-tech route. Fun fun fun! :-)

 Egon

 --
 Dr E.L. Willighagen
 Postdoctoral Researcher
 Institutet för miljömedicin
 Karolinska Institutet
 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


--
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Special issue of J Cheminf (PMR Symposium)

[Noel O'Boyle]

Hi all,

As Peter mentioned, I'll be working with Egon and also Rajarshi to
pull together information on the Blue Obelisk from the last number of
years. Once we have a deadline for the paper, we'll get some ideas
together and be back to this list to get feedback, and input from
others.

Regards,
   Noel

On 26 January 2011 17:58, Peter Murray-Rust pm...@cam.ac.uk wrote:
 We have arranged with J Cheminf. that there will be a special issue related
 to the PMR Symposium Visions of a semantic molecular future on Jan 17th
 2011. Noel gave an excellent 2-minute presentation at the symposium and I
 think it would be great to have a paper called the Blue Obelisk five years
 on or something similar. By default I'll suggest that Noel and Egon arrange
 something.

 Various BO people couldn't be there such as Egon who watched the symposium
 on his phone and Christoph, and of course most people outside Europe.

 This is an excellent opportunity for us to collect systematic information on
 the various Blue Obelisk programs, data and other activity. We should also
 use it as an opportunity to add BlueObelisk to our Readmes and even create a
 small graphic BO icon on web pages or graphics.

 If anyone wants to add another paper relating to the symposium or the Blue
 Obelisk let me and Charlotte know.




 --
 Peter Murray-Rust
 Reader in Molecular Informatics
 Unilever Centre, Dep. Of Chemistry
 University of Cambridge
 CB2 1EW, UK
 +44-1223-763069

 --
 Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
 Finally, a world-class log management solution at an even better price-free!
 Download using promo code Free_Logger_4_Dev2Dev. Offer expires
 February 28th, so secure your free ArcSight Logger TODAY!
 http://p.sf.net/sfu/arcsight-sfd2d
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss



--
Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
Finally, a world-class log management solution at an even better price-free!
Download using promo code Free_Logger_4_Dev2Dev. Offer expires 
February 28th, so secure your free ArcSight Logger TODAY! 
http://p.sf.net/sfu/arcsight-sfd2d
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Want to see your name or proejct on a Blue Obelisk poster?

[Noel O'Boyle]

Hi all,

I'm putting together a blue obelisk poster for PMR's hackfest on
Friday week. I'm thinking about including a wordle consisting of a
jumble of people's names and projects. If you want to see your name
added please email me off list or better still edit the public google
doc (which hopefully won't be spammed) at:

  
https://docs.google.com/document/d/1eM3kzRM7C88sNYK8CQo2UH1gX5mfDeYFy0Xf8sXPImU/edit?hl=enauthkey=CKHi6YAO

I'll be finalising the wordle tomorrow (Friday) in the morning (GMT)
so no need to edit it after that.

Regards,
   Noel

--
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and, 
should the need arise, upgrade to a full multi-node Oracle RAC database 
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Fwd: CCL:G: NWChem version 6.0 (Open Source) released

[Noel O'Boyle]

Great news.

The license is compatible with the GPL v3 but not v2
(http://www.gnu.org/licenses/license-list.html#GPLCompatibleLicenses).

- Noel

On 30 September 2010 08:06, Jérôme Pansanel j.pansa...@pansanel.net wrote:
 Hi,

 I've read the following on the CCL list. Is the Educational Community License
 2.0 a Free Software license ?

 Best regards,

 Jerome Pansanel

 --  Message transmis  --

 Sujet : CCL:G: NWChem version 6.0 (Open Source) released
 Date : mercredi 29 septembre 2010, 21:38:09

 We are pleased to announce the release of NWChem version 6.0. This version
 marks a transition of NWChem to an open-source software package. The software
 is being released under the [Educational Community License 2.0] (ECL 2.0).
 Users can download the source code and a select set of binaries from the new
 open source web site http://www.nwchem-sw.org



 New functionality, improvements, and bug fixes include:

 * Greatly improved memory management for TCE four-index transformation,
 CCSD(T), CR-EOMCCSD(T), and solver for EOMCCSD

 * Performance and scalability improvements for TCE CCSD(T), CR-EOMCCSD(T), and
 EOMCCSD

 * TCE based static CCSD hyperpolarizabilities

 * New exchange-correlation functionals available in the Gaussian DFT module

 * Range-separated functionals: CAM-B3LYP, LC-BLYP, LC-PBE, LC-PBE0, BNL. These
 functionals can also be used to perform TDDFT excited-state calculations

 * SSB-D functional

 * Double hybrid functionals (Semi-empirical hybrid DFT combined with
 perturbative MP2)

 * DFT response are now available for order 1 (linear response), single
 frequency, electric field and mixed electric-magnetic field perturbations

 * Greatly improved documentation for QM/MM simulations

 * Spin-orbit now works with direct and distributed data approaches

 * Plane-wave BAND module now has parallelization over k-points, AIMD, and
 Spin-Orbit pseudopotentials

 * Plane-wave modules have improved minimizers for metallic systems and
 metadynamics capabilities

 * Bug fix for DISP: Empirical long-range vdW contribution

 * Bug fix for Hartree-Fock Exchange contributions in NMR



 Please let us know if have any issues accessing the new website.



 Best wishes,



    Huub


 __
 Huub van Dam
 Scientist
 EMSL: Environmental Molecular Science Laboratory
 Pacific Northwest National Laboratory
 902 Battelle Boulevard
 P.O. Box 999, MSIN K8-91
 Richland, WA  99352 USA
 Tel:  509-372-6441
 Fax: 509-371-6445
 Hubertus.vanDam : pnl.gov
 www.emsl.pnl.gov



 ---

 --
 Start uncovering the many advantages of virtual appliances
 and start using them to simplify application deployment and
 accelerate your shift to cloud computing.
 http://p.sf.net/sfu/novell-sfdev2dev
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Fwd: [InChI-discuss] Licensing of InChI software

[Noel O'Boyle]

On 30 July 2010 19:51, Geoffrey Hutchison geo...@pitt.edu wrote:
 even if all the code was rewritten, the code ownership would not change
 at least if the changes are incremental. If this is true, you might be
 unable to relicense OpenBabel without permission from OpenEye even if
 all the original code is rewritten.

