The web link is fine for referencing T.E.S.T. I still use 1.0 release of CDK so not to break the JChemPaint linkage. In the web services version we will probably use a newer CDK version since we wont need JChemPaint for that. It wont be ready for about a year though.
Todd From: jay patel [mailto:[email protected]] Sent: Tuesday, August 16, 2016 11:01 AM To: Developers forum for discussion about the Chemistry Development Kit (CDK) <[email protected]>; Martin, Todd <[email protected]>; [email protected] Subject: Re: [Cdk-devel] CDK III paper: software using CDK 1.4 or 1.5? Hi Egon, US EPA's T.E.S.T also uses CDK libraries (https://www.epa.gov/chemical-research/toxicity-estimation-software-tool-test#pubs), so you can add that one to your list too. I know Todd is working on a new web services version of T.E.S.T, but I am not sure when are they releasing the new version. I have copied this mail to him in case he wants to elaborate on anything or if he has a paper on T.E.S.T which can be a better citation than the website link. Thanks, Jay Patel On Thu, Aug 11, 2016 at 3:50 AM, Egon Willighagen <[email protected]<mailto:[email protected]>> wrote: Hi all, I am finishing up a third CDK paper, which you can find the LaTeX source at [0]. The current draft PDF is attached. The introduction section lists a number of tools that are based on the CDK library, and currently reads something like: "For example, new tools expose CDK functionality, such as Cinfony [4], rcdk [5], and workflow plu- gins for Taverna [6] and KNIME [7]. Furthermore, projects with specific functional- ity have emerged building on the CDK, including jCompoundMapper [8], Scaffold- Hunter [9], OMG [10], Padel [11], AMBIT-SMARTS [12], AMBIT-Tautomer [13], and SMSD [14, 15]. Other tools used previous versions already, and follow newer releases of the CDK, such as Bioclipse [16, 17] and AMBIT [18]. While the above tools suggest that the CDK is primarily used to create general tools, it is important to note that it is also used to solve specific questions, like finding the maximally bridging rings in chemical structures [19]." I am keep on learning from more tools that have seen releases of CDK-based software in the last 2-3 years, using CDK 1.4 or better the 1.5 series. Please let me know if your software is not listed yet and you like it to be listed. If so, please send me a reply to this mailing list with the following information: 1. the full name of the software 2. a publication where the software is described (DOI) 3. which CDK version it is using 4. (preferably) a website about the software (If there is no publication yet, I will not cite it in the paper, but you are still strongly encouraged to mention it on the cdk-user@ mailing list!) Egon 0.https://github.com/cdk/cdk-paper-3 PS. Of course, if you like support with upgrading your software to CDK 1.5 (highly recommended, see the contents of the paper draft), we will be happy to help. -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohodev2dev _______________________________________________ Cdk-devel mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/cdk-devel
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