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FIlter list of strings by regex extracting... (1)

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then the two characters after the 'a' are included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['bc', 'xy'] is output.

Created: 2010-10-29

FIlter list of strings by regex with an un... (1)

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The workflow filters the five element list split from the first service and returns an empty list as no elements match.

Created: 2010-10-29

FIlter list of strings by regex with a sui... (1)

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The workflow filters the five element list split from the first service and returns the three elements that match the regular expression.

Created: 2010-10-29

Concatenate two strings (1)

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The concatenate two strings service takes the strings 'good' and 'bye' and returns the result 'goodbye'.

Created: 2010-10-29

Concatenate two strings - empty strings (1)

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The concatenate two strings service takes two empty strings and returns an empty string.

Created: 2010-10-29 | Last updated: 2010-10-29

Byte Array to string - non empty value (1)

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The beanshell converts the string 'hello' to a byte array which is then converted back to the string 'hello' by the Byte_Array_to_string service.

Created: 2010-10-29 | Last updated: 2010-10-29

Byte Array to string - empty value (1)

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The beanshell converts the empty string '' to a byte array which is then converted back to the empty string '' by the Byte_Array_To_string service.

Created: 2010-10-29 | Last updated: 2010-10-29

Echo_with_occasional_failure (1)

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The Sometimes_Fails service mostly echoes the string 'hello' to the out port. Sometimes, it throws a service failure.

Created: 2010-10-29 | Last updated: 2010-10-29

Always fails - two parameters (1)

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The always fails service generates a service failure when two parameter values are supplied.

Created: 2010-10-29 | Last updated: 2010-10-29

Always fails - one parameter (1)

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The always fails service generates a service failure when one parameter value is supplied.

Created: 2010-10-29 | Last updated: 2010-10-29

Always fails - no parameters (1)

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The always fails service generates a service failure when no parameter values are supplied.

Created: 2010-10-29 | Last updated: 2010-10-29

Get web page from URL - url and base (1)

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Fetches a web page from http://www.mygrid.org.uk/tools with the base parameter as "http://www.mygrid.org.uk" and the url as "/tools". Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Created: 2010-10-29 | Last updated: 2010-10-29

Get web page from URL - just url (1)

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Fetches a web page from http://www.mygrid.org.uk/tools using just the url parameter of the service. Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Created: 2010-10-29

Get image URLs from HTTP document - no images (1)

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Retrieve the web page at http://www.mygrid.org.uk/usermanual1.7/user_gettings_started.html and examine it for images. The workflow should return an empty list.

Created: 2010-10-29 | Last updated: 2010-10-29

Get image from URL - url and base specified (1)

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Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using both the url and base parameters

Created: 2010-10-29 | Last updated: 2010-10-29

Get image from URL - only url specified (1)

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Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using just the url parameter

Created: 2010-10-29

Remove duplicate strings (1)

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The remove duplicate strings service takes the list ['a','b','c','b','a','d'], strips out duplicate strings and outputs the result ['a','b','c','d'].

Created: 2010-10-29

Remove duplicate strings - empty list (1)

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The remove duplicate strings service takes the empty list [] and outputs the result [].

Created: 2010-10-29 | Last updated: 2010-10-29

Merge string list to string - empty list (1)

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The merge string list to string service takes an empty list [] and outputs an empty string ''.

Created: 2010-10-28

Merge string list to a string - default se... (1)

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The merge string list to string service takes the list ['a','b','c'] and outputs the string 'a b c'.

Created: 2010-10-28

Merge string list to string - colon separator (1)

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The merge string list to string service takes the list ['a','b','c'] and using the separator ':' outputs the string 'a:b:c'.

Created: 2010-10-28

Flatten list (1)

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The flatten_list service takes the list [['a'], ['b'], ['c'], ['d']] and outputs the list ['a', 'b', 'c', 'd', 'e'].

Created: 2010-10-28 | Last updated: 2010-10-28

Write text file - specified value (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes 'hello' into the file. 'hello' is also output by the service.

Created: 2010-10-28

Write text file - overwriting content (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file A service which writes the string 'hello' into the file. After service A has run, service B writes 'goodbye' into the file. The file is then read by the Read_Text_File service and its content, 'goodbye', output by the workflow.

Created: 2010-10-28

Write text file - empty string value (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes the empty string '' into the file. '' is also output by the service.

Created: 2010-10-28

Read text file - several lines (1)

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The beanshell write the string 'hello' four times separated by a new lineto a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello hello hello hello'.

Created: 2010-10-28

Read text file (1)

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The beanshell write the string 'hello' to a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello'.

Created: 2010-10-28

Read text file - empty file (1)

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The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the empty string ''.