 Actually, what Craig is referencing (I think) is an effort to totally scrap 
 the Open Babel core, in favor of a combined library written in collaboration 
 with RDKit. The pieces that we'd bring to the table would be things that have 
 been written since Open Eye and we clearly know the contributors.

 In any case, both your point and Craig's point is that life would be much 
 better if Open Eye were willing to discuss relicensing their code.

 Incidentally, I find it ironic that a few years ago, Open Eye was publicly 
 bashing InChI and now want to use it.

I think we can all agree that more widespread use of InChI is a good thing.

Also, if the technical objections are a real problem, then BSD
projects (as MolCore will be, and RDKit is) will have the same
problems using the InChI code as proprietary projects.

 -Geoff


 --
 The Palm PDK Hot Apps Program offers developers who use the
 Plug-In Development Kit to bring their C/C++ apps to Palm for a share
 of $1 Million in cash or HP Products. Visit us here for more details:
 http://p.sf.net/sfu/dev2dev-palm
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
The Palm PDK Hot Apps Program offers developers who use the
Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://p.sf.net/sfu/dev2dev-palm
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] BO dinner at the Boston ACS?

[Noel O'Boyle]

On 21 July 2010 15:25, Rajarshi Guha rajarshi.g...@gmail.com wrote:
 On Wed, Jul 21, 2010 at 9:59 AM, Noel O'Boyle baoille...@gmail.com wrote:
 I won't be in Boston, but I have a suggestion.

 During my ACS talk in March I mentioned the BO dinner (which had
 already taken place), and a couple of people came up afterwards to ask
 about it. Maybe you should consider advertising it more widely or
 perhaps having a slide at the end of talks by members of the BO.

 Also worth pointing out is that while we should try to include as many
 people as possible, it should be emphasised that it is not a general
 purpose networking event :-)

 This is a good idea - but the problem is that usually we need to make
 some form of reservation, so we need to know who's coming ahead of
 time. One possibility is to book a whole, say, bar or room. But that
 needs money, so it's unlikely

How about asking on the CCL in advance? Or posting on your blogs?

 --
 Rajarshi Guha
 NIH Chemical Genomics Center


--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] [open-science] Fwd: Silicos goes Open Source

[Noel O'Boyle]

On 21 July 2010 18:15, Peter Murray-Rust pm...@cam.ac.uk wrote:


 On Wed, Jul 21, 2010 at 2:18 PM, Bryan Bishop kanz...@gmail.com wrote:

 -- Forwarded message --
 From: Wilfried Langenaeker wilfried.langenae...@silicos.com
 Date: Wed, Jul 21, 2010 at 12:49 AM
 Subject: Silicos goes Open Source
 To: Bryan Bishop kanz...@gmail.com


 PRESS RELEASE:
 SILICOS NV PORTS ITS PROPRIETARY COMPUTATIONAL CHEMISTRY SOFTWARE INTO THE
 OPEN SOURCE DOMAIN

 On June 22, 2010, the Belgium-based computational chemistry company
 Silicos NV has made a
 strategic decision to port the majority of its proprietary software
 into the open source arena.

 What does majority mean? Is there a coherent OSS standalone library?

I guess they also have developed some other code which they are
retaining. The code they are open sourcing is full featured, as far as
I know.


 The
 decision has been made to port all of these tools and the
 corresponding C/C++ API's into the Open
 Babel environment under a GNU GPL licensing scheme.

 I'd be very interested in what the Open Babel environment means - can
 anyone on BO comment?
 [...]

Much of the code has already been added to OpenBabel (Tim
Vandermeersch has been involved here) and is available in SVN. Silicos
provide support. See
http://baoilleach.blogspot.com/2010/07/silicos-to-donate-code-to-open-babel.html
from 3 weeks ago.


 About Silicos' proprietary software tools

 Spectrophores™ are Silicos' patented 3D-field descriptors.

 What restrictions does this put on the use of the software?

None, in practice. And the patent expires next year and will not be renewed.

 This is clearly promising as it shows the commercial value of OSS-ing but
 the details will be important.

Silicos were happy to work with OB to adjust the wording of the
license to something acceptable to all parties.

 P.



 --
 Peter Murray-Rust
 Reader in Molecular Informatics
 Unilever Centre, Dep. Of Chemistry
 University of Cambridge
 CB2 1EW, UK
 +44-1223-763069

 --
 This SF.net email is sponsored by Sprint
 What will you do first with EVO, the first 4G phone?
 Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss



--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Blueobelisk QA at shapado

[Noel O'Boyle]

Hello all,

I want to bring the new BlueObelisk QA site to the attention of the
members of this list: http://blueobelisk.shapado.com/

Please help answer questions such as:
(1) What skills/background is necessary to contribute to open source
chemistry software?
(2) Open Data for mass spectrometry?
(3) Chemical database system for large compound DBs?

The nice thing about a QA website compared to the BO mailing list is
that it brings together the answers in a much more coherent way.

It doesn't take a lot to log in from time to time and answer a few
outstanding questions amd I hope people will do so (and ask questions
too!).

- Noel

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

[Noel O'Boyle]

On 31 March 2010 11:10, Peter Murray-Rust pm...@cam.ac.uk wrote:
 This is brilliant - thanks everyone. I had talked to some of the PSI people
 two years ago but had forgotten about it.

 On Wed, Mar 31, 2010 at 11:55 AM, Noel O'Boyle baoille...@gmail.com wrote:

 And of course, pyquante. Several packages use the Libint GPL library

 (http://www.files.chem.vt.edu/chem-dept/valeev/software/libint/libint.html)
 including the aforemention PSI3 and MPQC. So does ORCA, but through
 the magic of licenses, this is not open source!

 Pretty much every plane-wave pseudopotential code is open source
 (Quantum Espresso, etc.) but these are not much use to chemists.

 - Noel

 On 31 March 2010 10:40, Ganesh V tovgan...@gmail.com wrote:
  Hi Peter,
  I know of two codes that are opensource and quite mature too:
  PSI3: http://www.psicode.org/
  and MPQC: http://www.mpqc.org/
  ganesh
 

 I've briefly scanned the docs and they look great. So why don't we just
 start using them and promoting them? Is there a catch? They are, of course,
 compiled programs but this is a lot less painful than it used to be. I
 imagine it's possible to create static images for distribution if required -
 or indeed these probably exist.

 I would be keen to CML-ise these programs so that the output could be read
 directly into CML-aware programs. I've done this for MOPAC, CASTEP etc. PSI3
 and MPQC are well written and will be much easier to adapt.

