A step by step guide on how to build workflows in Taverna. Biology oriented but should be ok with other background with a 'tiny' Biology knowledge. I welcome your comments and suggestions.

File type: PowerPoint presentation

Comments: 0 | Viewed: 205 times | Downloaded: 286 times

Tags:

Workflow

Taverna 2

Uploader

Alan Williams

Get weather information (1)

Download

Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure.

Created: 2014-10-03

Credits: Alan Williams Franck Tanoh

Attributions: Get weather information

Workflow

Taverna 2

Uploader

tpacurtis

Fetch today's Johnny Wander Comic (1)

Download

Use the local java plugins and some filtering operations to fetch the comic strip image from http://www.johnnywander.com/ Based on the FetchDailyDilbert workflow & Fetch today's XKDC comic

Created: 2011-09-12 | Last updated: 2011-09-12

Credits: tpacurtis Franck Tanoh

Attributions: Fetch today's xkcd comic

Workflow

Taverna 2

Uploader

Alan Williams

GBSeq test (1)

Download

This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Franck Tanoh

Attributions: GBSeq test

Workflow

Taverna 2

Uploader

Alan Williams

Retrieve sequence in EMBL format (1)

Download

This workflow retrieves a sequence associated with its features in embl format

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Franck Tanoh

Attributions: Retrieve sequence in EMBL format

Workflow

Taverna 2

Uploader

Alan Williams

GBSeq test (1)

Download

This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Workflow

Taverna 2

Uploader

Alan Williams

Retrieve sequence in EMBL format (1)

Download

This workflow retrieves a sequence associated with its features in embl format

Created: 2010-07-04 | Last updated: 2010-07-04

Credits: Franck Tanoh

Workflow

Taverna 2

Uploader

Franck Tanoh

EntrezGeneId_to_GOFunction (1)

Download

The workflow takes a list of Entrez gene ids and returns the corresponding GO function definitions. Example value: 1306 486 4712 108 9912 7639 23786

Created: 2010-05-13 | Last updated: 2010-05-13

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

get_enzymes_by_gene (1)

Download

Retrieve all the EC numbers which are assigned to a given gene Input example: eco:b0002

Created: 2008-10-08

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

get_enzymes_by_compound (1)

Download

Retrieve all enzymes which have a link to a given compound id Input example: cpd:C00345

Created: 2008-10-08

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

get_elements_by_pathway (1)

Download

Retrieve all objects on specified pathway get_elements_by_pathway Input example: path:bsu00010

Created: 2008-10-08

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

get_element_relations_by_pathway (1)

Download

Retrieve all objects and relations on specified pathway Input example: path:bsu00010

Created: 2008-10-08

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

get_drugs_by_pathways (1)

Download

Retrieves all drugs on the specified pathway. input example: path:map07025 ; path:eco00020

Created: 2008-10-07

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

get_compounds_by_reaction (1)

Download

Retrieve all compounds which have a link to a given reaction_id Example on input: rn:R00100

Created: 2008-10-07

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

get_compounds_by_pathway (1)

Download

Retrieves all compounds on the specified pathway Example of input: path:eco00020

Created: 2008-10-07

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

get_best_best_neighbors_by_gene (1)

Download

Search the best-best neighbor of a gene in all organisms. Example of input: gene_id: eco:b0002 offset: 1 limit: 10

Created: 2008-10-02

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

color_pathway_by_objects (1)

Download

Color given objects on a pathway map with specified colors and return the URL of the colored image. In the KEGG pathway maps, a gene or enzyme is represented by a rectangle and a compound is shown as a small circle. Example of input: pathway_id: path:eco00260 object_list: (to add as list) eco:b0514 eco:b2913 fg_color: (to add as list) blue orange bg_color: (to add as list) red orange

Created: 2008-10-01 | Last updated: 2008-10-01

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

color_pathway_by_elements (2)

Download

Color the objects (rectangles and circles on a pathway map) corresponding to the given 'element_id_list' with the specified colors and return the URL of the colored image. Example of inputs: pathway_id: path:bsu00010 element_list: (to add as list) 78 79 fg_color_list:(to add as list) red blue bg_color_list: (to add as list) green yellow

Created: 2008-09-30 | Last updated: 2008-10-01

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

btit (1)

Download

Retrieve definitions of given database entries available on GenomeNet database. Example of input: hsa:1798 mmu:13478

Created: 2008-09-30 | Last updated: 2008-09-30

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

binfo (1)

Download

Show the version information of a specificied database. Example of input: "gb" for Genbank database "sp" for swissprot database "emb" for embl database

Created: 2008-09-30 | Last updated: 2008-09-30

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

bget (1)

Download

Retrieve database entries specified by a list of entry_id. Number of entry_id retrieves at a time is restricted up to 100 Example of input: eco:b0002 hin:tRNA-Cys-1

Created: 2008-09-29

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

bfind (1)

Download

Used for searching entries by keywords. User needs to specify a database from those which are supported by DBGET system before keywords. List of databases available at : http://www.genome.jp/dbget/ Example of input parameter: gb E-cadherin human

Created: 2008-09-29 | Last updated: 2008-09-29

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

bconv (1)

Download

Converts external IDs to KEGG IDs.External database: NCBI GI, NCBI GeneID, GenBank , UniGene , OMIM. Database prefix: ncbi-gi:, ncbi-geneid:, genbank: ,unigene: , uniprot: , omim: Example of input parameter: ncbi-gi:10047090 ncbi-geneid:14751

Created: 2008-09-29 | Last updated: 2008-09-29

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

Retrieve_abstract_from_Medline (1)

Download

This workflow retrieves Medline Abstracts given PMIDs (PubMed id) You can use: 9879 as input example to test this workflow

Created: 2008-09-17 | Last updated: 2008-09-17

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

BLASTP with simplified results returned (1)

Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers.

Created: 2008-07-22 | Last updated: 2008-07-22

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

Get weather information (3)

Download

Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure. The default value Stian's home country.

Created: 2008-06-17 | Last updated: 2008-06-20

Credits: Franck Tanoh Stian Soiland-Reyes

Attributions: Get weather information Get cities by country name

Workflow

Taverna 1

Uploader

Franck Tanoh

getUPIForSequence workflow (2)

Given a sequence retrieve the UPI (UniProt Archive (UniParc)) identifier.

Created: 2008-06-06 | Last updated: 2008-06-06

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Alan Williams

GBSeq test (2)

Download

This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2008-03-05 | Last updated: 2008-03-31

Credits: Franck Tanoh

Workflow

Taverna 1

Uploader

Franck Tanoh

Get weather information (1)

Download

Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure. The default value is my home town. To find out any supported city run the 'Get cities by country name' workflow