All content

Discover_proteins_from_text (2)

• Download

This workflow discovers proteins from plain text. It is built around the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

Created: 2007-11-15 | Last updated: 2007-11-15

Credits: Marco Roos AID

Retrieve Protein Sequence and BLAST (1)

Retrieves a protein sequence in Fasta format from Genbank and then performs a BLAST on that sequence

Created: 2007-11-09 | Last updated: 2008-06-05

Credits: Katy Wolstencroft

Back translate a protein sequence into a d... (2)

• Download

This workflow back translates a protein sequence into a DNA sequence. Example input for this workflow is: MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSSNSG SRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNILSRVLA RSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLTNTENT ASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEARLKRKLIR LFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDYGDVLRAVE KAATRHSLGLPRQQLQLLAQDAFRDVGVRLQERRHLDLIYNFGCHLTDDYRPGVDPALSD PTLARRLRENRTLAM...

Created: 2007-10-03 | Last updated: 2009-12-03

View Download

Open Data: Bilateral Perisylvian Polymicrogyria

Created: 2010-11-16 16:20:43 | Last updated: 2011-09-23 10:55:08

7 items in this pack

Comments: 0 | Viewed: 285 times | Downloaded: 50 times

Compare genome, extract proteins which are... (1)

• Download

  Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast NCBI Gi to Kegg Pathways color_pathway_by_objects

Multiple Protein Alignment Profiling(1) (4)

• Download

Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools.

Created: 2010-01-13 | Last updated: 2010-11-17

Credits: Carol Lushbough Alan Williams

Attributions: A workflow version of the EMBOSS tutorial

BioMart and Emboss Analysis (T2) (1)

• Download

This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158   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. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...

Created: 2009-09-15

Credits: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

Get Kegg Gene information (2)

• Download

This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.   Example input for this workflow is given below (new line separated): mmu:13163 hsa:1616

Created: 2009-01-26 | Last updated: 2009-12-14

Credits: Paul Fisher

Workflow Pattern - Structured Loop (2)

• Download

This workflow is a GWorkflowDL representation of a structured loop that updates the variable "x" in each iteration. This workflow is equivalent to the following pseudo code: x:=0; for ( i:=0; i<=99; i++) { x:=x+i; } x_result:=x; Please remark that this demonstration workflow does not invoke any external services at all. The calculation is done only by using the GWorkflowDL's syntax and semantics.

Created: 2008-12-09

Credits: Andreas Hoheisel

View Download

Installing java certificates for services using SSL

Created: 2008-10-15 09:05:44 | Last updated: 2009-02-16 07:37:39

Credits: Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Java archive

Comments: 1 | Viewed: 1757 times | Downloaded: 1485 times

QSAR workflow to measure the time used for... (1)

• Download

This workflow loads molecules from a database. Each molecule goes through the atom typing, gets its explecite hydrogens and the detection of the hueckel aromaticity. After that different qsar properties will be calculated. The output of this workflow will be a qsar vector as a csv file and a file which contains the time needed to calculate each qsar property.

Created: 2008-08-29 | Last updated: 2008-08-29

Credits: Thomasku

Nucleotide_ORF_translation (1)

• Download

From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length. EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview).

Created: 2008-06-06

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

EBI_Phobius (2)

• Download

The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing.

Created: 2008-06-01 | Last updated: 2008-06-02

Credits: Hamish McWilliam

EBI_NCBI_BLAST_with_prompts (1)

• Download

Run a BLAST analysis using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be use...

Created: 2008-05-31 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Attributions: EBI_NCBI_BLAST

feat (3)

This is an attempt to implement the feat application from the fsl fMRI package www.fmrib.ox.ac.uk/fsl/fsl/whatsnew.html into a Scufl workflow. Details are still being polished but the general structure is here. The main problem that we have with such workflows concerns data provenance. Each of the services is typically iterated on hundreds of data sets and keeping track of the produced files is a pain.

Created: 2008-03-18 | Last updated: 2008-05-19

Credits: Glatard

myExperimentBeanshellCollection (2)

• Download

Public collection of generic Beanshells curated by the myExperimentBeanshellCollection group on myExperiment. Visit http://www.myexperiment.org for details and updates. To use this collection of beanshells in Taverna: Right click "Available Processors" in the "Design Perspective" Choose "Add new Workflow scavenger..." Provide the URL to this beanshell collection on www.myExperiment.org or if you downloaded this to your hard disk, provide a "file" URL to the absolute path of this file (O...

