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

EDPS 6571 Week 1 Introduction (1)

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Week 1 Introduction

Created: 2018-04-25

EDPS 6751 Week 2 Problem Definition (1)

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Week 2: Problem Definition

Created: 2018-04-25

EDPS 6751 Week 3 Data Exploration (1)

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Week 3: Data Exploration

Created: 2018-04-25

List_CorrData (1)

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This test workflow demonstrates the ability to read a file.

Created: 2018-03-07

Credits: Divya Karade

Search Europe PMC and get ChEBI annotations (3)

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This workflow first conducts a search and downloads the PMIDs for all publications in PubMed and PMC that match a particular query using the Europe PMC Articles API. In a second phase, the workflow fetches the ChEBI annotations for all these publications using the Europe PMC Annotations API.

Created: 2018-02-09 | Last updated: 2018-02-12

Credits: Magnus Palmblad

demo-02 (1)

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Created: 2017-12-01

Credits: Barry Mitchell

demo-01 (1)

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this is a demo on how to upload a keplar file to myexperiment.org

Created: 2017-11-27

Credits: Barry Mitchell

zetasizer2excel (2)

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Arrrgh! The exported data file format for the Malvern Zetasizer is insane!Row1, x1,x2,x3,x4,....,y1,y2,y3,y4,....Row2, x1,x2,x3,x4,....,y1,y2,y3,y4,....Row3, x1,x2,x3,x4,....,y1,y2,y3,y4,....This workflow imports the txt file, takes each row and reformats as table with 3 columns: Size, Intensity, Volume. Then exports the data for each row to a new tab in Excel. Or you can just use KNIME to plot and prepare reports (to do).The TableRow2Variable node allows you to name the tabs in Excel from a ...

Created: 2017-11-20 | Last updated: 2017-11-20

Credits: sauberns

Hello World in CWL (1)

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Puts a message into a file using echo

Created: 2017-11-03

Credits: Stian Soiland-Reyes

Predador Presa v1 (1)

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Envia dois textos e três parâmetros numéricos para um web service, e recebe um texto como saída. O web service implementa um modelo de predador-presa.

Created: 2017-10-30 | Last updated: 2017-10-30

Credits: Johnathan Melo Neto

Tratamento de erro para WSDL (1)

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Verifica se web service está ativo antes de propriamente executá-lo, como forma de tratamento de erro, enviando mensagem de alerta caso erro ocorra.

Created: 2017-10-30

Credits: Johnathan Melo Neto

Variant Annotation with VEP (Variant Effec... (1)

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Here, from a list of g.vcf files, we execute GenotypeGVCFs command line GenotypeGVCFs perform joint genotyping on gVCF files produced by HaplotypeCaller Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Created: 2017-10-19

Credits: alabarga

RetroPath2.0-Mods-isomer-transformation-queue (2)

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The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. It is a modified version of "RetroPath2.0-Mods-isomer-transformation". It illustrates how to introduce a FIFO data structure for the source set and use it for iteratively firing rules on small chunks of structures. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.4.1 of Kni...

Created: 2017-10-12 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data RetroPath2.0-Mods-isomer-transformation

WSDL Calculator (1)

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Utiliza uma calculadora com métodos disponíveis via WSDL para somar dois números.

Created: 2017-10-10

Credits: Johnathan Melo Neto

8_nested_workflows (1)

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8_nested_workflows

Created: 2017-09-11

Credits: Kasikrit Damkliang

H1-2-H4-SLEEPDEMO (1)

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H1-2-H4-SLEEPDEMO

Created: 2017-09-11

Credits: Kasikrit Damkliang

QSAR-model-aminoglycosides (2)

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The workflow build a QSAR model with LOO cross-validation for antibacterial activities of aminoglycosides structures using RDKit fingerprints and random forest. See [1] for details. Antibacterial activities were compiled from Setny et al, JCIM, 2009. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCo...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

RetroPath2.0-Mods-iQSAR (2)

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The workflow allows one to search chemical structures in the chemical space optimizing biological activites. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

QSAR-model-Tg-prediction (2)