 Is there any reason why these should not become standard tools in chemistry
 labs and classes and replace the current closed systems that so many people
 are locked into?

 P

The biggest barrier to general usage is setting up the job. Do these
have user interfaces? If not, can Avogadro bump this up their priority
list? I'll work on it from the cclib end.

Another interesting piece of software is ASE, which provides a common
interface to setting up jobs for several of these programs. See
https://wiki.fysik.dtu.dk/ase/index.html. Perhaps Avogadro can
consider being a backend to this.

- Noel



 --
 Peter Murray-Rust
 Reader in Molecular Informatics
 Unilever Centre, Dep. Of Chemistry
 University of Cambridge
 CB2 1EW, UK
 +44-1223-763069


--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

[Noel O'Boyle]

Here's another one...Octopus
http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page

On 31 March 2010 13:28, Peter Murray-Rust pm...@cam.ac.uk wrote:


 On Wed, Mar 31, 2010 at 12:29 PM, Egon Willighagen
 egon.willigha...@gmail.com wrote:

 On Wed, Mar 31, 2010 at 12:23 PM, Noel O'Boyle baoille...@gmail.com
 wrote:
  The biggest barrier to general usage is setting up the job. Do these
  have user interfaces? If not, can Avogadro bump this up their priority
  list? I'll work on it from the cclib end.

 Bioclipse1 has a plugin [0] to run jobs via Ghemical, which interfaces
 to MOPAC7 and MPQC, and Ghemical itself is also of course a nice GUI
 for doing these things.

 Excellent. This influences my choice of MPQC...



 If someone is interested in porting the Bioclipse1 plugin to
 Bioclipse2, please let me know.

 BTW, I think it is important to note that several of these QM tools
 are distributed by Debian and Ubuntu, making them accessible to
 students easily. I wish more Blue Obelisk components were available as
 packages for Linux distributions...

 I think the time has come for us to review the BO components as we porbably
 have more than we realise. We also need to think about branding them. I'll
 kick off another thread on this

 P.


 Egon

 0.http://wiki.bioclipse.net/index.php?title=Ghemical_plugin
 1.http://www.uku.fi/~thassine/projects/ghemical/

 --
 Post-doc @ Uppsala University
 Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
 Homepage: http://egonw.github.com/
 Blog: http://chem-bla-ics.blogspot.com/
 PubList: http://www.citeulike.org/user/egonw/tag/papers



 --
 Peter Murray-Rust
 Reader in Molecular Informatics
 Unilever Centre, Dep. Of Chemistry
 University of Cambridge
 CB2 1EW, UK
 +44-1223-763069


--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

[Noel O'Boyle]

Did your expert try apt-get install mpqc? This works for me on an
old Ubuntu (9.04).

u...@ubuntu904desktop:~/Tools/cinfony$ apt-cache search mpqc
libopenbabel-dev - Chemical toolbox library (development files)
libopenbabel3 - Chemical toolbox library
gabedit - graphical user interface to Ab Initio packages
ghemical - A GNOME molecular modelling environment
mpqc - The Massively Parallel Quantum Chemistry Program
mpqc-support - Support programs and tools for MPQC
openbabel - Chemical toolbox utilities
python-openbabel - Chemical toolbox library (python bindings)

- Noel

On 31 March 2010 16:03, Peter Murray-Rust pm...@cam.ac.uk wrote:
 Many thanks Geoff

 Firstly I am excited that there are a significant number of Open packages
 and certainly enough for what I want to do (I think I have some exciting
 opportunities for the BO).

 I have just downloaded and compiled and run MPQC. Great!

 More accurately, however, I have watched while a compchem syadmin expert has
 spent an hour compiling MPQC. This requires the BLAS/LAPACK library which
 took him a considerable time to tame - and he's been through this before. If
 I'd had to do this myself (and I do know how to make make and configure in
 general terms) it would have taken me a week or probably longer. It was NOT
 trivial.

 I'm guessing that many BO users and followers would like a general-purpose
 approach to QM routines. For example I want to do gas-phase molecule
 optimization and possibly frequency calculation. This would also be a
 reasonable requirement for an undergraduate course. Is there a way that BO
 can remove some of the effort in evaluating or installing or customising
 Open QM programs, perhaps by choosing a preferred one because it is easier
 to understand/install/distribute or whatever. If so I suspect a lot of
 people would be grateful.

 P.

 --
 Peter Murray-Rust
 Reader in Molecular Informatics
 Unilever Centre, Dep. Of Chemistry
 University of Cambridge
 CB2 1EW, UK
 +44-1223-763069

 --
 Download Intel#174; Parallel Studio Eval
 Try the new software tools for yourself. Speed compiling, find bugs
 proactively, and fine-tune applications for parallel performance.
 See why Intel Parallel Studio got high marks during beta.
 http://p.sf.net/sfu/intel-sw-dev
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss



--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

[Noel O'Boyle]

On 31 March 2010 17:19, Peter Murray-Rust pm...@cam.ac.uk wrote:


 On Wed, Mar 31, 2010 at 5:43 PM, Geoffrey Hutchison geo...@pitt.edu wrote:

  More accurately, however, I have watched while a compchem syadmin expert
  has spent an hour compiling MPQC. This requires the BLAS/LAPACK library
  which took him a considerable time to tame - and he's been through this
  before. If I'd had to do this myself (and I do know how to make make and
  configure in general terms) it would have taken me a week or probably
  longer. It was NOT trivial.

 No offense, but if a compchem sysadmin expert has problems with
 BLAS/LAPACK and has done it before, they're not really an expert.
 BLAS/LAPACK (or ATLAS) are easy to install on every Linux workstation or
 server I have ever used. Indeed, on most compchem Linux machines, it's
 already installed.


 Well I won't go into it in detail, but the point is that there are people
 who find this easy and people who don't. Among other things we have to
 compile it on machine A in a static manner and transfer it to a grid where
 most of the libraries have been stripped off.

 But in any case *I* didn't find it easy. Firstly you have to *compile* the
 program. I've done a lot of compiling (but not recently). I went to
 http://www.mpqc.org/mpqc-snapshot-html/compile.html
 and tried to follow the instructions. I failed. I am not stupid or
 incompetent, simply ignorant. There are a lot of people like me who do not
 normally compile Linux programs and who get turned off very rapidly indeed
 by the compilation problem.

