{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2006/11/03/bioclipse-workshop-short-but.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/xf0q9-v4n97", "url": "https://chem-bla-ics.linkedchemistry.info/2006/11/03/bioclipse-workshop-short-but.html", "title": "Bioclipse Workshop: short but productive", "content_html": "

The Bioclipse Workshop\nhas ended and, for just three days, turned out quite productive.\nWe have first bits of scripting support for JavaScript using Rhino. At this moment the\nscripting plugin needs to explicit depend on plugins to be able to access their classpath, but we plan to solve that.\nAn example script:

\n\n
// to have short identifiers\nArray = Packages.java.lang.reflect.Array;\nString = Packages.java.lang.String;\nmsgBox = Packages.net.bioclipse.plugins.bc_rhino.ShowBcMsgBox;\nDbfetchServiceServiceLocator =\n  Packages.uk.ac.ebi.www.ws.services.urn.Dbfetch.DbfetchServiceServiceLocator;\n\n// get data\nservice = new DbfetchServiceServiceLocator();\nstrarray = service.getUrnDbfetch().fetchData(\"refseq:NM_210721\", \"refseq\", \"raw\");\n\n// make readable\nstr = new String();\nfor (i = 0; i < Array.getLength(strarray); i++) {\n  if (i != 0)\n  str = str + (\"\\n\");\n  str = str + strarray[i];\n}\n\n// show\nmsgBox.ShowStatic(str);\n
\n\n

It’s just a short example that uses webservice technology in Bioclipse to fetch a sequence.

\n\n

QSAR support

\n\n

QSAR support is getting along too, with a new DescriptorProvider extension point in trunk/\nand work is progressing on a wizard that allows selecting descriptors and a CDK backend. The output of the wizard is a matrix resource, for\nwhich we already have a rich editor. A JOELib plugin has been suggested,\nas it has a good deal of QSAR descriptors too; Jörg, interested in doing a tiny bit of Bioclipse hacking?

\n\n

A full proceedings is available online.

", "summary": "The Bioclipse Workshop has ended and, for just three days, turned out quite productive. We have first bits of scripting support for JavaScript using Rhino. At this moment the scripting plugin needs to explicit depend on plugins to be able to access their classpath, but we plan to solve that. An example script:", "date_published": "2006-11-03T00:00:00+00:00", "date_modified": "2025-02-16T00:00:00+00:00", "tags": ["bioclipse","qsar","javascript","conference"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }