myExperiment - Tags

Workflows (16)

Taverna 1 Original Uploader Peter Li	Mapping microarray data onto metabolic pathways (v1) Created: 14/11/07 @ 16:51:26 \| Last updated: 22/11/07 @ 10:39:32 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 509 times \| Downloaded: 172 times Tags (5): beanshell \| maxd \| microarray \| pathway \| sbml	View Download (v1)
Taverna 1 Original Uploader Duncan Hull	getSynonymsFromSBML (v1) Created: 09/06/09 @ 20:02:05 \| Last updated: 09/06/09 @ 20:08:02 Credits: Duncan Hull License: Creative Commons Attribution-Share Alike 3.0 Unported License This service takes an SBML file (for example from the Biomodels database) and extracts synonyms for each of the SBML species in the file, using ChEBI. Service is written and maintained by Neil Swainston at the MCISB. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 40 times \| Downloaded: 17 times Tags (8): biomodels \| chebi \| mcisb \| miriam \| neil-swainston \| sbml \| synonym \| systems biology	View Download (v1)
Taverna 1 Original Uploader Duncan Hull	getOntologyTerm (v1) Created: 09/06/09 @ 20:18:21 \| Last updated: 09/06/09 @ 20:19:29 Credits: Duncan Hull License: Creative Commons Attribution-Share Alike 3.0 Unported License This service takes a MIRIAM compliant URI and looks up all the synonyms for that URI using ChEBI and other services. Service developed and maintained by Neil Swainston at the MCISB in Manchester. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 78 times \| Downloaded: 19 times Tags (8): biomodels \| chebi \| miriam \| neil-swainston \| ontology \| sbml \| synonym \| term	View Download (v1)
Taverna 2 Original Uploader Peter Li	Construction of skeleton SBML model using a list of yeast ORF numbers (v1) Created: 26/03/10 @ 17:08:13 \| Last updated: 26/03/10 @ 17:13:15 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given list of yeast enzymes ORF numbers Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 17 times Tags (7): graph \| image \| model \| ORF \| pathways \| sbml \| yeast	View Download (v1)
Taverna 2 Original Uploader Peter Li	Construction of skeleton SBML model using subsystem term (v1) Created: 26/03/10 @ 17:11:26 \| Last updated: 26/03/10 @ 17:12:06 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given subsystem term. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 45 times \| Downloaded: 21 times Tags (6): graph \| image \| model \| sbml \| systems_biology \| yeast	View Download (v1)
Taverna 2 Original Uploader Peter Li	SBML model parameterisation (v1) Created: 26/03/10 @ 17:20:14 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow parameterises an SBML model generated by the qualitative SBML model construction workflow Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 57 times \| Downloaded: 23 times Tags (4): model \| r \| sbml \| systems_biology	View Download (v1)
Taverna 2 Original Uploader Peter Li	SBML model optimisation (v1) Created: 26/03/10 @ 17:21:53 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow modifies reaction kinetic parameters against experimental data stored in the MCISB key results database Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 51 times \| Downloaded: 19 times Tags (4): model \| model_optimisation \| sbml \| systems_biology	View Download (v1)
Taverna 2 Original Uploader Peter Li	Copasi time simulation of SBML model (v1) Created: 26/03/10 @ 17:23:25 Credits: Peter Li License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 75 times \| Downloaded: 35 times Tags (6): image \| model \| model_simulation \| sbml \| systems_biology \| user_interaction	View Download (v1)
Taverna 1 Original Uploader trybik	sbml2Prism Web service (v1) Created: 26/01/11 @ 21:59:36 \| Last updated: 26/01/11 @ 21:59:39 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License For example of the SBML to PRISM translation and the description of its details see http://www.prismmodelchecker.org/manual/RunningPRISM/SupportForSBML . Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 10 times \| Downloaded: 6 times Tags (6): format conversion \| prism \| sbml \| tav4sb \| translation \| web service	View Download (v1)