Created: 2010-10-28 | Last updated: 2010-10-28

List files by regex - single match (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file path to the one file matching 'c.*' i.e. starting with 'c' is output.

Created: 2010-10-28

List files by regex - several answers (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file paths matching the regular expression '.*i.*', i.e. those containing an 'i', are output.

Created: 2010-10-28

List files by regex - no matches (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service. Since no files match the regular expression 'x.*' i.e. no files have a name that starts with 'x', an empty list is output.

Created: 2010-10-28

List files by regex - empty directory (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_regex service. Since there are no files, an empty list is output.

Created: 2010-10-28 | Last updated: 2010-10-28

List files by extension - single match (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service and the file path to the one file ending in ".bin" is output.

Created: 2010-10-28 | Last updated: 2010-10-28

List files by extension - several matches (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service and the file paths to the three files ending in ".png" are output.

Created: 2010-10-28 | Last updated: 2010-10-28

List files by extension - no matches (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_extension service. Since no files end in ".fred", an empty list is output.

Created: 2010-10-28 | Last updated: 2010-10-28

List files by extension - empty directory (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The empty directory is examined by the List_files_by_extension service. Since no files end in ".png", an empty list is output.

Created: 2010-10-28

Get Environment Variables as XML (1)

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The Get_Environment_Variables_as_XML service returns an XML file containing a set of property elements each of which contains the name and value of an environment variable.The Get_Environment_Variables_as_XML service returns an XML file containing

Created: 2010-10-28

Execute cmd line app - unix - /bin/ls of t... (1)

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the args port of the execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls command on the temporary directory. The result is passed to its result port and then to the output port of the workflow.

Created: 2010-10-28 | Last updated: 2010-10-28

Execute cmd line app - unix - /bin/ls -R o... (1)

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Note that this workflow only works on Unix systems. The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the create_and_populate_list beanshell which creates a list of '-R' and the path. The resultant list is passed to the args port of the Execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'. The execute_cmd_line_app service runs the /bin/ls -R command on the temporary ...

Created: 2010-10-28 | Last updated: 2010-10-28

Concatenate files - multiple files (1)

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The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has no value, the results are not...

Created: 2010-10-28

Concatenate files - echo results but no files (1)

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The split_string_into_string_list_by_regular_expresson outputs an empty list since the string to be split is defaulted to ''. As there are no input values, the create_and_populate_temporary_file generates an empty list. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service does not write anything to the temporary output file. Because the displayresults port has been given a default value of 'true', the empty string is ...

Created: 2010-10-28

Concatenate files - echo results and multi... (1)

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The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell. The create_temporary_file beanshell creates a file to which the concatentation can be written. The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has been given a default value of...

Created: 2010-10-28

Transcribe DNA (1)

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The Transcribe DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding transcribed RNA sequence, in this example, 'gauccuccau'.

Created: 2010-10-28

Reverse complement DNA (1)

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The Reverse Complement DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding reverse complement sequence, in this example, 'atggaggatc'.

Created: 2010-10-28

Read SwissProt file (1)

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The Read_SwissProt_file service reads the file at the swiss_prot_file_url and converts the SwissProt data into Agave format. The result is then sent to the workflow's swiss_prot_data port.

Created: 2010-10-28 | Last updated: 2010-10-28

Read GenBank file (1)

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The Read_GenBank_file service reads the file at the genbank_file_url and converts the GenBank data into Agave format. The result is then sent to the workflow's gen_bank_data port.

Created: 2010-10-28 | Last updated: 2010-10-28

Encode byte[] to base64 (1)

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The encode byte[] to base 64 service encodes the bytes representing (in the local character set) 'hello'.

Created: 2010-10-28

Decode base64 to byte[] (1)

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The decode base64 to byte[] service decodes the base64 string. The byte array is then converted into the string 'Hello world'.

Created: 2010-10-28

Is Parameter Optimization Useful (1)

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This process compares two 10x10fold cross-validations with linear SVM for classification. One use the heuristic parameter choice C=1/avg(K(x,x)) and the other uses an internal 5fold cross-validation to tune the parameter C. Afterwards both performance values are compared via ANOVA and T-test to check whether there is a significant difference between both performance values. The behaviour of the optimized 10x10 XV is similar to that of the experiment 10x10fold_XV_with_optimizedSVM_classificat...

Created: 2010-10-28 | Last updated: 2010-10-28

10x10fold_XV_with_optimizedSVM_classification (1)

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This process performs 10 round of 10fold cross-validation for classification with a linear SVM. In each traning-phase the parameters C of the linear SVM is tuned by a 5fold cross-validation. The repetions are useful for estimating the real performance on a small sample high variance data set, e.g. microarray data.

Created: 2010-10-28