Workflows

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

Blastn-ClustalW (1)

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Created: 2010-10-27 | Last updated: 2010-10-27

Credits: Kalpana

Polygon buffer - Using pyWPS (1)

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Basic example on how to integrate a Web Processing Service (WPS) using  PyWPS's WSDL/SOAP The workflow will accept a GML file with featureCollection where polyon is described using gml:coordinate element structure. This GMl is easely generated with GDAL. The coodinate structure will be converted to WKT and used to create a polygon using shapely, the output will be a buffer polygon with a defined width. Output polygon will replace the orginal polygon and the existing XML will be return...

Created: 2010-10-26 | Last updated: 2010-10-26

Credits: Jorgejesus

Concatenate Examples (1)

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This process I'm using for preprocessing is concatenating the values of att2 for all the same values of att1 in att3. ps: Thanks to Matthias for his help.

Created: 2010-10-26 | Last updated: 2010-10-26

X-Validation with One-Class SVM (1)

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With this example process, I intend to show how one might validate predictions done with a one class classifier. RapidMiner includes the One-Class SVM (part of libsvm) as introduced by Schoelkopf. I'm very interested in feedback concerning problems with or errors in this experiment. Note that the data set (Sonar) is just a toy data set chosen for demonstration - learning a one class classifier on it won't give you any good results! DESCRIPTION The basic idea is to partition the data set...

Created: 2010-10-20 | Last updated: 2010-10-20

Find best feature selection method. (1)

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This processes searches for the best method for feature selection and the best feature subset size. Inside a parameter loop the number of selected features and the feature selection methods are evaluated with a 10fold cross-validation. The Feature Selection Extension ( https://sourceforge.net/projects/rm-featselext ) is required. BUGFIX: Please note that the plugin downloaded before 5th November contains a bug. Due to a bug in RM the TopK-operator sorted the features in the wrong direction. ...

Created: 2010-10-19 | Last updated: 2010-12-10

Recursive Feature Elimination with fully o... (1)

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The Process shows how you can use the RecursiveFeatureElimination-Operator of the Feature Selection Extension ( https://sourceforge.net/projects/rm-featselext) to select relevant features from a highdimensional dataset.

Created: 2010-10-19 | Last updated: 2010-12-10

Automatical Disabling / Enabling of Operat... (1)

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This meta process shows another possibility for automatically optimizing the process layout. The operator "OperatorEnabler" can be used to enable or disable one of its children. Together with one of the parameter optimization operators this can be used to check which operators should be used for optimal results. This is especially useful in order to determine which preprocessing operators should be used for a particular data set - learner combination or if you want to automatically test diffe...

Created: 2010-10-13

test P-GRADE wf (1)

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 This workflow serves only testing purposes.

Created: 2010-10-12 | Last updated: 2010-10-12

Credits: Pgtest

BioXSD example workflow (1)

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An attempt to implement in the BioXSD workflow described by Kalas et al., (2010) Bioinformatics 26:i540-6. The workflow only calls one BioXSD web service (BLAST) since the second service (ClustalW) in the example workflow is currently down :(

Created: 2010-10-12 | Last updated: 2010-10-12

Credits: Peter Li

Extended Operations for Nominal Values (1)

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This process shows examples for the extended operations for nominal values coming with one of the next RapidMiner updates (5.0.011 or 5.1.000). The operations are performed with the operator "Generate Attributes" and can be used directly within the expressions for the new attributes. The supported functions include Number to String [str(x)], String to Number [parse(text)], Substring [cut(text, start, length)], Concatenation [concat(text1, text2, text3...)], Replace [replace(text, what, by)],...

Created: 2010-10-05

DNA Shuffling Template - part 1: DNaseI di... (1)

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From Cameron Neylon's Bio-Blog a template for recording the data from a DNA shuffling experiment

Created: 2010-10-04 | Last updated: 2010-10-08

Credits: http://thebluerhino.myopenid.com/

Blastn-ClustalW (1)

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Created: 2010-09-29

Credits: Kalpana

Maptube mapper (2)

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Takes a URL of some spatially-aggregated data and a field/column name to map and generates a MapTube url to an online map of the data.

Created: 2010-09-22 | Last updated: 2011-01-10

Credits: Nick Malleson

Sff2Fasta_Blast_Blat_ParseBlast (1)

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Blast and Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/  

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga

Sff2Fasta_Blat (1)

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Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database http://www.bioinformaticslaboratory.nl/  

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga

Population projection transport simulation (1)

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Neiss Transport Sim Demo. Runs a population reconstruction model (PRM) from census data, then projects the simulation through time. Also runs a transport simulation before and after the projection.

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Nick Malleson

Sff2Fasta_Blast_ParseBlast (1)

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Blast Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/      

Created: 2010-09-22 | Last updated: 2010-09-22

Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga

RCOMM Challenge 3: Fibonacci Numbers (Inte... (1)

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At the RComm 2010 (www.rcomm2010.org), an unusual competition was held. Titled "Who Wants to Be a Data Miner", three challenges were issued to the participants of the conference. In all challenges, participants had to design RapidMiner processes as quickly as possible. This is the original solution I had in mind for Challenge 2: "Fibonacci Numbers". It defines a macro n, recurses by applying itself using an "Embed Process" operator on n-1 and n-2, appends the results (so the length is F(n-1)...

