Workflows

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

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 list of yeast enzymes ORF numbers

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

Credits: Peter Li

Sage bionetwork demo workflow (1)

This workflow performs key driver analysis and displays the results in Cytoscape.

Created: 2010-03-22

Credits: Peter Li

blastp of target vs source database (1)

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This worlflow allows the user to input two sets of proteins in fasta format. One file is converted to a database using formatdb, the set is blasted against this database to test for Blast hits. Users is able to set eValue and destination of files for database and blast file. Arguments can be added to either formatdb or blast in beanshell supplied. Blast and formatdb must be installed locally and the correct filepaths for these applications must entered into the workflow accordingly.

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

Credits: Ian Laycock nclteamc

Attributions: fetchEnsemblSeqsAndBlast

Kegg pathway diagrams (3)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - ...

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

BlastandParse2 (1)

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2010-03-19

Credits: Baywatch Solutions

Attributions: fetchEnsemblSeqsAndBlast

BlastandParse1 (1)

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2010-03-19

Credits: Baywatch Solutions

Attributions: fetchEnsemblSeqsAndBlast