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Items tagged with "analysis" (23)

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Workflows (23)
Original Uploader

Workflow Workflow for Protein Sequence Analysis (1)

Created: 09/01/08 @ 12:03:03 | Last updated: 09/01/08 @ 12:31:27

Credits: User M.B.Monteiro

Attributions: Workflow BLAST using DDBJ service Workflow Simplify a BLAST text file Workflow conditional branch

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 1795 times | Downloaded: 467 times

Tags (10):

Original Uploader

Workflow Analysing workflows (3)

Created: 06/05/09 @ 08:49:59 | Last updated: 06/05/09 @ 08:50:29

Credits: User Wassinki User Pieter Neerincx User Katy Wolstencroft User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 168 times | Downloaded: 64 times

Tags (9):

Original Uploader

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

Created: 05/04/10 @ 06:20:58

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 53 times | Downloaded: 23 times

Tags (5):

Original Uploader

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

Created: 05/04/10 @ 06:24:02

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 56 times | Downloaded: 37 times

Tags (5):

Original Uploader

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

Created: 05/04/10 @ 06:22:28

Credits: User cory (Kazuki Oshita)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 68 times | Downloaded: 27 times

Tags (5):

Original Uploader

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

Created: 05/04/10 @ 06:17:25 | Last updated: 09/01/11 @ 06:08:19

Credits: User cory (Kazuki Oshita)

License: GNU General Public License (GPL) 2.0

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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.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 42 times | Downloaded: 25 times

Tags (5):

Original Uploader

Workflow Biomart and EMBOSS analysis (1)

Created: 03/07/09 @ 14:18:28 | Last updated: 03/07/09 @ 14:19:32

Credits: User Stian Soiland-Reyes

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 98 times | Downloaded: 25 times

Tags (6):

Original Uploader

Workflow DNA sequence analysis pilot (Blat) (2)

Created: 20/11/09 @ 11:12:43 | Last updated: 30/11/09 @ 09:35:38

Credits: User Angela Luijf User Barbera van Schaik User Glatard

Attributions: Workflow DNA sequence analysis pilot

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 99 times | Downloaded: 23 times

Tags (7):

Original Uploader

Workflow M_Fetch_e-T_phylo_boot - (BETA) (1)

Created: 10/03/10 @ 15:44:02 | Last updated: 10/03/10 @ 15:49:06

Credits: User Achille Zappa User Hamish McWilliam

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 47 times | Downloaded: 19 times

Tags (12):

Original Uploader

Workflow odeSolver Web service (1)

Created: 26/01/11 @ 22:01:53 | Last updated: 26/01/11 @ 22:01:56

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 14 times | Downloaded: 10 times

Tags (7):

Original Uploader

Workflow prism Web service (1)

Created: 26/01/11 @ 21:53:24 | Last updated: 26/01/11 @ 21:53:25

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 16 times | Downloaded: 10 times

Tags (9):

Original Uploader

Workflow asynchronous prism Web service (1)

Created: 26/01/11 @ 21:57:02 | Last updated: 26/01/11 @ 21:57:04

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 17 times | Downloaded: 14 times

Tags (5):

Original Uploader

Workflow [deprecated] Simulate SBML-derived ODEs (1)

Created: 26/01/11 @ 22:10:31 | Last updated: 20/07/11 @ 14:05:59

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 27 times | Downloaded: 14 times

Tags (18):

Original Uploader

Workflow [deprecated] Probabilistic Model Checking ... (1)

Created: 26/01/11 @ 22:14:41 | Last updated: 20/07/11 @ 14:14:30

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 298 times | Downloaded: 9 times

Tags (6):

Original Uploader

Workflow Phylogenetic analysis workflow (1)

Created: 12/03/11 @ 07:10:59 | Last updated: 12/03/11 @ 07:12:22

Credits: User 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: 36 times | Downloaded: 25 times

Tags (7):

Original Uploader

Workflow Global Shape Analysis Workflow (1)

Created: 06/04/11 @ 00:18:59 | Last updated: 06/04/11 @ 00:19:03

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 18 times | Downloaded: 6 times

Tags (4):

Original Uploader

Workflow Local Shape Analysis (LSA) Workflow (1)

Created: 06/04/11 @ 00:40:19 | Last updated: 06/04/11 @ 00:40:26

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 14 times | Downloaded: 7 times

Tags (7):

Original Uploader

Workflow First Level within subject fMRI processing (1)

Created: 06/04/11 @ 01:41:51 | Last updated: 14/07/11 @ 00:33:54

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 26 times | Downloaded: 6 times

Tags (6):

Original Uploader

Workflow Multi-parameter sensitivity analysis (MPSA) (2)

Created: 14/07/11 @ 08:50:26 | Last updated: 21/07/11 @ 10:08:42

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 9 times | Downloaded: 48 times

Tags (7):

Original Uploader

Workflow Multi-parameter sensitivity analysis (MPSA... (2)

Created: 14/07/11 @ 08:59:23 | Last updated: 21/07/11 @ 10:08:07

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 9 times | Downloaded: 8 times

Tags (9):

Original Uploader

Workflow Simulate SBML-derived ODEs (2)

Created: 20/07/11 @ 13:57:19 | Last updated: 20/07/11 @ 14:02:43

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 15 times | Downloaded: 17 times

Tags (11):

Original Uploader

Workflow Probabilistic Model Checking (PMC): comput... (1)

Created: 20/07/11 @ 14:11:46 | Last updated: 20/07/11 @ 14:12:02

Credits: User trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 9 times | Downloaded: 6 times

Tags (6):

Original Uploader

Workflow Ice Class Map pixel analysis (NERSC) (1)

Created: 02/11/11 @ 10:08:05 | Last updated: 02/11/11 @ 10:10:50

Credits: User Jorgejesus

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 27 times | Downloaded: 9 times

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Non-Information Resource URI: http://alpha.myexperiment.org/tags/15


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