Computational Grid2011-11-22T12:34:46+00:00/groups/1022017-02-05T14:20:35+00:00Dr Kaveh Ostad Ali Askari joined the Computational Grid groupurn:uuid:64e01a1d-5630-4687-a479-6c0d9258fe98Dr Kaveh Ostad Ali Askari2011-05-18T09:23:33+00:00Alan Williams joined the Computational Grid groupurn:uuid:ab100fef-6b66-4cde-8306-a83038647d87Alan Williams2011-05-18T09:22:54+00:00Steffen Möller shared Example for external tools with gzip and gunzipThis workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File). The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later.urn:uuid:2b73cb11-2784-4ef2-acbb-d2acc0569482Steffen Möller2011-05-06T16:11:25+00:00Steffen Möller shared External Tool: Numerically adding two values with 'bc'.The workflow is an examples for the External Tools / UseCase plugin to integrate external tools. It wraps the "bc" command line calculator. Internally, it executes the following script: if [ ! -r "$1" ]; then echo "Cannot read file indicated by first argument '$1'." ; exit -1 ; fi ; if [ ! -r "$2" ];then echo "Cannot read file indicated by second argument '$1'." ; exit -1 ; fi if [ -x /usr/bin/bc ]; then a=$(cat $1|tr -d '\n') ; b=$(cat $2|tr -d '\n') ; echo "$a+$b" | bc | tr -d '\n'; else echo "The bc tool is not installed where expected, if installed at all." ; exit -1 ; fi To develop workflows in a similar manner, i.e. avoiding the specification of beans and gain complete flexibility for local or remote execution of the workflow, please follow instructions on http://www.mygrid.org.uk/dev …urn:uuid:ff418ed9-5e21-48ea-8cf2-9d78e4c297acSteffen Möller2011-01-08T11:18:11+00:00Julio Proaño joined the Computational Grid groupurn:uuid:c75fc9cb-b603-498c-87d0-b589b0295894Julio Proaño2008-09-22T01:05:37+00:00Steffen Möller shared dbfetch tutorialThis workflow eases entry in the world of Taverna with one of the key tasks - the retrieval of plain data. The dbfetch offers sequence and structure data from a large variety of sources. A first execution of this workflow informs about these in the "getSupportedDBs" output. Also the formats and styles are listed. The two inputs allow for the specification of a query that leaves the format with "default" (which is different for every database, "native" would be a better fit), the style is always "raw". With the output being presented as a list of strings, which is very slow for larger entries, the list of lines are merged into single strings for each entry prior to the display.urn:uuid:ee06b857-4090-4ecf-a934-a727cd4a0210Steffen Möller2008-09-18T14:44:54+00:00Steffen Möller shared echoThe workflow tests the standard-compliance of web service descriptions of ARC-1, a development of the EU project "KnowARC" to modernise the grid infrastructure ARC of the NorduGrid. Learn more about it on http://www.knowarc.eu and http://www.nordugrid.org . If you have computers in spare - join us - and help you very own and many other sciences. And you make many interesting contacts just en passent. No authorisation is required for this very experimental service.urn:uuid:e96a7f9d-3baf-443b-8f02-227bbed86f4dSteffen Möller2008-09-03T10:32:22+00:00Mike 'Mike' Jones joined the Computational Grid groupurn:uuid:c5dce709-821c-4227-a351-cf6a518fe773Mike 'Mike' Jones2008-09-02T14:59:24+00:00Steffen Möller shared Structural alignment of arbitrary number of protein structures.This grid-executed Mustang application performs a structural alignment of protein sequences. The number of arguments is variable, in principle, but is shown here for three. The application is executed via the Taverna-ARC plugin on a machine of the NorduGrid. Although your machine can be a part of it, you may prefer to wait for a later version of that interface that does not require grid certificates.urn:uuid:8315dbcc-edfe-449b-ae56-3d12c3f2fe25Steffen Möller2008-08-24T22:48:09+00:00Steffen Möller commented:The structural alignment with Mustang http://www.myexperiment.org/workflows/377 was contributed as a (partially) grid-executed workflow.urn:uuid:efa4e298-82f1-4b2f-a935-a7caa65615dbSteffen Möller2008-08-22T16:50:45+00:00Steffen Möller shared mustang provides structural alignment of two proteinsThis workflow experiments with the partial execution of jobs on a computational grid. The workflow elements "mustang" and "boxshade" are executed on grid nodes. Access to these resources is orchestrated with the plugin available on http://grid.inb.uni-luebeck.de . Please contact the author of this workflow for access permissions.urn:uuid:263b6e58-fae5-4474-901c-bb824d85a449Steffen Möller2008-08-21T12:35:45+00:00Steffen Möller created the Computational Grid groupurn:uuid:2eb5d535-5bb2-4809-923f-c0f2bf1ab358Steffen Möller