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The workflow (i) build a QSAR model for Tg prediction with LOO cross-validation and (ii) predict the Tg for enumerated isomers. See [1] for details. Tg values were compiled from Brown et al, JCIM, 2006. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. T...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

RetroPath2.0-Mods-isomer-transformation (2)

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The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licen...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

RetroPath2.0-Mods-isomer-augmentation (2)

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The workflow allows one to enumerate isomers using the isomer augmentation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/.Koch M, D...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

Scaffolds_trends_workflow_2 (1)

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Second part of the workflow for paper "The rise and fall of a scaffold: A trend analysis of scaffolds in the medicinal chemistry literature" by B. Zdrazil and R. GuhaIncludes grouping and filtering steps to retrieve the summary data needed for performing the scaffold trend, bioactivity, and liability analyses.

Created: 2017-06-22

Credits: Barbara Zdrazil

Scaffolds_trends_workflow_1 (1)

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First part of the workflow for paper "The rise and fall of a scaffold: A trend analysis of scaffolds in the medicinal chemistry literature" by B. Zdrazil and R. GuhaIncludes initial filtering steps, extraction of Murcko frameworks, inclusion of journal Impact Factors, and calculation of Z-Scores. The example of oxetane substructure search is also included.

Created: 2017-06-22 | Last updated: 2017-06-22

Credits: Barbara Zdrazil

Color auto balancing (1)

Color auto balancing of RGB image

Created: 2017-05-02

Credits: Christian S.

searchPublications_and_MapAffil (1)

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This is a workflow for spatiotemporal analysis of literature indexed in PubMed. The workflow takes an arbitrary Europe PMC search query, calls the Europe PMC Web service searchPublications and extracts the publication year and PubMed ID from the results. The first author affiliation is then geoparsed by the MapAffil Web server to get latitude and longitudes. The coordinates are then concatenated together with the publication year, to produce a single list of publication years, latitudes and ...

Created: 2017-04-19

Credits: Magnus Palmblad

profilePublications_over_time (1)

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This workflow takes a list of arbitrary Europe PMC search queries and generates the corresponding profiles of the number of matching publications per publication year.

Created: 2017-04-19

Credits: Magnus Palmblad

Quality Recognition Model (QRM) (1)

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Quality Recognition Model (QRM) is a SVM-based Machine Learning supervised classification model that assigns label to the evidentiary documents on the basis of rigorousness of the contents. It assigns the label Rigor if the document is of quality otherwise assigns the Non-Rigor. It uses two type of features: data and metadata. Data features include title and abstract while the metadata features include MeSH terms and publication type.

Created: 2017-03-11

A Montage workflow in DATAVIEW. (1)

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A sample workflow that implements the Montage workflow in DATAVIEW.

Created: 2017-02-22 | Last updated: 2017-02-22

Credits: Shiyong Lu

recommenderSystem (1)

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Complementary workflow for the modelBuild. It can read the trained model parameters in order to classify samples in another dataset.

Created: 2017-01-20 | Last updated: 2017-01-20

modelBuild (1)

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Using this workflow one can train a softmax regression model (a machine learning algorithm) and the learnt parameters are exported to files.

Created: 2017-01-20 | Last updated: 2017-01-20

dataExploration (1)

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This workflow allows the user to explore and process a dataset file.

Created: 2017-01-20 | Last updated: 2017-01-20

repoRead (1)

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Workflow created to perform a search over the Harvard Dataverse. It can also download datasets linked files.

Created: 2017-01-20 | Last updated: 2017-01-20

SNPs@PSU (1)

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Example file test workflows.

Created: 2016-12-03 | Last updated: 2016-12-03

Credits: Sittisak Krotasuwan

phage display techniques (1)

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Created: 2016-11-22

Credits: Candy Swift

The automatic integrated workflow for Phyl... (2)

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update server address

Created: 2016-11-08 | Last updated: 2016-11-24

Credits: Kasikrit Damkliang

Interactive Service (4)

Interactive service is developed to provide an interface for human users to intervene the execution process of scientific workflow. This allows that certain steps in workflow can be operated by human users rather than an end-to-end automatic process. This is helpful for activities in the workflow that currently cannot be executed by automatic process, and for the inspection activities.The workflow here utilized a set of REST web services, HTML pages, authentication services, client ...