Created: 2008-03-06 | Last updated: 2008-03-25

Credits: myExperimentBeanshellCollection

Demonstration of configurable iteration (1)

• Download

This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2008-03-05 | Last updated: 2008-03-25

Credits: Tomoinn

Daily Dilbert (2)

• Download

Retrieves the Daily Dilbert image ....to start the day with

Created: 2007-10-03 | Last updated: 2008-03-06

ProteinSynonymsToQuery (2)

• Download

This workflow uses Martijn Schuemie's protein synonym service to produce synonyms and a new query string from the input query term. The service is limited to proteins, enzymes and genes. An input query that is a boolean string will be split and processed, but the boolean logic of the input query will be lost. Workflow URL: http://rdf.adaptivedisclosure.org/~marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml

Created: 2007-10-03 | Last updated: 2007-11-13

Credits: Marco Roos Martijn Schuemie AID

Dummy example of looping (3)

• Download

Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast. createJob creates a temporary file with the content "0". Filename retuirned as a "job ID". checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. (As no actual job is being run) getResults reads the file content, with...

Created: 2010-01-27 | Last updated: 2013-10-08

Credits: Stian Soiland-Reyes

Phylogeny Bootstrapped Algorithm (2)

• Download

Bootstrapped sequences algorithm reads in a data set, and produces multiple data sets from it by bootstrap resampling. http://pro.genomics.purdue.edu/cgi-bin/emboss/help/fseqboot

Created: 2010-01-13 | Last updated: 2010-11-17

Credits: Carol Lushbough

Pathways and Gene annotations for QTL region (2)

• Download

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the Pig, Sus scrofa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...

Created: 2009-11-20 | Last updated: 2009-11-20

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

SigWin-detector Config-Basic (2)

• Download

Detects significant windows in a sequence. Input: A space-delimited file with (at least) one column containing the input sequence E= {E1, E2, …, EN}. A two-line header should precede the data. Input file example. Output: (1) A file containing the detected significant windows for each label. Each data row represents a stretch of consecutive significant windows. Column 1 gives the window size and columns 2 and 3 give the first and last significant windows in the stretch. Output file e...

Created: 2009-10-09 | Last updated: 2010-04-23

Credits: Adambel

DNA sequence analysis pilot (1)

• Download

  http://amc-app1.amc.sara.nl/twiki/bin/view/         Workflow-based  DNA sequence analysis on the Dutch Life Science Grid, presented as Application Showcase at the NBIC Conference 2009, Lunteren, The Netherlands, 17 & 18 March 2009. http://www.biomedgrid.it/programme may 15th 2009. Hands on workflow: grid-enabled medical imaging  (Johan Montagnat – Tristan Glatard)  

Created: 2009-07-10 | Last updated: 2009-11-30

Credits: Angela Luijf Glatard

Using CQL to query protein sequence data (1)

• Download

To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600

Created: 2009-05-07

Credits: Stian Soiland-Reyes

Attributions: Using CQL to query protein sequence data

DOI Record Generator (1)

• Download

This workflow generates DOI record files for deposit, using data set metadata for the FLOSSmole project. It reads in an input file generated from a SQL query from an eprints database, and transforms the parts of the source file as necessary to create a comprehensive DOI deposit record. It also generates DOIs for the data sets. These metadata are inserted into an XML record template (based on the std-doi.xsd schema) and the individual resources are aggregated into a single file.

Created: 2009-04-29

Credits: Andrea Wiggins

Attributions: Data Set Metadata Generator

Run XMPP cloud services. (2)

• Download

Basic workflow indicating how a XMPP service can be called with XML input and output. Source code for the activity is available from: github.com/egonw/xws-taverna/tree/master That page explains you how to install the plugin you must install on top of Taverna 2.0. The workflow will not work otherwise.

Created: 2009-04-25 | Last updated: 2010-03-22

Credits: Egon Willighagen

Workflow Pattern - Structured Discriminato... (1)

• Download

This workflow is an alternative GWorkflowDL representation of a structured discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored for the same data group. Other tokens on the place "begin" can be processed recurrently if they belong to another data group. Please note that the transitions "C" and "ignore" have different priorities (not shown in the graph) that make the net determ...

Created: 2009-01-20

Credits: Andreas Hoheisel

Workflow Pattern - Structured Loop (C) (2)

• Download

This workflow is a GWorkflowDL representation of a structured loop that counts from 0 to 99.   This workflow is equivalent to the following pseudo code: for ( i:=0; i Please remark that this demonstration workflow does not invoke any external services at all.