 If I had been wanting to run it on a Windows machine what would I have done?
 There is no binary on the MPQC site and no indication of how to compile it
 in Windows. It's not trivial.

 So I reiterate my problem. Many people want to use compchem programs and
 don't know where to start or how to proceed. There is currently a priesthood
 of compchemists which makes it very difficult when you don't have one at
 hand.

 I have no idea what apt-get is and it's not on the MPQC compile page.

 The point I am trying to make is that I am suggesting the BO try to make it
 easy for chemists, not Linux / Ubuntu / Debian experts ,  to run a small
 number of Open programs. I don't want to compile them, only run them. I know
 what the programs do. I do not know and I don't want to know what the
 compilers do. Is there a way the BO can help?

I do agree. All C++ open source projects (OpenBabel included) should
make use of the OpenSUSE build system to provide binaries for all of
the Linux distributions.

Apologies for the reference to apt-get which wasn't very clear. I
should have said that MPQC is included in the Debian and Ubuntu
repositories. This means that the binary is already available. You
just need to find the package manager on your menu. There have been
some movements towards adding the appropriate button to websites so
that the package manager is automatically invoked when you click on
install it! but as far as I understand, this does not work for most
of the major Linux distributions.

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Where to meet for the Blue Obelisk Dinner in SF?

[Noel O'Boyle]

On 8 March 2010 17:50, Geoffrey Hutchison ge...@geoffhutchison.net wrote:
 any suggestions regarding where to meet for the Blue Obelisk Dinner in SF?


 Buca di Beppo? It's close to the Moscone Center, although I didn't check if 
 it's also close to the hotel. I'd like to make sure we can get back to the 
 Sci-Mix posters.

 If people are OK with Italian, I'll look into reservations.

I have no reservations about Italian.

 -Geoff
 --
 Download Intel#174; Parallel Studio Eval
 Try the new software tools for yourself. Speed compiling, find bugs
 proactively, and fine-tune applications for parallel performance.
 See why Intel Parallel Studio got high marks during beta.
 http://p.sf.net/sfu/intel-sw-dev
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

[Noel O'Boyle]

On 2 March 2010 11:23, Greg Landrum greg.land...@gmail.com wrote:
 Dear Noel,

 Thanks for the repost; this helps.

 My 2 cents are below.

 On Tue, Mar 2, 2010 at 11:34 AM, Noel O'Boyle baoille...@gmail.com wrote:
 On 2 March 2010 09:40, Peter Murray-Rust pm...@cam.ac.uk wrote:
 Thanks,
 This is a useful initiative

 On Tue, Mar 2, 2010 at 9:14 AM, Noel O'Boyle baoille...@gmail.com wrote:

 (Reposted from my blog following Greg's suggestion )

 Hello all,

 Right now, I'm adding stereo (i.e. double bond stereochemistry, and
 chirality) to the MDL Mol format in OpenBabel. There are three places
 where stereochemical information can be stored in these files: the
 coordinates, the atom parity (in the atom block), the bond stereo (in
 the bond block).

 My current understanding is that where 3D coordinates are present,
 there's no need to store stereochemical information in either the atom
 parity or the bond block. I think I'll probably set the atom parity
 anyway (since I've already written the code, and it helps when you
 look at the file to be able to easily identify the chiral centers).

 Agreed that setting parity is a useful service to human readers but,
 as is already mentioned below, the spec is quite clear that these
 flags should be ignored on read.



 The main problem is lack of information as to whether the geometry (2D or
 3D) is definitive or arbitrary. It is impossible to construct a 3D model of
 (say) alanine without a perceived stereochemistry at the Carbon. Similarly
 most modern 2D graphic programs will draw a double bond as cis or trans (not
 normally linear although this was common in typesetting). If the (arbitrary)
 geometry is then transmitted without details of authoring, then the reader
 may assume a definitive stereochemistry. Put another way, there is no way of
 indicating by coordinates alone that stereochemistry is unknown. I thinks
 it's very important not to use the geometry as definitive unless it is clear
 that the author specified it (which normally only comes from crystal
 structures or computational chemistry).

 Sure, but I think this is outside the scope here.

 I'm not sure I agree. I think this is one of the critical points when
 doing CTABs: when writing 3D or 2D coordinates how do you indicate
 what you *don't* know as well as indicating what you *do* know.

 In2D (and 3D) the problem is stereochemistry around double bonds: the
 coordinates provided in the output determine the stereochemistry.
 Luckily here the CTAB spec provides a way to indicate what isn't
 known: you use the 4th field in the bond line to indicate that the
 bond is an either bond (value 3). Technically this is what should be
 done by any toolkit that builds a molecule from the SMILES CC=CC.

 With atomic stereochemistry in 3D structures, the coordinats again
 determine the stereochemistry. As far as I know, the CTAB spec doesn't
 provide specific guidance about what to do when you have a
 stereocenter that's undetermined in your molecule. One possibility is
 to make sure that the bonds from that atom have 0 in field 4. Maybe
 it's polite to assign an either bond here as well (value 4 in this
 case) to make explicit to the viewer that the stereochemistry isn't
 known. But either of these raise the question of what to do if you
 *do* know the stereochemistry. My opinion here, and I'm aware it's one
 that many people do not share, is that it's best to treat the 3D case
 the same as the 2D one and use a wedged bond to mark atoms where the
 stereochemistry is known. It's somewhat ugly, but it has the advantage
 of being consistent (yes, yes, I know, when foolish it's the hobgoblin
 of little minds... but I don't think it's foolish here).

 P.


 For 2D coordinates, there's no need to store the bond stereochemistry
 (as this can be worked out from the coordinates), but chirality needs
 to be stored explicitly. The normal way to store this is not using
 atom parity (but I'll set this anyway for the same reasons as above),
 but by setting one of the bonds on the tetrahedral center to up or
 down.

 For 0D coordinates, there are no guidelines. I propose to store
 cis/trans stereo using the bond stereo (you know, UP [or DOWN] at both
 ends of a double bond means cis), and chirality using the atom parity.
 The MDL spec states that atom parity should be ignored when read,

 I know this is the spec and I don't want to get into more arguments about
 whether it should be changed. At this stage I think it is useful if programs
 have the capability to read and interpret this field.

 I think that I may move this to an option. So, if you don't explicitly
 ask for it, you will just get what the spec says - i.e. no
 stereochemistry will be stored if there are no coordinates.

