http://blog.gmane.org/gmane.science.chemistry.blue-obelisk hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1692 <pre>Dear all I am an organic chemist at the Zurich University of Applied Sciences. A couple of months ago we published an article in the Journal of Cheminformatics about the beginnings of a purely functional cheminformatics toolkit written in Scala (the article can be found here: http://www.jcheminf.com/content/4/1/38/abstract). So far, this toolkit only supports SMILES parsing and representing molecules in a basic, immutable graph data structure. I am now looking for people interested in pushing this project forward. The toolkit, which we called 'chemf', is open-source (the source code is hosted on github: https://github.com/stefan-hoeck/chemf) but it hasn't seen much activity lately since so far I have been the only person working on it. So, I am looking for people helping me implement the typical algorithms needed for a fully fledged cheminformatics toolkit in a purely functional, referentially transparent way. The algorithms may be implemented in an imperative style in the background, but they need to be designed to work with immutable data structures and produce such data structures as output. I am aware that there are already quite a few cheminformtaics toolkits out there, but to the best of my knowledge, those rich in functionality like CDK or Open Babel provide algorithms that require mutable data structures to work properly. Note, that people wishing to contribute to this project do not necessarily need to be able to write Scala code since if one sticks to Scala's imperative side, Java source code can typically be transferred to Scala source code quite easily. Please excuse if this is not the right way or place to address the Blue Obelisk community with such a request. Any help or input on this matter is highly appreciated. Best regards Stefan Höck ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr_______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f&lt; at &gt;public.gmane.org https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss </pre> Stefan Hoeck 2013-04-24T08:13:38 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1690 <pre>Hello, all, I would like to design a database to support group contribution methods. Since the model is the primary focus of this project at the moment, I only need a primitive DB, with main requirement of being able to represent the groups correctly. If anyone can offer any tips, thoughts, references, links; those would be highly appreciated. Great thanks.------------------------------------------------------------------------------ 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-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f&lt; at &gt;public.gmane.org https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss </pre> Alex Gorbounov 2013-04-08T17:09:08 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1676 <pre>Blue Obelisk members, I am not sure whether any of you intend to attend the ACS Indianapolis meeting in the fall? If so, can I suggest that you might have some valuable comments and presentations for the session that Bob Lancashire and I are co-chairing. The title is below Session Code: CINF013 Session Title: Exchangeable Molecular and Analytical Data Formats and Their Importance in Facilitating Data Exchange If you have a presentation that you believe might fit into the session please do join us. The deadline for submissions is March 18th. Thanks Antony Williams PhD, FRSC Phone: +1 (919) 201-1516 Email: williamsa-LFlALxTm1og&lt; at &gt;public.gmane.org&lt;mailto:williamsa-LFlALxTm1og&lt; at &gt;public.gmane.org&gt; My LinkedIn Profile: http://www.linkedin.com/in/antonywilliams/ My ScientistsDB page: www.scientistsdb.com/index.php?title=Antony_John_Williams&lt;http://www.scientistsdb.com/index.php?title=Antony_John_Williams&gt; My ORCID ID: http://orcid.org/0000-0002-2668-4821 My Blog: www.chemconnector.com&lt;http://www.chemconnector.com/&gt; Twitter: http://twitter.com/ChemConnector About.me: http://about.me/ChemConnector DISCLAIMER: This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening. The Royal Society of Chemistry is a charity, registered in England and Wales, number 207890 - Registered office: Thomas Graham House, Science Park, Milton Road, Cambridge CB4 0WF------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar_______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f&lt; at &gt;public.gmane.org https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss </pre> Antony Williams 2013-03-14T04:56:30 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1671 <pre>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 </pre> Egon Willighagen 2013-03-06T15:52:05 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1666 <pre>Mcule.com &lt;https://mcule.com&gt;, the online drug discovery platform, is pleased to announce the release of the easiest molecular docking solution online: 1-Click Docking&lt;https://mcule.com/apps/1-click-docking/?utm_source=blueobelisk&amp;utm_medium=maillist&amp;utm_campaign=1-click-docking&gt; . Molecular docking predicts the binding orientation and affinity of a ligand to a target. 