Created: 2016-10-26 | Last updated: 2016-10-26

Credits: Kewei Duan

Metavisitor: Spades test in Use Case 2-2 (1)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-10-10 | Last updated: 2016-10-10

Metavisitor: Trinity test in Use Case 2-2 (1)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server 

Created: 2016-10-10 | Last updated: 2016-10-10

Metavisitor: Workflow for small RNA profil... (1)

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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence dataReadthedocMississippi Galaxy server

Created: 2016-10-10 | Last updated: 2016-10-10

RapidMiner: Use a Macro at Detect Outliers... (1)

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a reply to @paavopdf 's question on twitter "Anyone having an idea how I can use a macro at "Detect Outliers" for the no. outliers in @RapidMiner? #rapidminer #DataScience"

Created: 2016-10-03

VCaP RNA-Seq Fusion gene detection with ST... (1)

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The end-to-end workflow starts by obtaining paired-end RNA-Seq data of the VCaP cell line via EGA. Galaxy determines the file type automatically with its built-in format detection system. The reads will be clipped before an alignment with STAR and STAR produces several output files that can be used for different analysis. The last tool is STAR-Fusion which was able to confirm the TMPRSS2-ERG fusion gene. 

Created: 2016-08-31 | Last updated: 2016-08-31

Credits: Y. Hoogstrate

vir-representative (1)

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Retrieve from NCBI and reduce redundancy in the viral database.

Created: 2016-08-09 | Last updated: 2016-08-09

Credits: Juliana Pegoraro

Test (1)

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Test

Created: 2016-08-02

Credits: Sue Tairaku

CARACTERÍSTICAS GEOQUÍMICAS DE LOS SEDIMEN... (1)

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Esta investigación tuvo como objetivo, evaluar algunos parámetros geoquímicos de los sedimentos superficiales de la laguna costera La Restinga, ubicada en la Isla de Margarita, estado Nueva Esparta, Venezuela. Utilizando metodología clásica para estudios geoquímicos, se analizó la composición granulométrica y textura del sedimento, porcentaje de carbono orgánico y materia orgánica total, así como, carbonato de...

Created: 2016-08-01

Credits: William Senior

ASPECTOS GEOQUÍMICOS Y AMBIENTALES DE LOS ... (1)

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Created: 2016-08-01 | Last updated: 2016-08-01

Credits: William Senior

TRPV1 Bioactivity from ChEMBLdb13 and ChEM... (1)

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This workflow allows to extract bioactivity data stored in ChEMBLdb for human TRPV1. Ensure you have installed Chembl and RDKit extensions to run the workflow.

Created: 2016-07-27 | Last updated: 2016-07-27

Credits: Daria Goldmann

KNIME workflow without hERG labels include... (1)

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KNIME workflow used to retrieve and process data from Open PHACTS for three targets of interest (hSERT, hDAT, hERG). Further, Murcko scaffolds are computed and selectivity trends towards hSERT and hDAT can be studied. Cutt off's for separating actives/inactives are tailored to the specific target and endpoint.Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community Contributions (2....

Created: 2016-07-20 | Last updated: 2016-07-20

Credits: Barbara Zdrazil Open PHACTS

KNIME workflow with hERG labels included f... (1)

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KNIME workflow used to retrieve and process data from Open PHACTS for three targets of interest (hSERT, hDAT, hERG). Further, Murcko scaffolds are computed and selectivity trends towards hSERT and hDAT can be studied. Compounds/scaffold series are flagged by their ability to also inhibit hERG.Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community Contributions (2.11)': EMBL-EBI No...

Created: 2016-07-20 | Last updated: 2016-07-20

Credits: Open PHACTS

An example BRAIN api call (1)

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An example brain API call.Note: This workflow require RServe library. Please refer to this link for the instructions to install RServer    

Created: 2016-07-11 | Last updated: 2016-07-11

Credits: Rajireturn

KEGG:Get PW for met (1)

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The purpose of the workflow is to retrieve all the pathways that the input metabolite(s) participates in.

Created: 2016-06-21

Credits: Kristina Hettne Harish Dharuri

Attributions: KEGG:Pathway Scheme