 This is what I would suggest. Anything else involves introducing
 conventions that will work with OB, but that may or may not work with
 other toolkits. Since there's no clear answer, or anything that even
 really makes much sense, it's

[BlueObelisk-discuss] Stereochemistry in MDL files

[Noel O'Boyle]

(Reposted from my blog following Greg's suggestion )

Hello all,

Right now, I'm adding stereo (i.e. double bond stereochemistry, and
chirality) to the MDL Mol format in OpenBabel. There are three places
where stereochemical information can be stored in these files: the
coordinates, the atom parity (in the atom block), the bond stereo (in
the bond block).

My current understanding is that where 3D coordinates are present,
there's no need to store stereochemical information in either the atom
parity or the bond block. I think I'll probably set the atom parity
anyway (since I've already written the code, and it helps when you
look at the file to be able to easily identify the chiral centers).

For 2D coordinates, there's no need to store the bond stereochemistry
(as this can be worked out from the coordinates), but chirality needs
to be stored explicitly. The normal way to store this is not using
atom parity (but I'll set this anyway for the same reasons as above),
but by setting one of the bonds on the tetrahedral center to up or
down.

For 0D coordinates, there are no guidelines. I propose to store
cis/trans stereo using the bond stereo (you know, UP [or DOWN] at both
ends of a double bond means cis), and chirality using the atom parity.
The MDL spec states that atom parity should be ignored when read, but
the alternative is to just forget the stereochemistry, or else to
store both cis/trans stereo *and* chirality in the bond block, which
may just about be possible but is likely to be a real mess.

Any thoughts?

- Noel

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

[Noel O'Boyle]

On 2 March 2010 09:40, Peter Murray-Rust pm...@cam.ac.uk wrote:
 Thanks,
 This is a useful initiative

 On Tue, Mar 2, 2010 at 9:14 AM, Noel O'Boyle baoille...@gmail.com wrote:

 (Reposted from my blog following Greg's suggestion )

 Hello all,

 Right now, I'm adding stereo (i.e. double bond stereochemistry, and
 chirality) to the MDL Mol format in OpenBabel. There are three places
 where stereochemical information can be stored in these files: the
 coordinates, the atom parity (in the atom block), the bond stereo (in
 the bond block).

 My current understanding is that where 3D coordinates are present,
 there's no need to store stereochemical information in either the atom
 parity or the bond block. I think I'll probably set the atom parity
 anyway (since I've already written the code, and it helps when you
 look at the file to be able to easily identify the chiral centers).


 The main problem is lack of information as to whether the geometry (2D or
 3D) is definitive or arbitrary. It is impossible to construct a 3D model of
 (say) alanine without a perceived stereochemistry at the Carbon. Similarly
 most modern 2D graphic programs will draw a double bond as cis or trans (not
 normally linear although this was common in typesetting). If the (arbitrary)
 geometry is then transmitted without details of authoring, then the reader
 may assume a definitive stereochemistry. Put another way, there is no way of
 indicating by coordinates alone that stereochemistry is unknown. I thinks
 it's very important not to use the geometry as definitive unless it is clear
 that the author specified it (which normally only comes from crystal
 structures or computational chemistry).

Sure, but I think this is outside the scope here.

 P.


 For 2D coordinates, there's no need to store the bond stereochemistry
 (as this can be worked out from the coordinates), but chirality needs
 to be stored explicitly. The normal way to store this is not using
 atom parity (but I'll set this anyway for the same reasons as above),
 but by setting one of the bonds on the tetrahedral center to up or
 down.

 For 0D coordinates, there are no guidelines. I propose to store
 cis/trans stereo using the bond stereo (you know, UP [or DOWN] at both
 ends of a double bond means cis), and chirality using the atom parity.
 The MDL spec states that atom parity should be ignored when read,

 I know this is the spec and I don't want to get into more arguments about
 whether it should be changed. At this stage I think it is useful if programs
 have the capability to read and interpret this field.

I think that I may move this to an option. So, if you don't explicitly
ask for it, you will just get what the spec says - i.e. no
stereochemistry will be stored if there are no coordinates.


 but
 the alternative is to just forget the stereochemistry, or else to
 store both cis/trans stereo *and* chirality in the bond block, which
 may just about be possible but is likely to be a real mess.

 Is it ambiguous or merely complicated? If the latter then we should use it
 to remove ambiguity.

As it is (for 2D), it's already ambiguous. The interpretation of a
hash or wedge bond between two stereocentres is ambiguous (as in one
toolkit may interpret as describing the stereo only at the start,
while another might interpret it as describing the stereo at the
beginning and end). In the case of 0D, if you cram all of the
stereochemical information into the bond block it will only get worse;
you will have situations like a stereochemical center attached to a
double bond. Can the same single bond be used to indicate both
cis/trans across the double bond, and the chirality of the center? All
of these problems can be avoided using conventions, but the spec
doesn't go that far.





 --
 Peter Murray-Rust
 Reader in Molecular Informatics
 Unilever Centre, Dep. Of Chemistry
 University of Cambridge
 CB2 1EW, UK
 +44-1223-763069


--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

[Noel O'Boyle]

On 2 March 2010 11:23, Greg Landrum greg.land...@gmail.com wrote:
 Dear Noel,

 Thanks for the repost; this helps.

 My 2 cents are below.

 On Tue, Mar 2, 2010 at 11:34 AM, Noel O'Boyle baoille...@gmail.com wrote:
 On 2 March 2010 09:40, Peter Murray-Rust pm...@cam.ac.uk wrote:
 Thanks,
 This is a useful initiative

 On Tue, Mar 2, 2010 at 9:14 AM, Noel O'Boyle baoille...@gmail.com wrote:

 (Reposted from my blog following Greg's suggestion )

 Hello all,

 Right now, I'm adding stereo (i.e. double bond stereochemistry, and
 chirality) to the MDL Mol format in OpenBabel. There are three places
 where stereochemical information can be stored in these files: the
 coordinates, the atom parity (in the atom block), the bond stereo (in
 the bond block).

 My current understanding is that where 3D coordinates are present,
 there's no need to store stereochemical information in either the atom
 parity or the bond block. I think I'll probably set the atom parity
 anyway (since I've already written the code, and it helps when you
 look at the file to be able to easily identify the chiral centers).