1-Click Docking&lt;https://mcule.com/apps/1-click-docking/?utm_source=blueobelisk&amp;utm_medium=maillist&amp;utm_campaign=1-click-docking&gt;is easy to use and it’s FREE! Draw a ligand, select a target, click on Dock and start browsing the results! Click here to try 1-Click Docking now!&lt;https://mcule.com/apps/1-click-docking/?utm_source=blueobelisk&amp;utm_medium=maillist&amp;utm_campaign=1-click-docking&gt; Have a nice docking! Robert Kiss CSO, mcule.com rkiss-JmRbqXAs0MsAvxtiuMwx3w&lt; at &gt;public.gmane.org --- About mcule.com: DO EARLY PHASE DRUG DISCOVERY LIGHTNING FAST! Mcule.com is the online drug discovery platform. It offers a unique solution for pharma and biotech companies by providing molecular modelling tools and the highest quality purchasable compound database. ------------------------------------------------------------------------------ Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d_______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f&lt; at &gt;public.gmane.org https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss </pre> Róbert Kiss 2013-01-29T14:25:20 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1653 <pre>Thanks to Tim, there is a new version of the OpenSMILES specification, in both HTML and PDF formats: http://www.opensmiles.org Tim did a great deal of reformating with nice style sheets, and there is a whole new section on stereo centers. I'm leaving on vacation so I haven't had time to review it, but I invite everyone to read it and make comments. This message is cross-posted to several mailing lists. If you're on the BlueObelisk-SMILES list, please reply to that list. If you're not on that list but have comments, post them where you can; perhaps someone can cross-post them to the BO-SMILES list. Craig ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d_______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f&lt; at &gt;public.gmane.org https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss </pre> Craig James 2012-12-14T17:25:06 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1649 <pre>Hi, And now for something completely different ... I'm looking for an image of a DNA strand that's quite long and that I can manipulate. Is there an editor program and a template that I could use to create such a thing? What I'm looking for is a DNA strand that on the macroscopic level is also spiral, so that it can be made to look like it's wrapping around a tree a bit like a snake. This is for art, not chemistry. Seriously! Thanks! Craig (P.S. I have an alter ego. This has nothing to do with eMolecules.) ------------------------------------------------------------------------------ Keep yourself connected to Go Parallel: VERIFY Test and improve your parallel project with help from experts and peers. http://goparallel.sourceforge.net_______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f&lt; at &gt;public.gmane.org https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss </pre> Craig James 2012-11-29T16:50:13 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1644 <pre>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 </pre> Egon Willighagen 2012-09-18T10:15:27 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1641 <pre>Has anyone compiled a set of UTF-8 codepoints (characters) that are essential for chemistry specifically in Anglophone countries and aimed at machine processing? [Note I am not including the glyphs in this mail in case of corruption] For example chemistry uses over half of the printing characters in the range 32-127, probably most of the Greek characters (they can be used for locants), some of the ISO-latin, plus-minus (for racemates) , middot (e.g. Et2O.BF3) [http://en.wikipedia.org/wiki/Interpunct]. I would exclude personal names (e.g. Hueckel) and units (e.g. Angstrom) as they are used elsewhere. Where possible it would be valuable to have a normalized value. Thus IMO machine-processable chemical names should use '-' (char #45, hyphen-minus http://en.wikipedia.org/wiki/Hyphen ) rather than true minus, or dashes. Similarly minus should also use this character. </pre> Peter Murray-Rust 2012-09-13T10:21:05 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1614 <pre>Many of us use Java for code and some (e.g Jmol) use applets. Does anyone have any indication what we should do about http://www.kb.cert.org/vuls/id/636312 ? </pre> Peter Murray-Rust 2012-08-30T22:08:41 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1608 <pre>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/ </pre> Noel O'Boyle 2012-08-30T10:56:45 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1593 <pre> Here is text which I think helps fill in the "Open Data", "Open Source", "Open Specification" pages of the Blue Obelisk pages. Please note that I have changed some of the Blue Obelisk terms to be more acceptable to my views and understanding. For example, I do not believe that an Open Standard essentially requires "community process." Cheers, Andrew dalke-DxsMES/F/+GyoL73aWPbVUEOCMrvLtNR&lt; at &gt;public.gmane.org =============== http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Open_Source