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Items tagged with "analysis" (23)

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Workflows (23)

Taverna 1 Original Uploader M.B.Mon...	Workflow for Protein Sequence Analysis (v1) Created: 09/01/08 @ 12:03:03 \| Last updated: 09/01/08 @ 12:31:27 Credits: M.B.Monteiro Attributions: BLAST using DDBJ service Simplify a BLAST text file conditional branch License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis. Rating: 4.0 / 5 (2 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1495 times \| Downloaded: 404 times Tags (10): analysis \| BLAST \| homology \| multiple sequence alignment \| phylogenetic tree \| protein \| sequence \| tree \| wpsa	View Download (v1)
Taverna 1 Original Uploader Wassinki	Analysing workflows (v3) Created: 06/05/09 @ 08:49:59 \| Last updated: 06/05/09 @ 08:50:29 Credits: Wassinki Pieter Neerincx Katy Wolstencroft Marco Roos License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site The amount of services used The amount of local processors used The amount of scripting tasks The amount of sub workflows Furthermore it classifies the local services based on their intended function. The workflow has two inputs: ... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 145 times \| Downloaded: 57 times Tags (9): analysis \| beanshell \| localworker \| moby \| myexperiment \| rshell \| scripting \| taverna \| web services	View Download (v3)
Taverna 2 Original Uploader cory	G-language Genome Analysis Environment - GC skew analysis (basic) (v2) Created: 05/04/10 @ 06:20:58 Credits: cory License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 37 times \| Downloaded: 17 times Tags (5): analysis \| g-language \| genome \| sequence \| workflow	View Download (v2)
Taverna 2 Original Uploader cory	G-language Genome Analysis Environment - GC skew analysis (sequence retrieval via togoWS) (v2) Created: 05/04/10 @ 06:24:02 Credits: cory License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 44 times \| Downloaded: 33 times Tags (5): analysis \| g-language \| genome \| sequence \| workflow	View Download (v2)
Taverna 2 Original Uploader cory	G-language Genome Analysis Environment - GC skew analysis (multiple) (v2) Created: 05/04/10 @ 06:22:28 Credits: cory License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 23 times Tags (5): analysis \| g-language \| genome \| sequence \| workflow	View Download (v2)
Taverna 2 Original Uploader cory	G-language Genome Analysis Environment - GC skew analysis (AT skew) (v3) Created: 05/04/10 @ 06:17:25 \| Last updated: 09/01/11 @ 06:08:19 Credits: cory License: GNU General Public License (GPL) 2.0 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 18 times Tags (5): analysis \| g-language \| genome \| sequence \| workflow	View Download (v3)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and EMBOSS analysis (v1) Created: 03/07/09 @ 14:18:28 \| Last updated: 03/07/09 @ 14:19:32 Credits: Stian Soiland-Reyes Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 80 times \| Downloaded: 22 times Tags (6): alignment \| analysis \| sequence \| services \| soaplab \| workflow	View Download (v1)
Taverna 1 Original Uploader Angela Luijf	DNA sequence analysis pilot (Blat) (v2) Created: 20/11/09 @ 11:12:43 \| Last updated: 30/11/09 @ 09:35:38 Credits: Angela Luijf Barbera van Schaik Glatard Attributions: DNA sequence analysis pilot License: Creative Commons Attribution-Share Alike 3.0 Unported License http://amc-app1.amc.sara.nl/twiki/bin/view/ Workflow-based DNA sequence analysis on the Dutch Life Science Grid. This workflow is based on http://www.myexperiment.org/workflows/840 , the last component (Blast analysis) is replaced by Blat analysis Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 76 times \| Downloaded: 19 times Tags (7): analysis \| DNA \| grid \| moteur \| sequence \| taverna 1 \| workflow	View Download (v2)
Taverna 1 Original Uploader Achille Zappa	M_Fetch_e-T_phylo_boot - (BETA) (v1) Created: 10/03/10 @ 15:44:02 \| Last updated: 10/03/10 @ 15:49:06 Credits: Achille Zappa Hamish McWilliam License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 11 times Tags (12): alignment \| analysis \| clustal \| consensus \| fetch \| ml \| muscle \| nj \| phylogeny \| protein \| sequence \| tree	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	prism Web service (v1) Created: 26/01/11 @ 21:53:24 \| Last updated: 26/01/11 @ 21:53:25 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License PRISM model checking (http://www.prismmodelchecker.org/manual/RunningPRISM/ModelChecking). The '-fixdl' switch is used, which means that all deadlock states in model are fixed by addition of self-loops. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 6 times Tags (9): analysis \| model checking \| prism \| tav4sb \| web service	View Download (v1)