 Agreed that setting parity is a useful service to human readers but,
 as is already mentioned below, the spec is quite clear that these
 flags should be ignored on read.



 The main problem is lack of information as to whether the geometry (2D or
 3D) is definitive or arbitrary. It is impossible to construct a 3D model of
 (say) alanine without a perceived stereochemistry at the Carbon. Similarly
 most modern 2D graphic programs will draw a double bond as cis or trans (not
 normally linear although this was common in typesetting). If the (arbitrary)
 geometry is then transmitted without details of authoring, then the reader
 may assume a definitive stereochemistry. Put another way, there is no way of
 indicating by coordinates alone that stereochemistry is unknown. I thinks
 it's very important not to use the geometry as definitive unless it is clear
 that the author specified it (which normally only comes from crystal
 structures or computational chemistry).

 Sure, but I think this is outside the scope here.

 I'm not sure I agree. I think this is one of the critical points when
 doing CTABs: when writing 3D or 2D coordinates how do you indicate
 what you *don't* know as well as indicating what you *do* know.

 In2D (and 3D) the problem is stereochemistry around double bonds: the
 coordinates provided in the output determine the stereochemistry.
 Luckily here the CTAB spec provides a way to indicate what isn't
 known: you use the 4th field in the bond line to indicate that the
 bond is an either bond (value 3). Technically this is what should be
 done by any toolkit that builds a molecule from the SMILES CC=CC.

 With atomic stereochemistry in 3D structures, the coordinats again
 determine the stereochemistry. As far as I know, the CTAB spec doesn't
 provide specific guidance about what to do when you have a
 stereocenter that's undetermined in your molecule. One possibility is
 to make sure that the bonds from that atom have 0 in field 4. Maybe
 it's polite to assign an either bond here as well (value 4 in this
 case) to make explicit to the viewer that the stereochemistry isn't
 known. But either of these raise the question of what to do if you
 *do* know the stereochemistry. My opinion here, and I'm aware it's one
 that many people do not share, is that it's best to treat the 3D case
 the same as the 2D one and use a wedged bond to mark atoms where the
 stereochemistry is known. It's somewhat ugly, but it has the advantage
 of being consistent (yes, yes, I know, when foolish it's the hobgoblin
 of little minds... but I don't think it's foolish here).

 P.


 For 2D coordinates, there's no need to store the bond stereochemistry
 (as this can be worked out from the coordinates), but chirality needs
 to be stored explicitly. The normal way to store this is not using
 atom parity (but I'll set this anyway for the same reasons as above),
 but by setting one of the bonds on the tetrahedral center to up or
 down.

 For 0D coordinates, there are no guidelines. I propose to store
 cis/trans stereo using the bond stereo (you know, UP [or DOWN] at both
 ends of a double bond means cis), and chirality using the atom parity.
 The MDL spec states that atom parity should be ignored when read,

 I know this is the spec and I don't want to get into more arguments about
 whether it should be changed. At this stage I think it is useful if programs
 have the capability to read and interpret this field.

 I think that I may move this to an option. So, if you don't explicitly
 ask for it, you will just get what the spec says - i.e. no
 stereochemistry will be stored if there are no coordinates.

 This is what I would suggest. Anything else involves introducing
 conventions that will work with OB, but that may or may not work with
 other toolkits. Since there's no clear answer, or anything that even
 really makes much sense, it's

Re: [Blueobelisk-discuss] Web-based Community Forum: http://blueobelisk.stackexchange.com/

[Noel O'Boyle]

There is already a SO for science. General chemistry questions can be
asked there: http://sciencestack.com/

2009/11/11 Peter Murray-Rust pm...@cam.ac.uk:
 This is a fantastic idea. Well done Egon. (I was considering myself but
 somehow had failed to connect BO and SO).

 I am an addict for SO and I think the rep model is addictive. I have spent
 the last few eeks thinking about how it could be adopted for chemistry. FWIW
 I went to areal-life SO meeting in Cambridge 2 weeks ago.

 The question of availability of SW is unclear but I think we should
 definitely go with what Egon has set up. I had seen wider questions like:
 * what is a good introduction to Lewis structures?
 * what are the restrictions on using controlled substances int he laboratory
 * why has F-F a weak bond?
 * what is the accepted melting point of glycerol
 * what software can build a reliable 3D model of SF4?

 I'm an optimist and see this as gaining critical mass. I had thought it was
 harder to get the SO software stack than it is.

 I'd say - go for it and lets' invite a whole range of questions. I have a
 fairly good idea of what works on SO and how it could translate to
 chemistry.

 We should publicize it, santize the questions to start with (we have to
 moderate non-chemistry questions like - Why did Obama win the election?
 and argumentaive like why does program X suck?

 I think it has HUGE potential if we get it right.

 Peter M-R (http://stackoverflow.com/users/130964/peter-murray-rust on SO -
 you can see the Q's I have asked and answered).

 A series of responsible open answers to chemistry questions could have
 enormous value in chemistry.

 Main question is can we run it as it scales?

 We need to set up BO moderators at the start so some of us need particular
 permissions.

 BTW where is it mounted? SO have made quite a play about there hardware
 stack - they have done it themselves.

 P.



 On Wed, Nov 11, 2009 at 11:41 AM, Egon Willighagen
 egon.willigha...@gmail.com wrote:

 On Wed, Nov 11, 2009 at 12:37 PM, Egon Willighagen
 egon.willigha...@gmail.com wrote:
  Oh, and questions like Who is going to Conf Z and wants to meet up
  for a BO dinner/lunch/wii event? are very much encouraged too, in my
  opinion :)

 Is website/product BAR ODODOS or not? ++

 (and I will now shut up...)

 Egon

 --
 Post-doc @ Uppsala University
 Homepage: http://egonw.github.com/
 Blog: http://chem-bla-ics.blogspot.com/
 PubList: http://www.citeulike.org/user/egonw/tag/papers


 --
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008
 30-Day
 trial. Simplify your report design, integration and deployment - and focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss



 --
 Peter Murray-Rust
 Reader in Molecular Informatics
 Unilever Centre, Dep. Of Chemistry
 University of Cambridge
 CB2 1EW, UK
 +44-1223-763069


--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [Blueobelisk-discuss] Introducing Ganesh Venkateshwara and MeTA Studio

[Noel O'Boyle]

Hello Ganesh,

Only an admin can create an account. I'll contact you off list with a
username and password

- Noel

2009/11/10 Egon Willighagen egon.willigha...@gmail.com:
 On Tue, Nov 10, 2009 at 12:38 PM, Ganesh V tovgan...@gmail.com wrote:
 Thanks for your mails. Yup I would like to join the community and also
 would like MeTA Studio to be included in the Blue Obelisk category.