We use "Open Source" to encompass free [http://www.gnu.org/philosophy/free-sw.html] and open source [http://opensource.org/docs/definition.php] software as well as software in the public domain [http://en.wikipedia.org/wiki/Public_domain]. (ODFOSOS doesn't have the same simplicity to it). We believe that open source is an essential prerequisite for useful peer review, we believe that open source research software is the best way to advance and disseminate knowledge, and we encourage people to release their own software under an open license. Do you want to release your software as Open Source? The principles of free and open source software is based in copyright law. Software is essentially text, and in most countries you, or perhaps your employer, automatically have the right to prevent others from copying that text. You must actively either grant others a license to make copies or give up your copyright and put it into the public domain. The book "Producing Open Source Software" has an excellent summary of how to choose a license [http://producingoss.com/en/license-quickstart.html]. Our recommendation is to use the GNU GPL [http://www.gnu.org/licenses/#GPL], the MIT / X Window System License [http://opensource.org/licenses/mit-license.php] if you are interested in a simple license, and the Apache License 2.0 [http://www.apache.org/licenses/LICENSE-2.0] for a permissive license which also explicitly grants a patent license. If you want to put your software into the public domain then we recommend you either use the text from the SQLite public domain dedication [http://www.sqlite.org/copyright.html] or use the CC0 public domain dedication [http://creativecommons.org/about/cc0]. Be aware that "public domain" doesn't have a well-defined internationally recognized meaning, so many people prefer instead the certainty of a license. =============== http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Open_Data We use "Open Data" to apply to data sets which are part of the open scientific literature, including data sets which are published on research web sites. We believe that facts and collections of facts must be in the public domain, or at the very least distributed by a data license which adheres to the Panton Principles [http://pantonprinciples.org/]. We believe all published data sets, including those which contain material covered under copyright, should be released under a permissive data license which allows anyone to copy, process, analyze, modify, and redistribute that data, for any purpose. We specifically exclude personally identifying information from this belief, and have no position about data which might be seen a posing a public hazard. Do you want to release your data as Open Data? A fact is something like "the triple point of water is 273.16 K" or "the SMILES for methane is [CH4]". While gene patents come close, facts concerning the natural world are not, by themselves, protectable. There must be some transformative or creative step to make a fact protectable under patent or copyright law. The difficulty is that a collection of facts might be protected. For example, if you've used creative thought and expert opinion in order to select the elements in the data set, then you may have a specific database right. If you've arranged the data in a novel and creative fashion, then that is also protected. The specific details depends on your country's legal system; in the UK, a database right exists if there is a "substantial investment in obtaining [or] verifying" the data in the database. You can easily see how that might apply to scientific data. You can make your data Open Data by putting it in the public domain. This is called a public domain dedication or waiver, and it is not a license. The easiest and best solution is to use the CC0 public domain dedication [http://creativecommons.org/about/cc0]. You may think it's okay to use a simpler version, like a variation of the SQLite [http://www.sqlite.org/copyright.html] or PDB PDB [http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/policies_references.html] dedications. The problem is that these only cover copyright and not the database, moral, or other related rights which might also be in the data set. You need to be careful. Just because you collected a bunch of data doesn't mean that you have the right to dedicate it to the public domain. For one, your employer or university might be the legal rights holder, so check with them first. You need to be careful that you don't violate the legal rights of others. For example, suppose you develop a crowed-sourced collection of chemical protocols, where commentary on each of the protocols was contributed by others. Those people have a copyright interest in the result, so you can't distribute your data set without their permission. For this case we recommend that you require that contributors license their contribution under the Attribution-ShareAlike 3.0 Unported License [http://creativecommons.org/licenses/by-sa/3.0/]. And importantly, don't take someone else's proprietary data set, extract a lot of the of records, and release it. Even if you add a lot of new data, that's