This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. org.embl.ebi.escience.scuflworkers.java.StringConcat org.embl.ebi.escience.scuflworkers.java.SplitByRegex org.embl.ebi.escience.scuflworkers.java.SplitByRegex org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge \n org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates mus_musculus org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates kegg pathway org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); nonEmpty.add(trimmed); } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + "ncbi-geneid:" + (String) (nonEmpty.elementAt(i) + "\n"); } input output String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); nonEmpty.add(trimmed); } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + "uniprot:" + (String) (nonEmpty.elementAt(i) + "\n"); } input output String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output http://soap.genome.jp/KEGG.wsdl bconv String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); String[] trimmedSplit = trimmed.split("\t"); if (trimmedSplit.length > 2) { nonEmpty.add(trimmedSplit[1].trim()); } } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + (String) (nonEmpty.elementAt(i) + "\n"); } input output http://soap.genome.jp/KEGG.wsdl btit String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); } input output result = ensemblGeneId + "," + entrezGeneId + "," + externalGeneId + "," + chromoName + "," + geneStart + "," + geneEnd + "," + ensemblTranscriptId + "," + uniprotAcc; ensemblGeneId entrezGeneId externalGeneId chromoName geneStart geneEnd ensemblTranscriptId uniprotAcc result Mus musculus genes (NCBIM36) http://soap.genome.jp/KEGG.wsdl bconv http://soap.genome.jp/KEGG.wsdl binfo This workflow removes any null values from a list of strings This workflow removes any null values from a list of strings String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\t"); } input output \n org.embl.ebi.escience.scuflworkers.java.StringListMerge http://soap.genome.jp/KEGG.wsdl btit http://phoebus.cs.man.ac.uk:8081/axis/EnsemblListner.jws?wsdl lister org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge String pathway_id_input = pathway_ids.trim(); String gene_id_input = gene_id.trim(); String output = ""; output = gene_id_input + "\t" + pathway_id_input; pathway_ids gene_id output org.embl.ebi.escience.scuflworkers.java.SplitByRegex http://soap.genome.jp/KEGG.wsdl get_pathways_by_genes Retrieves the current databases from ENSEMBL for a species http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.getcurrentdatabase