Taverna 1 Original Uploader trybik	asynchronous prism Web service (v1) Created: 26/01/11 @ 21:57:02 \| Last updated: 26/01/11 @ 21:57:04 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License Asynchronous version of the Prism Web service. Results XML list is sent via email. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 8 times Tags (5): analysis \| model checking \| prism \| tav4sb \| web service	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: 76 times \| Downloaded: 5 times Tags (6): analysis \| example \| model checking \| prism \| sbml \| tav4sb	View Download (v1)
BioExtract Server Original Uploader Yosr Bouhlal	Phylogenetic analysis workflow (v1) Created: 12/03/11 @ 07:10:59 \| Last updated: 12/03/11 @ 07:12:22 Credits: Yosr Bouhlal License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow provides a simple phylogenetic analysis starting from a protein query using "MrBayes" program and according to the maximum likelihood model Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 12 times Tags (7): analysis \| phylogeny \| protein \| workflow	View Download (v1)
LONI Pipeline Original Uploader Pipeline	Global Shape Analysis Workflow (v1) Created: 06/04/11 @ 00:18:59 \| Last updated: 06/04/11 @ 00:19:03 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes raw un-skull-stripped volumes in multiple groups/populations, or a Study-Design, and generates a scene file containing the models of the ROIs where the groups are different. It also reports the global 56 regional p-values. Problem addressed by this workflow Identifying the group differences between 2 populations in the global shapes of 56 cortical and sub-cortical ROIs. This workflow also generates DX models of all 56 ROIs which can be viewed as a scene in Sh... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 5 times Tags (4): analysis \| brain \| pipeline \| shape	View Download (v1)
LONI Pipeline Original Uploader Pipeline	Local Shape Analysis (LSA) Workflow (v1) Created: 06/04/11 @ 00:40:19 \| Last updated: 06/04/11 @ 00:40:26 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes raw un-skull-stripped volumes in 2 groups/populations and an ROI index to generate a color-coded shape object using the per-vertex local p-values of some local shape-measure (e.g., displacement, atrophy, Jacobian, curvature, etc). It also outputs the p-values color-map superimposed on the mean shape. Problem addressed by this workflow Identifying local group differences between 2 populations in one specific ROI. This workflow also generates mean-shape DX mo... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 8 times \| Downloaded: 3 times Tags (7): analysis \| brain \| brain imaging \| image \| local \| pipeline \| shape	View Download (v1)
LONI Pipeline Original Uploader Pipeline	First Level within subject fMRI processing (v1) Created: 06/04/11 @ 01:41:51 \| Last updated: 14/07/11 @ 00:33:54 Credits: Pipeline License: Creative Commons Attribution-Share Alike 3.0 Unported License Overview - fMRI-FEAT workflow This is a simple with-in subject fMRI analysis workflow. It takes 3D fMRI images and structural images of a subject and performs FSLmerge, BET (if the data is not already skull stripped) and first level FEAT processing. Problem addressed by this workflow FSLMerge, BET and FEAT first level analysis can be performed using this workflow on one or more subjects that require the same processing. The design FSF file is generate using the FSL FEAT inte... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 4 times Tags (6): analysis \| fmri \| functional mri \| imaging \| magnetic resonance imaging \| pipeline	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: 23 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)
Taverna 2 Original Uploader Jorgejesus	Ice Class Map pixel analysis (NERSC) (v1) Created: 02/11/11 @ 10:08:05 \| Last updated: 02/11/11 @ 10:10:50 Credits: Jorgejesus License: Creative Commons Attribution-Share Alike 3.0 Unported License NERSC ice classification workflow. Avaible images for a specific date will be fecthed from the WPS service, and their color table changed to allow for a user to easly identify specific areas. Statistical analysis also run using the r.stats module. Worflow uses a list of image, the list will flow thru the workflow for process resulting in mutiple outputs Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 12 times \| Downloaded: 5 times Tags (7): analysis \| classification \| color \| grass \| ice \| nersc \| pixel	View Download (v1)