just plain illegal under copyright law. =============== http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Open_Standards We believe that Open Standards are necessary to promote scientific data exchange, analysis services, and data archiving. By Open Standards we mean that data formats, and control and exchange protocols must be documented in such a way that person "skilled in the art" [http://en.wikipedia.org/wiki/Person_having_ordinary_skill_in_the_art] can produce software which can read, write, and exchange data with other software which implements those Open Standard. Open Standards must be available on non-discriminatory terms, must not require patent, trademark, or other licensing, must not require a royalty fee of any sort, must not be protected using DRM or other technical means, and must not prohibit reverse engineering. For historical reasons, we acknowledge that older standards published in the open literature and available through public research libraries and the publishers, may be included as an Open Standard. Otherwise, Open Standards must not require an access fee, registration, or license agreement in order to access and use the documentation, and must not prevent redistribution of copies of the standard, including by DRM or copyright restrictions. We take no position on if Open Standards must allow derivative works. We specifically exclude trademark issues so long as software may use the Open Standard without trademark permission. We take no position on if an Open Standard requires public involvement or feedback. Do you want to release your data as an Open Standard? A standard is just documentation. The easiest way to make it an Open Standard is to release the document under one of the open content licenses. Do you want others to be able to develop variations of the standard? Then we suggest using the Attribution 3.0 (CC BY 3.0) [http://creativecommons.org/licenses/by/3.0/] or Attribution-ShareAlike 3.0 (CC BY-SA 3.0) [http://creativecommons.org/licenses/by-sa/3.0/] licenses. Otherwise, if you want to control the standards document (which is not the same as controlling the standard) then we suggest the Attribution-NoDerivs 3.0 (CC BY-ND 3.0) [http://creativecommons.org/licenses/by-nd/3.0/]. Unfortunately, standards may depend on patents, and patent issues are not part of the above licenses. You need to be aware if your standard requires any patent. You may also need to require that participants in the standards development waive their patent claims before joining, but so far a lack of patent waiver has not caused problems. You may also release a reference implementation or validation dataset as part of the specification. These should be released as Open Source [http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Open_Source] and Open Data [http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Open_Data], respectively. ------------------------------------------------------------------------------ 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/ </pre> Andrew Dalke 2012-08-29T13:47:36 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1573 <pre>I recently published the "Structure Query Collection", at https://bitbucket.org/dalke/sqc This is a collection of different SMILES and SMARTS used as queries against a small molecule database. I include the original data in as raw a form as I can manage, and a processed form which extracts only the SMILES/SMARTS and may include some cleanup of the original data. I have been struggling with how to define a license for the SQC data, or even if one is needed. 1) BindingDB The largest data sets in the collection by far come from BindingDB. This contains almost a decade of user-submitted queries from BindingDB. They were extracted from the log files. As best as I can tell, in the US there would be no legal protection for this data because there's no creative effort in its extraction. The SMILES are too short and non-notable to have individual protection by the submitter, and the US (see Feist) does not recognize database rights. BindingDB is from the US. Therefore, I do not believe that those dataset are covered under copyright, patent, trademark or other sui generis rights. (Assuming that I understand the phrase 'sui generic' correctly.) There is a niggling detail as I live in Sweden. However, I don't think my two days of work could be described as a "substantial investment in either the obtaining, verification or presentation of the contents", which is the text of "Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases". Should I include a disclaimer anyway, and if so, is there a suggested style? 