Workflows

Building a knowledge base for data mining ... (7)

• Download

Scientific workflow for creating the knowledge base. 

Created: 2013-10-03 | Last updated: 2018-09-20

Credits: respinosa

Attributions: Measuring data quality criteria in arff files Data Mining Algorithms

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

DataBiNS with Kegg ID (3)

• Download

Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene

Created: 2009-07-09 | Last updated: 2010-11-22

Credits: Mark Wilkinson Fong Chun Chan

A workflow version of the EMBOSS tutorial (1)

• Download

Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: A workflow version of the EMBOSS tutorial

Fetch today's xkcd comic (1)

• Download

Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Fetch today's xkcd comic

Biomart and EMBOSS analysis (1)

• Download

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: BiomartAndEMBOSSAnalysis

EBI InterproScan T2 (1)

• Download

This T2 version of the Interpro scan workflow is an example of the while loop in action. This is used to poll the async EBI service for the result (busy waiting)

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

KEGG Gene IDs to KEGG Pathways (1)

• Download

this is a simplified version of Paul's workflow (linked?) that is designed to be provenance-friendly

Created: 2009-06-04 | Last updated: 2010-01-07

Credits: Paolo

Attributions: Pathways and Gene annotations for QTL region

Download pathways for external references ... (2)

• Download

Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format.

Created: 2009-02-03

Credits: Thomaskelder