Workflows

Fail if true - false value (1)

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The fail if true service executes without an exception if given the value 'false'.

Created: 2008-09-27

Credits: Alan Williams

Fail if false - non false value (1)

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The fail if true service executes without an exception if given a non-false value such as 'fred'.

Created: 2008-09-27

Credits: Alan Williams

Fail if false - true value (1)

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The fail if true service executes without an exception if given the value 'true'.

Created: 2008-09-27

Credits: Alan Williams

Create lots of strings (1)

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The create lots of strings service returns a list containing a large number of strings.

Created: 2008-09-27 | Last updated: 2008-09-27

Credits: Alan Williams

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: 2008-09-27

Credits: Alan Williams

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: 2008-09-27

Credits: Alan Williams

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: 2008-09-27

Credits: Alan Williams

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: 2008-09-27

Credits: Alan Williams

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: 2008-09-27

Credits: Alan Williams

Choose - single element list (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a' and outputs the list ['a']. The choose service displays a dialog with 'Some title' and 'Some message'. The user is only able to choose the value 'a'. When the user presses OK 'a' is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Choose - title and message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with 'Some title' and with 'Some message'. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Choose - title parameter (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with 'Some title' but no message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Choose - no title or message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The choose service displays a dialog with no title or message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Byte[] 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[]_to_string service.

Created: 2008-09-27

Credits: Alan Williams

Byte[] 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[]_to_string service.

Created: 2008-09-27

Credits: Alan Williams

Ask - title and message parameters (1)

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The ask service displays a prompt with 'Some title' and the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Ask - just message parameter (1)

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The ask service displays a prompt with no title but with the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Ask - just title parameter (1)

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The ask service displays a prompt with the title 'Some title' but no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Ask - no parameters (1)

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The ask service displays a prompt with no title and no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

linking3.xml (1)

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This workflow links between a specified EMBL accesion number to corresponding identifiers in the MEDLINE database.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

metabolic.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_ontology_diagram.xml (1)

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This workflow builds up a subgraph of the Gene Ontology (http://www.geneontology.org) to show the context for a supplied term or terms. It shows this context by colouring all ancestors of the term, all children and all siblings. By default, ancestors of the supplied term or terms are coloured orange, siblings purple and direct children teal. Other terms appear in the default wheat colour.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

BlastComparer.xml (1)

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Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

interpro_url.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Example of an alternate processor (1)

Trivial workflow which will initially fail, retry twice then fall over to the alternative specified for the FailingThing process.

Created: 2008-05-28

Credits: Jfogel

Mitochondrial genome assembly _V2 (1)

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Created: 2021-12-14 | Last updated: 2021-12-14

Credits: Yash Munnalal Gupta

Recetas Saludables (1)

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Diagrama de Flujo de recetas de comidas saludables

Created: 2021-09-06 | Last updated: 2021-09-06

Credits: Karen

Random Forest based Feature Weightage (1)

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Features can be assigned weightage through the random forest model. In this regard, RapidMiner's Auto Model comes quite handy. Divide the original data into training and testing datasets before applying the workflow to it.  

Created: 2020-06-30 | Last updated: 2020-06-30

Credits: Imran Ali Syed

Gradient Boosting Trees based Feature Weig... (1)

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Features can be assigned weightage through the gradient boosting trees model. In this regard, RapidMiner's Auto Model comes quite handy. Divide the original data into training and testing datasets before applying the workflow to it. 

Created: 2020-06-30 | Last updated: 2020-06-30

Credits: Imran Ali Syed

CHART based Feature Weightage (1)

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Features can be assigned weightage through the decision tree model. In this regard, RapidMiner's Auto Model comes quite handy. Divide the original data into training and testing datasets before applying the workflow to it. 

Created: 2020-06-30 | Last updated: 2020-06-30

Credits: Imran Ali Syed

cutadapt+BWA-MEM-mis1-i2,2-gapex2,2+filter... (1)

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This workflow is designed to genotype trinucleotide repeats from sequencing reads that span the repeat and its flanksDetailed description as follows:1. Input fastq sequencing reads files (Galaxy tool: Input dataset)Input files for the workflow are single-end MiSeq reads (R1 produced using the protocol from Ciosi et al. 2018) or PacBio reads of insert (ROI) in fastq files format.2. Removing Illumina sequencing adaptor sequence in 3’ of the MiSeq reads (Galaxy tool: Cutadapt 1.16)Cutadapt...

