Workflows

Microarray CEL file to candidate pathways (2)

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This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Created: 2007-10-03

querySWS_minimalQuery (2)

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SRS by WS (SWS) is a set of Web Services allowing to retrieve database entries from libraries included in public SRS sites. The querySWS service implement a search on the basis of the database name (lib) and the term to be searched (query). It automatically identifies the best site to query. Additional parameters include in_fields (in which part of the record the terms are searched), out_fields (which information is returned) and site (the SRS site). This workflow is just a demonstration ...

Created: 2007-10-03

Fetch Dragon images from BioMoby v2 (2)

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demonstration to ISSGC07

Created: 2007-10-03

Python script for face and smile detection (1)

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Created: 2019-05-16 | Last updated: 2019-09-27

Credits: George Kargas

Integrated workflow for MSA, Similarity sc... (3)

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Integrated workflow for MSA, Similarity score estimation, and gaps trimming using Clustal Omega and web services at http://bioservices.sci.psu.ac.th/ We demonstrate the workflow using example fasta seqs.

Created: 2016-02-28 | Last updated: 2017-08-16

Credits: Kasikrit Damkliang

Explain concept scores (7)

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Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: Reinout van Schouwen

RDKit-pains-parallel (2)

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If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows RDKit-pains, and Indigo-pains.*** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries ****** This version contains Parallel processing nodes to take advantage of mutil-core processors ***Implementation of the PAINS filters[1] using the RDKit (3.0.0.201511131320) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. This workflow contains the S...

Created: 2011-10-13 | Last updated: 2015-12-01

Credits: sauberns

Attributions: RDKit-pains

EBI_NCBI_BLAST (4)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now wo...

Created: 2011-01-17 | Last updated: 2013-05-30

Credits: Katy Wolstencroft Hamish McWilliam

Attributions: EBI_NCBI_BLAST

caDSR Data service query in caGrid (3)

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This workflow is used as an example in this wiki article: https://wiki.cagrid.org/display/knowledgebase/How+to+Create+CaGrid+Workflow+Using+Taverna+2   Tested with Taverna 2.1.2 as of 6/10/2010

Created: 2010-05-25 | Last updated: 2010-06-11

Credits: Wei Tan

Support-Vector-Machine (SVM) based data cl... (2)

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Support-Vector-Machine based data classificationSupport-Vector-Machine based data classification using genePattern SVM service, the input should be in genePattern STATML format.

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: Wei Tan

G-language Genome Analysis Environment - S... (2)

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This workflow calculates the Student's T-test and Pearson/Spearman correlations. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew (by default, for keto bases, with window size of 1000) of a given genome sequence identifier. Here the genome sequence in Fasta format is downloaded through the Togo Web Service with RefSeq identifier. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew of a given genome sequence (for the entire genome, for only the coding sequences, for only the intergenic regions, and for only the third codon positions), as well as the GC content with sliding windows. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (2)

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This workflow calculates and graphs the GC skew of a given genome sequence. Use this as a template for using more than 100 analysis programs implemented in G-language Genome Analysis Environment, which can be used in a similar manner. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - G... (3)

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This workflow calculates and graphs the AT skew of a given genome sequence, using options of gcskew program. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05 | Last updated: 2011-01-09

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - B... (2)

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Given a numerical vector (array), this workflow calculates the maximum value (max) and its index (maxdex), minumum value (min) and its index (mindex), mean, sum, median, and standard deviation. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - B... (2)

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This workflow shows simple sequence manipulation functions of G-language GAE, such as random shuffling, obtaining a reverse complement, and translation of nucleotide sequences, and showing basic composition statistics for nucleotide and amino acid sequences. See http://www.g-language.org/ for more information about the G-language Genome Analysis Environment.

Created: 2010-04-05 | Last updated: 2010-04-05

Credits: cory (Kazuki Oshita)

G-language Genome Analysis Environment - B... (2)

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Given an identifier for genome sequence (by default, genome of Mycoplasma genitalium: refseq:NC_000908) or raw sequence data in FASTA format, this workflow calculates and graphs the following properties using the G-language Genome Analysis Environment: GC skew (gcskew), cumulative GC skew (gcskew_cumulative), GC skew of coding/intergenic/GC3 (genomicskew), GC content with sliding windows (gcwin), replication origin and terminus (find_ori_ter), codon usage table (codon_usage), the Codon Adapta...

Created: 2010-04-05 | Last updated: 2010-04-05

Credits: cory (Kazuki Oshita)

XSTAR (3)

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This is a simple workflow designed to run XSTAR with an user selected input. XSTAR is a computer program for calculating the physical conditions and emission spectra of photoionized gases. More information can be found here: - XSTAR home page: http://heasarc.nasa.gov/lheasoft/xstar/xstar.html - XSTAR on the Spinet client (Soaplab2): http://caoba.ivic.ve:8180/soaplab2-axis/

Created: 2010-04-02 | Last updated: 2011-02-27

Select items from list (1)

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This workflow pops up a window containing an input list of strings. The user is invited to select one or more strings for downstream processing.

Created: 2010-03-30

Credits: Peter Li

Copasi time simulation of SBML model (1)

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Uses the synchronous Copasi time simulation web service to predict the concentrations of species over a time period. The results from Copasi are provided in SBRML format which is visualised as a graph using an R script.

Created: 2010-03-26

Credits: Peter Li

SBML model optimisation (1)

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This workflow modifies reaction kinetic parameters against experimental data stored in the MCISB key results database

Created: 2010-03-26

Credits: Peter Li

SBML model parameterisation (1)

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This workflow parameterises an SBML model generated by the qualitative SBML model construction workflow

Created: 2010-03-26

Credits: Peter Li

Construction of skeleton SBML model using ... (1)

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This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given subsystem term.

Created: 2010-03-26 | Last updated: 2010-03-26

Credits: Peter Li