Taverna 1 Original Uploader trybik	odeSolver Web service (v1) Created: 26/01/11 @ 22:01:53 \| Last updated: 26/01/11 @ 22:01:56 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License SBML ODE Solver Library (http://www.tbi.univie.ac.at/~raim/odeSolver/) Web service. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 8 times \| Downloaded: 7 times Tags (7): analysis \| ode \| sbml \| simulate \| simulations \| tav4sb \| web services	View Download (v1)
Taverna 1 Original Uploader trybik	[deprecated] Simulate SBML-derived ODEs (v1) Created: 26/01/11 @ 22:10:31 \| Last updated: 20/07/11 @ 14:05:59 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2264.html . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 9 times Tags (18): analysis \| example \| experiment \| graph \| mathematica \| ode \| plot \| sbml \| simulate \| simulations \| tav4sb	View Download (v1)
Taverna 1 Original Uploader trybik	[deprecated] Probabilistic Model Checking (PMC): compute results (v1) Created: 26/01/11 @ 22:14:41 \| Last updated: 20/07/11 @ 14:14:30 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License This is a Taverna 1 version; if you're using latest Taverna 2 workbench please use: www.myexperiment.org/workflows/2266.html . Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) PRISM model translation and model checking Web service operations. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 81 times \| Downloaded: 5 times Tags (6): analysis \| example \| model checking \| prism \| sbml \| tav4sb	View Download (v1)
Taverna 2 Original Uploader trybik	Multi-parameter sensitivity analysis (MPSA) (v2) Created: 14/07/11 @ 08:50:26 \| Last updated: 21/07/11 @ 10:08:42 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA, ODEs simulations are basis of analysis of SBML model parameters space. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 3 times \| Downloaded: 25 times Tags (7): analysis \| example \| mpsa \| ode \| sbml \| sensitivity analysis \| tav4sb	View Download (v2)
Taverna 2 Original Uploader trybik	Multi-parameter sensitivity analysis (MPSA) with PMC (v2) Created: 14/07/11 @ 08:59:23 \| Last updated: 21/07/11 @ 10:08:07 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA PRISM probabilistic model checking is basis of analysis of SBML model parameters space. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1 time \| Downloaded: 6 times Tags (9): analysis \| example \| model \| model checking \| mpsa \| prism \| sbml \| sensitivity analysis \| tav4sb	View Download (v2)
Taverna 2 Original Uploader trybik	Simulate SBML-derived ODEs (v2) Created: 20/07/11 @ 13:57:19 \| Last updated: 20/07/11 @ 14:02:43 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 4 times \| Downloaded: 8 times Tags (11): analysis \| example \| experiment \| graph \| mathematica \| ode \| plot \| sbml \| simulate \| simulations \| tav4sb	View Download (v2)
Taverna 2 Original Uploader trybik	Probabilistic Model Checking (PMC): compute results (v1) Created: 20/07/11 @ 14:11:46 \| Last updated: 20/07/11 @ 14:12:02 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) PRISM model translation and model checking Web service operations. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 5 times \| Downloaded: 5 times Tags (6): analysis \| example \| model checking \| prism \| sbml \| tav4sb	View Download (v1)

Packs (1)

Creator:

Peter Li

Systematic integration of experimental data and models in systems biology

Created: 25/03/10 @ 20:31:36 | Last updated: 26/03/10 @ 17:23:44

A pack of workflows for the construction, parameterisation, optimisation and simulation of SBML models.

5 items in this pack

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Groups (1)

Administrator:

Peter Li

SBML

Created: Thursday 29 November 2007 @ 11:46:44 (GMT)

For people interested in doing SBML-related stuff in workflows

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Files (1)

Uploader:

Paul Dobson

ONDEX Graph from the Yeast Jamboree SBML

Created: 10/02/09 @ 10:51:58 | Last updated: 10/02/09 @ 12:48:52

Credits: Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The oxl file represents in ONDEX the SBML reconstruction of yeast metabolism produced in the "Jamboree", as described in the following paper. PMID 18846089 A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology. 2008 Oct;26(10):1155-60. Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Lieb...

File type: GNU Zip Archive

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Items tagged with "sbml" (19)