Created: 2020-06-01 | Last updated: 2020-06-01

deneme (1)

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Created: 2020-04-27

Credits: mevlüt Aydemir BAIBU

Deriving factual information from WHO COVI... (1)

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 WHO has posted a CSV that's frequently updated with COVID abstracts. A simple PubMed search reveals thousands of abstracts too. So here's an NLP pipeline to mine these and extract meaningful sentences/facts using Stanford Open Information Extractor and Biological entity tagging. #knime #naturallanguageprocessing #textanalytics #textmining #covid19 #nlp #datascience #WHO 

Created: 2020-04-12

Credits: Insilicoconsulting

Antiviral activity multiclass Predictor (1)

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A simple multi-class antiviral activity predictor based on expanded Pubchem fingerprints and random forest algorithm. Seems to work well to perform quick screens for antiviral molecules.Download training data from CTD (http://ctdbase.org/downloads/) or  use this preprocessed version https://www.myexperiment.org/files/2285.html. Write to me at rajeev.gangal@gmail.com regarding any queries.I make no claim that the predictive model is accurate for clinical hypotheses or that it will find mo...

Created: 2020-03-23 | Last updated: 2020-03-25

Credits: Insilicoconsulting

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS proteomics Analysis of human medulloblastoma cell line (DAOY cell line)15 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment20 pH8 fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS proteomics Analysis of human medulloblastoma cell line (DAOY cell line)5 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment20 pH8 fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS phosphoproteomics Analysis of human medulloblastoma cell line (DAOY cell line)15 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment13 HILIC fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS phosphoproteomics Analysis of human medulloblastoma cell line (DAOY cell line)5 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment12 HILIC fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Untargeted metabolomics reveals molecular ... (1)

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Normal 0 false false false EN-US X-NONE AR-SA ...

Created: 2019-06-21

Credits: David_MTX

Integrative data mining of chemical compou... (1)

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This workflow downloads ligand data for hepatic Organic Anion Transporting Polypeptides (OATPs) from five different open sources (CHEMBL, Metrabase, USFC-FDA Transportal, IUPHAR, and Drugbank) in an semi-automatized fashion. This workflow can be adopted to any other ligand data showing an (in)activity against membrane transporter. If missing, structural file format is mapped via PubChem webservices. Pre-curated compounds are subjected to standardization procedure (Atkinson standardization scr...

Created: 2018-12-10 | Last updated: 2018-12-10

Credits: Alzbeta Tuerkova

Genetic Algorithms for BIOISOSTERIC Struct... (1)

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Genetic algorithm workflow to generate novel structures by recombination and mutation and that uses an ML model as a fitness function. Both the fitness function and the fingerprints modified in the model should be the same. ML model cannot have any descriptors other than given fingerprint.Reverse molecular mapping/generation is not part of this workflow and can be done by creating a large Structure-FP database.

Created: 2018-11-06

Credits: Insilicoconsulting

Substructure querying | R-group decomposit... (1)

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This workflow creates maximum common substructure (MCS) out of the provided structures and then substructure mining using MCS as a structural query is performed. Obtained hits are then subjected to R-group decomposition to explore their functional groups. Optionally, physicochemical descriptors for individual functional groups can be calculated.

Created: 2018-10-25

Credits: Alzbeta Tuerkova Barbara Zdrazil

Scaffold Analysis | Statistical analysis o... (1)

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This workflow performs an extraction and statistical analysis of Murcko scaffolds for compounds being active against (a) different target(s). Specifically, target-wise detection of Murcko Scaffolds in active versus inactive compounds, filtering steps by removing too generic scaffold (i.e., number of rings equals to one OR number of heteroatoms in a ring is zero or one), calculating the frequency of a particular scaffold which appears frequently in the active over inactive class, applying Fish...

Created: 2018-10-25

Credits: Alzbeta Tuerkova Barbara Zdrazil

Find concept-literature relationships and ... (1)

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This Bioclipse script (dev version) searches articles titles for the given concept and creates QuickStatements to create Wikidata statements that that article is about that concept.

Created: 2018-09-01

Credits: Egon Willighagen

Human MSH3 exon 1 variant genotyping (1)

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This workflow is designed to genotype 9 bp tandem repeat region in MSH3 exon 1 as well as flanking variants described in Flower and Lomeikaite et al. (2018). Detailed description as follows:1. Input files.Input files for the workflow are demultiplexed fastq files from MiSeq Illumina sequencing. 2. Read merging.To enable obtaining haplotype information, forward and reverse paired-end reads are merged using Pear with default settings. 3. Demultiplexing.Merged reads are demul...

Created: 2018-08-22 | Last updated: 2018-08-22

KNIME Workflow for RetroRules and Retropat... (3)

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Created: 2018-07-26 | Last updated: 2018-08-11

Credits: Pablo Carbonell

KNIME Workflow for RetroRules and Selenzyme (4)

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Created: 2018-07-24 | Last updated: 2018-08-11

Credits: Pablo Carbonell

EDPS 6751 Week 6 Decision Tree Classifier (1)

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Week 6: Decision Tree Classifier

Created: 2018-04-26

EDPS 6751 Week 5 Unsupervised Learning (1)

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Week 5: Unsupervised Learning

Created: 2018-04-26

EDPS 6751 Week 4 Data Preparation (1)

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Week 4: Data Preparation

Created: 2018-04-25