2) SMARTS collections from RDKit This is probably the easiest to deal with. Two SMARTS data sets derive from files found in RDKit, which is distributed under a BSD/MIT-style license. I trivially transformed the data into a simple list of SMARTS. I don't believe I need to worry about these two data sets at all because I include the RDKit license in the distribution. However, is the extracted data set even covered under copyright and/or database rights at all? 3) SMARTS from Ehrlich and Rarey's recent J. Cheminformatics paper Ehrlich and Rarey published a list of 1235 SMARTS in Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2. Hans-Christian Ehrlich and Matthias Rarey. Journal of Cheminformatics 2012, 4:13 doi:10.1186/1758-2946-4-13 These SMARTS were used as their benchmark. I am trying to figure out if these SMARTS are covered under copyright or database rights. At first thought, one might conclude that the copyright is owned by Ehrlich and Rarey as the paper is published under the Creative Commons Attribution License 2.0. However, the SMARTS themselves were extracted from various other sources. Some of the sources include: - the Daylight documentation - works published in the other journals, including: J Chem Inf Comput Sc Adv Drug Delivery Rev J Comput Aided Mol Des This implies that neither the authors nor the Journal of Cheminformatics regard those original SMARTS as being protected under copyright or database rights. I have no idea if the work they did to assemble the SMARTS patterns means that their 1235 SMARTS are protected in the EU under a database right. I will presume that they are not. My conclusion is that the actual SMARTS and SMILES patterns from these different sources are not covered under copyright or database rights, and hence I do not need permission from the source providers in order to distribute the SQC. Likewise, the SQC data itself does not need a statement which grants additional rights to others, because the data is not protected under any law. Is my understanding correct? I also believe that people will look at the SQC and expect that there is a license statement of some sort - even though one is not required for the data. What is the proper way to disclaim copyright and (more importantly) database rights? I was thinking: Andrew Dalke and Andrew Dalke Scientific AB disclaim any additional copyright, database right, or other legal protections to the SMILES and SMARTS data sets included in the Structure Query Collection. Perhaps the Blue Obelisk "Open Data" page could describe what one should do in order to make their datasets open, or to disclaim any legal protections to data sets? Andrew dalke-DxsMES/F/+GyoL73aWPbVUEOCMrvLtNR&lt; at &gt;public.gmane.org ------------------------------------------------------------------------------ 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/ </pre> Andrew Dalke 2012-08-27T10:14:06 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1569 <pre>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/ </pre> Noel O'Boyle 2012-08-13T20:25:00 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1568 <pre>Are we planning a dinner at ACS? P. </pre> Peter Murray-Rust 2012-07-25T09:54:49 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1561 <pre>Mat Todd has raised the exciting idea of a Craigslist for molecules - "I would like some of *this*". His post is at http://intermolecular.wordpress.com/2012/04/20/molecular-craigslist/ We'll be discussing this at the OKFN hackathon tomorrow. Any ideas would be very welcome. Since many would be new molecules (and presumably organic) we can use InChI but we need a nice Open interface. We'll be looking at some of the latest OKF tools and maybe they will create most of what is necessary. Do we have a JS-enabled molecular viewer for InChIs, for example to embed in web pages? </pre> Peter Murray-Rust 2012-07-06T16:52:18 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1561 <pre>Mat Todd has raised the exciting idea of a Craigslist for molecules - "I would like some of *this*". His post is at http://intermolecular.wordpress.com/2012/04/20/molecular-craigslist/ We'll be discussing this at the OKFN hackathon tomorrow. Any ideas would be very welcome. Since many would be new molecules (and presumably organic) we can use InChI but we need a nice Open interface. We'll be looking at some of the latest OKF tools and maybe they will create most of what is necessary. Do we have a JS-enabled molecular viewer for InChIs, for example to embed in web pages? </pre> Peter Murray-Rust 2012-07-06T16:52:18 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1548 <pre>OK, I'm stumped. How does one get to Rule d? Does anyone know if this code was ever tested? 03131 if (b-&gt;GetBond &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBAtom.html#a1383e1d49338b8ee6784b8b9ef889ba4&gt;(c)-&gt;IsAromatic &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBBond.html#a737ac5dd55e68e9d29f6d368b403c7b1&gt;()) {03132 double Ub, Uc, pi_bc, beta;03133 Ub = GetUParam &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a4dd261dbea68ff31a17a777e3a9efc8f&gt;(b);03134 Uc = GetUParam &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a4dd261dbea68ff31a17a777e3a9efc8f&gt;(c);03135 03136 if (!HasPilpSet &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a01072db9ce803fb91ff6b73cd62ac03a&gt;(type_b) &amp;&amp; !HasPilpSet &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a01072db9ce803fb91ff6b73cd62ac03a&gt;(type_c))03137 pi_bc = 0.5;03138 else03139 pi_bc = 0.3;03140 03141 if (((GetVal &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#adf66fb6159cb5cfb695ef10ea85f9c43&gt;(type_b) == 3) &amp;&amp; (GetVal &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#adf66fb6159cb5cfb695ef10ea85f9c43&gt;(type_c) == 4)) ||03142 ((GetVal &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#adf66fb6159cb5cfb695ef10ea85f9c43&gt;(type_b) == 4) &amp;&amp; (GetVal &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#adf66fb6159cb5cfb695ef10ea85f9c43&gt;(type_c) == 3)))03143 beta = 3.0;03144 else03145 beta = 6.0;03146 03147 torsioncalc.v1 &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBFFTorsionCalculationMMFF94.html#a56e54b9521cb38b2eaec90d6530ca46b&gt; = 0.0;03148 torsioncalc.v2 &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBFFTorsionCalculationMMFF94.html#af5a97920571660315ee3a8bbbd8c90a0&gt; = beta * pi_bc * sqrt(Ub * Uc);03149 torsioncalc.v3 &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBFFTorsionCalculationMMFF94.html#a2cf47c38afaedf54148e8ff0eae629f8&gt; = 0.0;03150 found_rule = true;03151 } else {03152 // rule (c) page 63103153 double Ub, Uc, pi_bc, beta;03154 Ub = GetUParam &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a4dd261dbea68ff31a17a777e3a9efc8f&gt;(b);03155 Uc = GetUParam &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a4dd261dbea68ff31a17a777e3a9efc8f&gt;(c);03156 03157 if (((GetMltb &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a8d8291470b39dfecb4c66362b5e302c4&gt;(type_b) == 2) &amp;&amp; (GetMltb &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a8d8291470b39dfecb4c66362b5e302c4&gt;(type_c) == 2)) &amp;&amp; a-&gt;GetBond &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBAtom.html#a1383e1d49338b8ee6784b8b9ef889ba4&gt;(b)-&gt;IsDouble &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBBond.html#a51a42be9b514d0250330eb4204276d35&gt;())03158 pi_bc = 1.0;03159 else03160 pi_bc = 0.4;03161 03162 beta = 6.0;03163 torsioncalc.v1 &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBFFTorsionCalculationMMFF94.html#a56e54b9521cb38b2eaec90d6530ca46b&gt; = 0.0;03164 torsioncalc.v2 &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBFFTorsionCalculationMMFF94.html#af5a97920571660315ee3a8bbbd8c90a0&gt; = beta * pi_bc * sqrt(Ub * Uc);03165 torsioncalc.v3 &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBFFTorsionCalculationMMFF94.html#a2cf47c38afaedf54148e8ff0eae629f8&gt; = 0.0;03166 found_rule = true;03167 }03168 03169 // rule (d) page 63203170 if (!found_rule)03171 if (((GetCrd &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a7c08f7eff3b784428708f49582334a5c&gt;(type_b) == 4) &amp;&amp; (GetCrd &lt;http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBForceFieldMMFF94.html#a7c08f7eff3b784428708f49582334a5c&gt;(type_c) == 4))) {03172 double Vb, Vc;03173 </pre> Robert Hanson 2012-05-18T03:03:46 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1537 <pre>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-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f&lt; at &gt;public.gmane.org https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss </pre> Noel O'Boyle 2012-04-23T18:10:45 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1535 <pre>Hi all, thanx to Peter Maas, Chemical blogspace is still up and running: http://cb.openmolecules.net/ While I was looking for citations of "OpenMolecule RDF" (http://rdf.openmolecules.net/) I noted that Cb was cited a few months ago in this paper: Buchanan, Robert A. (2011) "Beyond the Chemistry Web," Sci-Tech News: Vol. 65: Iss. 2, Article 11. Available at: http://jdc.jefferson.edu/scitechnews/vol65/iss2/11 Grtz, Egon </pre> Egon Willighagen 2012-04-15T13:12:30 http://comments.gmane.org/gmane.science.chemistry.blue-obelisk/1530 <pre>As a result of the "Semantic Physical Science" workshop earlier this year ( http://www-pmr.ch.cam.ac.uk/wiki/Semantic_Physical_Science) we are writing a paper for J.Cheminformatics on "Building a code library for CML". We'd like information from anyone who has implemented a toolset to read and/or write CML. The paper will analyse some of these in depth and record others. The minimal amount of information is probably the coverage (through the usage of CML Elements) , the language and a few additional fields (this are mainly tickboxes). At present we are covering: - Neylon/Python - VTK - Avogadro - Chem4Word - OpenBabel - CDK/JChemPaint - FoX - Jmol - JUMBO-system We'd very much like others to contribute - it can be closed source as well as Open, We are generally interested in systems that use Schema2.4 or Schema3.0 as previous versions are deprecated. Note that Schema 2.4 has been used by the community for about 5 years with no emendations. Schema3 does not introduce new functionality but has a more modern approach using conventions rather than content-models. We are creating a spreadsheet and it may be simplest to share this in a dropbox. If you write a section on your code then this will generally mean that you are listed as an author. We only want descriptions of the CML interface/API/coverage - not the greater functionality of the program/library If you aren't on the list above, please mail either this list or me. Hoping for contributions </pre> Peter Murray-Rust 2012-03-29T09:11:12 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.chemistry.blue-obelisk