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_posts/2008-10-24-git-eclipse-integration.markdown

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blogger-link: https://chem-bla-ics.blogspot.com/2008/10/git-eclipse-integration.html
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doi: 10.59350/sejc5-h3m89
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tags: git eclipse
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image: /blog/assets/images/gitEclipse.png
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image: /assets/images/gitEclipse.png
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---
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Recently, I have been blogging about [Git](http://git.or.cz/):
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One concern expressed by people was the lack of integration with IDEs. Now, an [Eclipse plugin](http://git.or.cz/gitwiki/EclipsePlugin)
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seems well on its way:
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![](/blog/assets/images/gitEclipse.png)
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![](/assets/images/gitEclipse.png)
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With a experimental update site ([http://www.jgit.org/update-site](http://www.jgit.org/update-site)),
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the plugin is just an Eclipse reboot away.

_posts/2008-10-25-bioclipse2-scripting-1-from-smiles-to.markdown

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blogger-link: https://chem-bla-ics.blogspot.com/2008/10/bioclipse2-scripting-1-from-smiles-to.html
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doi: 10.59350/5azgt-k8a94
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tags: bioclipse cml cdk jmol eclipse github cheminf
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image: /blog/assets/images/mashupCmldomJmolCDK.png
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image: /assets/images/mashupCmldomJmolCDK.png
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After some difficulties this week with making an export of [CDK](http://cdk.sf.net/) plugins in the
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A variation of this script is visible in the following screenshot:
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![](/blog/assets/images/mashupCmldomJmolCDK.png)
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![](/assets/images/mashupCmldomJmolCDK.png)
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This and other Bioclipse2 scripts I will post in [Gist](http://gist.github.com/), a sort of [pastebin](http://en.wikipedia.org/wiki/Pastebin)
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supporting version history, and I'll tag them with *bioclipse gist* on [delicious](http://delicious.com/egonw/), so that you can always

_posts/2008-10-31-next-generation-asynchronous.markdown

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blogger-link: https://chem-bla-ics.blogspot.com/2008/10/next-generation-asynchronous.html
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doi: 10.59350/7gx9j-dn554
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tags: bioclipse xmpp soap http inchikey:VPPJLAIAVCUEMN-GFCCVEGCSA-N
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image: /blog/assets/images/cdkxwsPsi.png
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image: /assets/images/cdkxwsPsi.png
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---
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Johannes joined a [Bioclipse Workshop](http://wiki.bioclipse.net/index.php?title=Outcome_of_the_Bioclipse_autumn_workshop_2006) a long time
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[CDK](https://cdk.github.io/). This brings me to [cdk-xws](https://cdk.svn.sourceforge.net/svnroot/cdk/cdk-xws/trunk@12888), which is
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the project to bring CDK functionality online as webservices using IO-DATA.
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![](/blog/assets/images/cdkxwsPsi.png)
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![](/assets/images/cdkxwsPsi.png)
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This shows three nodes, the first being the CDK service, with two functions, of which I only implemented one yet.
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_posts/2008-11-03-embrace-workshop-in-uppsala.markdown

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blogger-link: https://chem-bla-ics.blogspot.com/2008/11/embrace-workshop-in-uppsala.html
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doi: 10.59350/wh1bq-ptb19
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tags: bioclipse openscience justdoi:10.5281/zenodo.2647677 web
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image: /blog/assets/images/bioclipseWebserviceEmbrace.png
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image: /assets/images/bioclipseWebserviceEmbrace.png
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This Monday and Tuesday I will attend the EMBRACE workshop [Understanding, creating and deploying EMBRACE compliant WebServices](http://teacher.bmc.uu.se/webservicesworkshop/Welcome.html).
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I will present there the ongoing work in Bioclipse to support services and web services in particular. The sheets of the presentation will look like:
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[![](/blog/assets/images/bioclipseWebserviceEmbrace.png)](https://doi.org/10.5281/zenodo.2647677)
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[![](/assets/images/bioclipseWebserviceEmbrace.png)](https://doi.org/10.5281/zenodo.2647677)