Created: 2010-09-17 | Last updated: 2010-09-17

RCOMM Challenge 3: Fibonacci Numbers (Impr... (1)

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At the RComm 2010 (www.rcomm2010.org), an unusual competition was held. Titled "Who Wants to Be a Data Miner", three challenges were issued to the participants of the conference. In all challenges, participants had to design RapidMiner processes as quickly as possible. This is the winning process of Challenge 2: "Fibonacci Numbers" by Matko Bošnjak. This was the task: The n-th Fibonacci number is F(n)=F(n-1)+F(n-2), and F(0)=0, F(1)=1. Create a process that creates an example set with F(n)...

Created: 2010-09-17 | Last updated: 2010-09-17

RCOMM Challenge 2: Broken Iris (1)

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At the RComm 2010 (www.rcomm2010.org), an unusual competition was held. Titled "Who Wants to Be a Data Miner", three challenges were issued to the participants of the conference. In all challenges, participants had to design RapidMiner processes as quickly as possible. This is the winning process of Challenge 2: "Broken Iris" by Nico Piatkowski. This was the task: You are given a decision tree model (M) designed on the well-known Iris data set and unlabelled data (U) on which the model is t...

Created: 2010-09-17

RCOMM Challenge 2: Broken Iris (Preparation) (1)

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This workflow creates the input for the RCOMM 2010 Challenge 2. The solution and description are in workflow "RCOMM Challenge 2: Broken Iris"

Created: 2010-09-17

RCOMM Challenge 1: 99 bottles of beer (1)

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At the RComm 2010 (www.rcomm2010.org), an unusual competition was held. Titled "Who Wants to Be a Data Miner", three challenges were issued to the participants of the conference. In all challenges, participants had to design RapidMiner processes as quickly as possible. This is the winning process of Challenge 1: "99 bottles of beer" by Sebastian Land. This was the task: Design a process that produces an example set the rows of which form the lyrics of the well-known song "99 bottles of beer...

Created: 2010-09-17

BowtieToPileup (1)

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This example workflow aligns short sequencing reads to a reference genome using Bowtie and generates a SAMtools pileup file. By analysing an actual data set (SNP detection in N. vitripennis) and translating this analysis pipeline into a Taverna workflow, I was able to come up with an easy way of using Taverna for such analysis. I created a Java API (with my limited Java experience) that wraps the command line programs used in the analysis pipeline: Bowtie and some of the SAMtools. Instead of ...

Created: 2010-09-16

From PDF to lemmatized text (1)

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This workflow uses the web service stationed in JSI (IJS Slovenia), which is based on Matjaž Juršič's LemmaGen - lemmatization engine. The workflow accepts a PDF file as an input an uses James Eales's wrokflows to preprocess the data. The workflow interactively asks the user of which language is the text, since the lemmatization process is language based. The output is a string in Taverna Workbench.

Created: 2010-09-16 | Last updated: 2012-01-18

Credits: Netr James Eales

Attributions: PDF to plain text Clean plain text

retrive dpas data for all ics instruments ... (1)

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This workflow demonstrates the standard query where events for a period of time are requested from the HEC service, available instruments for this time come from the ICS and data only for the times of the events are requested from the DPAS. In this version data from only 3 random events (out of the HEC list) will be requested from the DPAS.

Created: 2010-09-14 | Last updated: 2010-09-14

Credits: Anja Le Blanc

Attributions: retrive dpas data for all ics instruments for HEC event data

retrive dpas data for all ics instruments ... (1)

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This workflow demonstrates the standard query there events for a period of time are requested from the HEC service, available instruments for this time come from the ICS and data only for the times of the events are requested from the DPAS.

Created: 2010-09-14 | Last updated: 2010-09-14

Credits: Anja Le Blanc

Attributions: Extracting data from VOTable format by using XPath query Retrieve all data for all instruments for a given periode of time

Generate percentages from absolute values (1)

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This process demonstrates how to calculate the percentages of absolute values of one data record. The process first creates an aggregation attribute SumAll and then loops over the absolute value attributes and creates a new relative attributes. Tags: relative, absolute, values, percentage, loop attributes, generate aggregation

Created: 2010-09-14 | Last updated: 2010-09-14

Example workflow for REST and XPath activi... (1)

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Note that this workflow depends upon the REST and XPath plugins. This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch d...

Created: 2010-09-13 | Last updated: 2010-09-13

Credits: Sergejs Aleksejevs

Principle Component Analysis (PCA) over mi... (1)

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Principle Component Analysis (PCA) over microarray data. Data is uploaded through caGrid transfer ultility.

Created: 2010-09-10 | Last updated: 2010-09-10

Credits: Wei Tan

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2010-09-06

Credits: George

Attributions: Multiple Choice Quiz

11111 (1)

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Reads collections of text from a set of directories, assigning each directory to a class (as specified by parameter text_directories), and transforms them into a TF-IDF or other word vector. Finally, an SVM is applied to model the input texts.

Created: 2010-09-04

222 (1)

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This process shows how several different classifiers could be graphically compared by means of multiple ROC curves.

Created: 2010-09-04