 Great! Welcome :)

 Have subscribed to the BO mailing list... does this enable me to
 change the wiki page?

 I think you still need to create an account... that's ancient for
 me... can you try to do that on this page:

 http://blueobelisk.sourceforge.net/wiki/index.php?title=Special:Userlogin

 Does that work?

 Egon

 --
 Post-doc @ Uppsala University
 Homepage: http://egonw.github.com/
 Blog: http://chem-bla-ics.blogspot.com/
 PubList: http://www.citeulike.org/user/egonw/tag/papers

 --
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
 trial. Simplify your report design, integration and deployment - and focus on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [Blueobelisk-discuss] SourceForge problems

[Noel O'Boyle]

The issue has been resolved. I logged in to my settings page, and was
able to change my name from Noel O'Boyle to Noel O'Boyle. My
displayed name changed from Noel O\'Boyle to Noel O'Boyle and
there was no problem accessing https://sf.net.

- Noel

2009/8/17 Greg Landrum greg.land...@gmail.com:
 On Mon, Aug 17, 2009 at 1:31 PM, Noel O'Boylebaoille...@gmail.com wrote:
 Hello all,

 When I access http://sf.net without logging in (in Firefox 3.0 or IE
 on WinXP), it's fine. However, if I log into SourceForge, I get Error
 500. This is new for me.

 Can anyone check whether they have the same problem before I log a
 support request? I have a feeling it's because of the apostrophe in my
 name :-)

 Logged in without problems this morning using openid from safari and
 firefox, but I don't have any funny characters in my name. :-)

 -greg


--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
trial. Simplify your report design, integration and deployment - and focus on 
what you do best, core application coding. Discover what's new with 
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [Blueobelisk-discuss] Fwd: the story for you

[Noel O'Boyle]

2009/5/19 Geoffrey Hutchison geo...@pitt.edu:
 I was surprised to see Amber mentioned as being funded by the NIH.
 Isn't this commercial and proprietary?


 No, Amber is GPL'ed now -- I think as of Amber version 10.
 http://ambermd.org/

 A surprising number of NIH-funded software is now open source. There's even
 a push to have all US-funded software become open source in some fashion. (I
 don't recall whether it's gaining traction under the new administration.)

AmberTools appears to be GPL. Amber is $400 for academics, and the
license states:  You may not distribute copies of the Software to
others outside of your site.

- Noel

--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables 
unlimited royalty-free distribution of the report engine 
for externally facing server and web deployment. 
http://p.sf.net/sfu/businessobjects
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [Blueobelisk-discuss] Wikipedia page

[Noel O'Boyle]

Not to discourage you, but several (if not the majority) of the
references to the BO paper are by people trying to find a citation for
OpenBabel. I am hoping that this problem will eventually be resolved
:-)

- Noel

2009/5/18 Egon Willighagen egon.willigha...@gmail.com:
 Hi all,

 I was just blogging about Open Data, and wanted to link to the WP
 page, which has nicely grown, when I saw that the Blue Obelisk did not
 have a page yet... the paper is cited 50+ times, so I think it is not
 just a mere hype...

 So, I added: http://en.wikipedia.org/wiki/Blue_Obelisk

 Please contribute.

 Egon

 --
 Post-doc @ Uppsala University
 http://chem-bla-ics.blogspot.com/

 --
 Crystal Reports - New Free Runtime and 30 Day Trial
 Check out the new simplified licensing option that enables
 unlimited royalty-free distribution of the report engine
 for externally facing server and web deployment.
 http://p.sf.net/sfu/businessobjects
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables 
unlimited royalty-free distribution of the report engine 
for externally facing server and web deployment. 
http://p.sf.net/sfu/businessobjects
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [Blueobelisk-discuss] Wikipedia page

[Noel O'Boyle]

2009/5/18 Egon Willighagen egon.willigha...@gmail.com:
 On Mon, May 18, 2009 at 10:11 AM, Noel O'Boyle baoille...@gmail.com wrote:
 Not to discourage you, but several (if not the majority) of the
 references to the BO paper are by people trying to find a citation for
 OpenBabel. I am hoping that this problem will eventually be resolved
 :-)

 Sure. But they clearly feel that they want to support the Blue Obelisk
 initiative because of OpenBabel associating with the Blue Obelisk...
 They could otherwise just have cited the webpage...

 They might have been encouraged, but at least someone agreed that when
 that cite was made the Blue Obelisk is something good... not?

That's certainly true. As a unrelated question, should we encourage
the participating projects/bloggers to place the logo somewhere on
their homepage?

 Egon

 --
 Post-doc @ Uppsala University
 http://chem-bla-ics.blogspot.com/


--
Crystal Reports - New Free Runtime and 30 Day Trial
Check out the new simplified licensing option that enables 
unlimited royalty-free distribution of the report engine 
for externally facing server and web deployment. 
http://p.sf.net/sfu/businessobjects
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [Blueobelisk-discuss] Java and pdf or powerpoint

[Noel O'Boyle]

No, but would http://polyview.cchmc.org/polyview3d.html help for your
purpose? It can make animated gifs for PPT.

- Noel

2009/2/23 Jan H. Jensen jhjen...@kemi.ku.dk:
 Hi,

 does anyone have any experience with embedding java scripts (ideally
 Jmol) in pdf or powerpoint files?

 Best regards, Jan
 --
 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
 Jan H. Jensen   Associate Research Professor
 Department of Chemistry jhjen...@kemi.ku.dk
 University of CopenhagenPhone: +45 35 32 02 39
 Universitetsparken 5FAX:   +45 35 32 02 14
 2100 Copenhagen Denmark
 http://propka.ki.ku.dk/~jhjensen
 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

 --
 Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
 -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
 -Strategies to boost innovation and cut costs with open source participation
 -Receive a $600 discount off the registration fee with the source code: SFAD
 http://p.sf.net/sfu/XcvMzF8H
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


--
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[Blueobelisk-discuss] New Orleans meeting summary

[Noel O'Boyle]

I've added a page on the recent BO meeting at the NO ACS at:
http://blueobelisk.sourceforge.net/wiki/Spring_ACS_Conference_in_New_Orleans

If you were there, let me know if you want the original images.