_posts/2008-11-04-next-generation-asynchronous.markdown

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blogger-link: https://chem-bla-ics.blogspot.com/2008/11/next-generation-asynchronous.html
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doi: 10.59350/esdth-ef628
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tags: xmpp java bioclipse web
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image: /blog/assets/images/autogeneration.png
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image: /assets/images/autogeneration.png
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Getting back to some webservice stuff (see [part #1 of this series](https://chem-bla-ics.blogspot.com/2008/11/next-generation-asynchronous.html))...
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The Bioclipse xws4j plugin actually puts the data model in my workspace, so that I can easily introspect the API:
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![](/blog/assets/images/autogeneration.png)
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![](/assets/images/autogeneration.png)
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The last three lines invoke the function (synchronously, as it's cheap), and get the mass from the function output. BTW, I should
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stress that a function does not require any specific implementation regarding synchronous or asynchronous calls. You write **one**

_posts/2008-11-07-opendatasourcestandards-is-not-enough.markdown

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blogger-link: https://chem-bla-ics.blogspot.com/2008/11/opendatasourcestandards-is-not-enough.html
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doi: 10.59350/kmk49-mj610
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tags: odosos chemspider workflow cdk bioclipse cml debian eclipse rdf jmol blue-obelisk
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image: /blog/assets/images/registry.png
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image: /assets/images/registry.png
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The [Blue Obelisk](http://blueobelisk.sourceforge.net/wiki/Main_Page) mantra [ODOSOS](http://blueobelisk.sourceforge.net/wiki/ODOSOS),
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[WDSL entry](http://prints.cs.man.ac.uk:8081/service/massspecapi) for [a workspace](http://www.myexperiment.org/workflows/97)
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I [uploaded](http://chem-bla-ics.blogspot.com/2007/11/metabolomics-workflows-in-taverna.html) about a year ago to MyExperiment:
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![](/blog/assets/images/registry.png)
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![](/assets/images/registry.png)
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BTW, ChemSpider has an Advisory Board of which I am member, but it is also a classical (and intentional) Cathedral project. We do share common interests though, which makes us collaborate.
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[Chemical MIME Data](http://packages.debian.org/lenny/chemical-mime-data),
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[Kalzium](http://packages.debian.org/lenny/kalzium) and [OpenBabel](http://packages.debian.org/lenny/openbabel)):
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![](/blog/assets/images/debichem.png)
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![](/assets/images/debichem.png)
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This data analysis helps the projects being analyzed.
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_posts/2008-11-18-solubility-data-in-bioclipse-1.markdown

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blogger-link: https://chem-bla-ics.blogspot.com/2008/11/solubility-data-in-bioclipse-1.html
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doi: 10.59350/ydgw3-52978
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tags: bioclipse rdf
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image: /blog/assets/images/bioclipseRDF.png
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image: /assets/images/bioclipseRDF.png
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I am working on converting [Jean-Claude](http://usefulchem.blogspot.com/)'s [Solubility](https://spreadsheets.google.com/ccc?key=plwwufp30hfq0udnEmRD1aQ&hl=en)
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[Bioclipse](http://www.bioclipse.net/) will be the workbench in which this will be visualized, and just got graph depiction online using
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[Zest](http://www.eclipse.org/gef/zest/). The screenshot does not show the RDF yet, but that will follow soon:
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![](/blog/assets/images/bioclipseRDF.png)
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![](/assets/images/bioclipseRDF.png)
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Next stops:
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_posts/2008-11-20-scripting-jchempaint.markdown

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blogger-link: https://chem-bla-ics.blogspot.com/2008/11/scripting-jchempaint.html
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doi: 10.59350/yhdxa-ft783
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tags:
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image: /blog/assets/images/jcpScripting.png
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image: /assets/images/jcpScripting.png
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Today and tomorrow, Stefan, [Gilleain](http://gilleain.blogspot.com/), Arvid and I are having a [JChemPaint Developers Workshop](https://apps.sourceforge.net/mediawiki/cdk/index.php?title=JChemPaintWorkshop2008)
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A simple script could look like: Or, as screenshot:
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![](/blog/assets/images/jcpScripting.png)
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![](/assets/images/jcpScripting.png)

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