Created: 2008-12-09

Credits: Andreas Hoheisel

Attributions: Workflow Pattern - Structured Loop (B)

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: 2008-11-14

Credits: Thomaskelder

Attributions: CloneItemsInList

AppendToFile (2)

• Download

Processor to add content to a (existing)  file. The content is added to the end of the file. The inputs: Filename: the file name of a file, if the file does not exists, a new file is added Content: the string to append NewLine [default = true]: if true, a newline is added to the end of the line (useful if you want to add a record each time)   The processor supports Multi-Threading since version 2.

Created: 2008-11-11 | Last updated: 2008-11-11

Credits: Wassinki

Blat against ENSEMBLE Danio_rerio_Genome (1)

• Download

The blat workflow invokes the blat services provided at www.bioinformatics.nl (author Pieter Neerincx). As input, it takes a database name (for example, Danio_rerio_Genome for Zebra Fish) and one or more sequences in Fasta format. The output will be a tab separated output of the blat. An eValue string constant is added to filter on the e-Value. Note, the e-Value is not exactly the same as the blast e-Value. To run this workflow, a certificate to access www.bioinformatics.nl needs to instal...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: Wassinki

View Download Add New Item

WikiPathways workflows

Created: 2008-09-16 11:43:57 | Last updated: 2009-02-03 12:47:00

5 items in this pack

Comments: 0 | Viewed: 227 times | Downloaded: 54 times

Data Set Metadata Generator (1)

• Download

This workflow generates ePrints XML import files with data set metadata for the FLOSSmole project. It reads in an input file generated from a Notre Dame SourceForge dump SQL query and uses regular expressions to parse the filename for the data set's source repository, download URL, and basic description. It also translates the epoch date into a sql format suitable for import, and the file size from bytes into larger units, e.g. GB, MB, etc. These data are inserted into an XML eprint record te...

Created: 2008-08-19 | Last updated: 2008-08-19

Credits: Andrea Wiggins

Retrieve Protein Sequence (1)

• Download

Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

Created: 2008-07-30 | Last updated: 2009-12-03

Credits: Katy Wolstencroft

Fasta_string_to_fasta_list (1)

• Download

Split a string containing a set of sequences in fasta format into a list for fasta formated sequences.

Created: 2008-06-06

Credits: Hamish McWilliam

EBI_FASTA (1)

• Download

Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). Note: the WSFasta service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement FASTA services (REST or SOAP) should be used instead.  

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Fetch today's xkcd comic (1)

Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.  I just uploaded this example so I can play around with the myexperiment api.

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

Credits: Alan Williams

Attributions: Fetch today's xkcd comic

Unique tags (2)

• Download

This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".

Created: 2008-03-11 | Last updated: 2008-03-11

Credits: Don Cruickshank

Attributions: Viking boat

Fetch PDB flatfile from RCSB server (1)

• Download

Given aPDB identifier such as '1crn', this workflow fetches the PDB format flatfile from the RCSB

Created: 2008-01-25 | Last updated: 2008-03-05

Credits: Katy Wolstencroft

Retrieve SNPs from regions around known genes (1)

• Download

Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position)

Created: 2007-11-07

Example of a conditional execution workflow (2)

• Download

If the input is true the workflow returns the temperature in Celsius, if false the temperature in Fahrenheit is returned.

Created: 2007-10-03 | Last updated: 2008-01-27

BLASTP with simplified results returned (2)

• Download

This workflow Performs a blastp search on protein sequence, extracts sequence id within the blast report and retrives the corresponding seuqences.

Created: 2007-10-03 | Last updated: 2008-03-06

Parse UniProt text file (2)

• Download

This workflow performs a search through the SRS linking system to find the text files for a particular UniProt identifier. This UniProt text file is then parsed to extract a small list to summarise the file, primarily consisting of external identifiers. Example input for this workflow is: O35613

Created: 2007-10-03 | Last updated: 2009-12-03

Remove null values (2)

• Download

This workflow removes any null values from a list of strings

Created: 2007-10-03 | Last updated: 2007-11-13

DOI2PMID (2)

• Download

Converts Digital Object Identifiers into their corresponding PubMed identifiers, if they exist.

Created: 2007-10-03

NCBI Gi to Kegg Pathways (1)

• Download

User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image.

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Attributions: color_pathway_by_objects NCBI Gi to Kegg Pathways

find events in xray and radio (7)

• Download

instruments: hessiEC, phoenix2 attention: hessi name has changed!

Created: 2010-03-16 | Last updated: 2010-03-16

Credits: Anja Le Blanc