Noel

-
This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
Don't miss this year's exciting event. There's still time to save $100. 
Use priority code J8TL2D2. 
http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [Blueobelisk-discuss] BO dinner in New Orleans

[Noel O'Boyle]

To find out, you need to attend the CINF welcome reception. It's all
very cloak and dagger. Or just ask Christoph :-)

On 03/04/2008, David Wild [EMAIL PROTECTED] wrote:
 By the way, was a location ever set for Harry's Party?


  David


  On Apr 1, 2008, at 4:02 PM, Noel O'Boyle wrote:


  For the record I note that there's a CINF reception at 6pm to 8pm on
   Tuesday, and another at a similar time on Sunday.  There's also
   Harry's Party on the Monday from 5 pm - 7 pm.
  
   Any day is fine for me, though. :-)
  
   Noel
  

  --

  ---
   Check out the new SourceForge.net Marketplace.
   It's the best place to buy or sell services for
   just about anything Open Source.
   http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/
   marketplace
   ___
   Blueobelisk-discuss mailing list
   [EMAIL PROTECTED]



-
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[Blueobelisk-discuss] Making a screencast

[Noel O'Boyle]

(Follow-on from Daresbury meeting...)

I've created a BO wiki page on making and uploading screencasts at
http://blueobelisk.sourceforge.net/wiki/How_to_make_Screencasts

Does anyone have experience of making screencasts. Can anyone comment
on the easiest way to record screencasts on Linux and on Windows? If
anyone already has an available screencast at an appropriate website,
please add a link on the wiki.

Please edit the BO wiki page rather than replying here. (If you need
an a/c please ask an existing user to create one for you.)

Noel

-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[Blueobelisk-discuss] Mediawiki and chemistry

[Noel O'Boyle]

I am not involved in Wikipedia Chemistry, but those of you that are
might like to look at:
http://it.wichemia.org/wiki/index.php?title=Main_Page

It seems to be a mediawiki installation that automatically converts
SMILES -- PNG (using proprietary software).

Noel

-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[Blueobelisk-discuss] Sourceforge password change

[Noel O'Boyle]

From SF:

 In support of improved security, all SourceForge.net user passwords
 have been expired and must be changed upon next login. CVS, Subversion
 and Shell users will need to login to the site to change their
 password before they will be able to access these services.


 Noel

-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[Blueobelisk-discuss] Blueobelisk-discuss] [Patch] Missing documentation for discoveryDate

[Noel O'Boyle]

 Message: 6
 Date: Wed, 30 Jan 2008 12:07:45 +0100
 From: Carsten Niehaus [EMAIL PROTECTED]
 Subject: [Blueobelisk-discuss] [Patch] Missing documentation for
 discoveryDate
 To: blueobelisk-discuss@lists.sourceforge.net
 Message-ID: [EMAIL PROTECTED]
 Content-Type: text/plain; charset=us-ascii

 Moin

 The attached patch adds the missing documentation for discoveryDate.

 For some reasons I cannot commit myself... My username should be cniehaus.

Could you verify that you are using the correct address for the SVN
repository, which should be of the form:
projectname.svn.sourceforge.net
(It changed some time ago, but you may still be using the old name
which is now no longer working...)

 Please apply.

-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[Blueobelisk-discuss] Postdoctoral Researcher / Senior Research Fellow in Free and Open Source Software (Limerick)

[Noel O'Boyle]

In case any of you are interested, there's a position going in
University of Limerick (Ireland) to do research on FOSS. Quite an
unusual type of post, I would say.

Full details are at:
http://www.lero.ie/Aboutlero/Vacancies/SeniorresearchfellowResearchFellowinFreeOpenSource.html
but here's a summary:

Postdoctoral Researcher / Senior Research Fellow in Free and Open
Source Software (Specific Purpose Contract)

Lero

Department of Computer Science and Information Systems

Lero, the Irish Software Engineering Research Centre has been jointly
established by the University of Limerick, Dublin City University,
University College Dublin and Trinity College Dublin to advance the
state of the art in Software Engineering in Ireland. Lero is supported
by Science Foundation Ireland under the CSET Centres for Science
Engineering and Technology programme.

To strengthen its research in the Free and Open Source Software
research area, Lero is seeking productive, committed and visionary
researchers focusing on this topic.

Essential

* PhD in software engineering, information systems or related topic
* Demonstrated ability to publish peer-reviewed research
* Demonstrated knowledge of research in free and open source software

Desirable

* Knowledge of software product lines, global software development
and agile methods
* Knowledge of automotive or medical device software engineering
* Post-graduate research supervision

Noel

-
SF.Net email is sponsored by: The Future of Linux Business White Paper
from Novell.  From the desktop to the data center, Linux is going
mainstream.  Let it simplify your IT future.
http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[Blueobelisk-discuss] Blue Obelisk website down

[Noel O'Boyle]

For the record, the addresses, http://blueobelisk.org and
http://blueobelisk.sourceforge.net are no longer responding. I think
this is due to changes made by Christoph.

The main page of the wiki can still be reached at:
http://blueobelisk.sourceforge.net/wiki/index.php/Main_Page

Noel

-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

Re: [Blueobelisk-discuss] Blue Obelisk website down

[Noel O'Boyle]

Working fine for me now...sorry about the panic.

Noel

On 21/09/2007, Christoph Steinbeck [EMAIL PROTECTED] wrote:
 I think this is working now, but the redirect issue is a pain in the neck.

 Cheers,

 Chris

 Noel O'Boyle wrote:
  For the record, the addresses, http://blueobelisk.org and
  http://blueobelisk.sourceforge.net are no longer responding. I think
  this is due to changes made by Christoph.
 
  The main page of the wiki can still be reached at:
  http://blueobelisk.sourceforge.net/wiki/index.php/Main_Page
 
  Noel
 
  -
  This SF.net email is sponsored by: Microsoft
  Defy all challenges. Microsoft(R) Visual Studio 2005.
  http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
  ___
  Blueobelisk-discuss mailing list
  Blueobelisk-discuss@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


 --
 PD Dr. Christoph Steinbeck
 Lecturer in Chemoinformatics
 Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany
 Phone: (+49/0) 7071-29-78978   Fax: (+49/0) 7071-29-5091

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


-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2005.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
Blueobelisk-discuss mailing list
Blueobelisk-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss