myExperiment - Content

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Life Table Response Experiments Year Effect in One Location or Place workflow provides an environment to analyse two or more matrices from different years in one location. The objective of this workflow is to determine the effects of the research years (2 or more) in one place on λ. This workflow performs a fixed LTRE, one way design (Caswell 2001).LTRE is a retrospective analysis (Caswell 1989),...

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Galaxy

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Ylebras

Tuto Galaxy 2013 : CPB2012 - BasicProtocol... (1)

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Workflow used when applying the CPB2012 Basic Protocol 1 tutorial from Galaxy team. It permits to filter Exons with the most SNP density.

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Galaxy

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Ylebras

NGS : Pair reads assembly with Velvet Work... (1)

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Paired-end reads assembly after fastQ groomer using a Migale (France INRA core facility https://migale.jouy.inra.fr/) modified version of Velvet tool suite descriptors

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

Galaxy

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Ylebras

Tuto Galaxy 2013 : CPB2012 - BasicProtocol... (1)

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Workflow used when applying the CPB2012 Basic Protocol 3 tutorial from Galaxy team. It calls peaks for ChIP-seq data using MACS14.

Created: 2014-02-27 | Last updated: 2014-06-10

Credits: Ylebras

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M. Kirsh

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Science, the Virtual and the Actual: a real stand-off

Created: 2014-02-23 01:00:13

Credits: M. Kirsh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Abstract: The World Wide Web is a source of social encounter occurring over undefined distances. If physical parameters of social encounter are considered uncontrollable for studies in a natural setting, the internet world, when dissected philosophically with respect to physical witnessibility of engaged identities, provides a model in which distance is absent. Upon comparison of meaning in science method and theory as it is necessarily rooted to common perceptional experience, it is proposed...

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M. Kirsh

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Determining the Determined State : a sizing of size ...

Created: 2014-02-23 00:50:50

Credits: M. Kirsh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Abstract: A philosophical exploration is presented that considers entities such as atoms, electrons, protons, reasoned (in existing physics theories) by induction, to be other than universal building blocks, but artifacts of a sociological struggle that in elemental description is identical with that of all processes of matter and energy. In a universal context both men and materials, when stressed, struggle to accomplish/maintain the free state. The space occupied by cognition, inferred to b...

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anthropology and science
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change
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civilization
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correspondances in nature
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cultural and biological evolution
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distance
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egg
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einstein
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emergence
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energy form and surface
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energy matter and geometrical form
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environmental disturbance
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ethics in science
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explanatory gap
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form in nature
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frame of reference
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free floating geometry for space
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genetic transmission
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graph of an egg
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human behavior and history
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illogic
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imagination
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induction and imagination
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infinite and eternal
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language and nature
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laws
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legality arbitration and nature
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light
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logic of nature.universal consciousness.cognitive representation.natural processes.uniqueness in nature.mobius strip.one sided surface genes and evolution
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mass
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matter
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mind matter form and energy
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mirror symmetry
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modern and old societies
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natural balance and pathology
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natural ethic
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nature and ethics
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nature and society
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newtons laws of motion
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numbers and kinds
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observation interpretation and common causes
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parallelism
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passive and active reflection
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path cause and effect
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perception and the external
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plot of an egg
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relativity space volume and culture
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religion and science
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representation of nature
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science discourse and power
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simultaneity
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social equality and mathematical inequality
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sociological and scientific process
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symbolism in science
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symmetry
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the concept
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the concept and physical parallels
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theory in anthropology
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theory in social sciences
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theory of nature
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time
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transcendental object
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unified theory of nature
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uniqueness
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universal consciousness
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universal form
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universal shape
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universals and constants
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velocity
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volume and space

Taverna 2

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Bolette Jurik

Slim Migrate And QA mp3 to Wav Using Hadoo... (4)

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This workflow migrates an input list (available on HDFS) of mp3 files (available on NFS) to wav files (in output directory on NFS) using an ffmpeg Hadoop job. The workflow then compares content of the original mp3 and the migrated wav by first converting the two files to wav using an mpg123 Hadoop job and the identity function respectively, and then using an xcorrSound waveform-compare Hadoop job. The needed Hadoop jobs are available from https://github.com/statsbiblioteket/scape-audio-qa-ex...

Created: 2014-02-21 | Last updated: 2014-06-30

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Maria Paula Balcazar-Vargas

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Life Table Response Experiments Fixed design year ef...

Created: 2014-02-21 13:12:33 | Last updated: 2014-08-21 08:06:21

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Life Table Response Experiments year effect for multiple places workflow provides an environment to analyse two or more matrices (e.g., two or more matrices of different years of one place) of two or more different locations. The objective of this workflow is to determine the effects of the research years (2 or more) on λ. This workflow performs a fixed LTRE, one way design (Caswell 2001).LTRE is...

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Taverna 2

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Markus Plangg

Imagemagick convert - image2tiff - compres... (1)

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Converts images supported by imagemagick to tiff using imagemagick convert with the provided compression

Created: 2014-02-14

Credits: Markus Plangg

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Norman Morrison

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Embedding an R Script in a Workflow Exercise

Created: 2014-02-13 17:47:42 | Last updated: 2014-02-13 17:52:17

This pack has all the files for the problem based learning exercise of embedding an R Script in a workflow

4 items in this pack

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Norman Morrison

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Taverna Tool Service

Created: 2014-02-13 17:40:54 | Last updated: 2014-02-13 17:42:58

Taverna Tool service tutorial pack

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Tim Booth

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Rserve on Bio-Linux

Created: 2014-02-13 14:55:21

Credits: Tim Booth

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The recommended way to run Rserve on Bio-Linux is to install the "r-cran-rserve" package - ie:$ sudo apt-get install r-cran-rserve(Note - this wasn't working on the morning of the 13th but has now been fixed in version 1.7-3-0biolinux2)If you install the library by using install.packages("Rserve") it will work but it will not get updated and will mask the system version of Rserve, which could cause you hard-to-diagnose problems down the line. My recommendation is...

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Taverna 2

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Renato De Giovanni

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loop_until_progress_complete (4)

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Loops until an asynchronous openModeller Web Service job is finished, i.e., keeps calling getProgress until it returns 100 (completed), -2 (aborted) or -3 (cancelled). NOTE: this is a "low level" component that was created to be used by other existing components, so end users may never need to use it at all.

Created: 2014-02-13 | Last updated: 2015-05-11

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Norman Morrison

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An introduction to designing and executing workflows...

Created: 2014-02-13 08:46:17

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial uses Bioinformatics exercises as an introduction to designing and executing workflows with Taverna.

File type: PowerPoint presentation

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Taverna 2

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Kraxner

Converts any ImageMagick supported image f... (1)

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SCAPE Migration Component

Created: 2014-02-12

Credits: Markus Plangg

Taverna 2

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Julian Garrido

Curves Exploration (1)

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Exploration of curves of cubes that contain galaxy observations

Created: 2014-02-12

Credits: Julian Garrido

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Norman Morrison

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Working with the BioVeL Portal

Created: 2014-02-11 16:12:36

Credits: Norman Morrison Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

In this exercise we will upload and run a simple workflow that we created in the previous exercises on the BioVeL portal.

File type: PowerPoint 2007 presentation

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Norman Morrison

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Setup instructions for BioLinux VM

Created: 2014-02-11 16:01:51 | Last updated: 2014-02-13 11:06:17

Credits: Norman Morrison quevedo79

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Version2

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Norman Morrison

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Embedding an R Script in a Workflow Exercise

Created: 2014-02-11 15:42:26

Credits: Norman Morrison

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This exercise is designed as a problem based learning task to understand how to embed R Scripts in workflows in Taverna.

File type: PowerPoint presentation

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Norman Morrison

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Using R Shell in Taverna workbench

Created: 2014-02-11 14:55:12 | Last updated: 2014-02-13 17:54:04

Credits: Norman Morrison Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

In this tutorial we wil perform some simple statistical analyses using the RShell processor

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Talend

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Francois Belleau

A Talend mashup to discover PARP proteins ... (3)

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A Talend workflow to answer this specific question :What is known about PARP family proteins involved in pathway according to Reactome ?by fetching RDF data from Bio2RDF`s HGNC, UniProt REST service and EBI Reactome SPARQL endpoint, all Semantic Web public resources.

Created: 2014-02-10 | Last updated: 2014-04-07

Credits: Francois Belleau

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Norman Morrison

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Exploring the Taverna workflow engine

Created: 2014-02-10 14:45:48 | Last updated: 2014-02-10 14:46:54

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

In this tutorial we will explore the Taverna workflow engine, including: 1) iteration; 2) looping; 3) parallel invocation.

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Norman Morrison

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An introduction to designing and executing workflows...

Created: 2014-02-06 16:42:14 | Last updated: 2014-02-06 16:44:14

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Part 2 - An introduction to designing and executing workflows with Taverna. Importing and exporting data.

File type: PowerPoint presentation

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Norman Morrison

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Supplementary material for "An Introduction to Desig...

Created: 2014-02-06 16:10:58 | Last updated: 2014-02-06 16:11:35

Supplementary material for "An Introduction to Designing and Executing Workflows with Taverna - Part 2".

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Norman Morrison

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03E_species_list_2.xls

Created: 2014-02-06 16:09:11

Credits: Norman Morrison

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This data file is supplementary material for "An Introduction to Designing and Executing Workflows with Taverna - Part 2".

File type: Trident (Package)

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Norman Morrison

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03D_species_2.txt

Created: 2014-02-06 16:08:26

Credits: Norman Morrison

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This data file is supplementary material for "An Introduction to Designing and Executing Workflows with Taverna - Part 2".

File type: Plain text

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Norman Morrison

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03C_species_list_1.xls

Created: 2014-02-06 16:02:27

Credits: Norman Morrison

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This data file is supplementary material for "An Introduction to Designing and Executing Workflows with Taverna - Part 2".

File type: Trident (Package)

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Norman Morrison

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03B_species_1.txt

Created: 2014-02-06 15:19:41 | Last updated: 2014-02-06 16:03:18

Credits: Norman Morrison

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This data file is supplementary material for "An Introduction to Designing and Executing Workflows with Taverna - Part 2".

File type: Plain text

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Norman Morrison

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An introduction to designing and executing workflows...

Created: 2014-02-06 14:52:19 | Last updated: 2014-02-06 16:45:12

Credits: Norman Morrison Katy Wolstencroft Aleksandra Pawlik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Part 1 - An introduction to designing and executing workflows with Taverna. Building a simple workflow.

File type: PowerPoint presentation

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Taverna 2

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Magnus Palmblad

RTCalc Retention Time Prediction and Outli... (1)

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This workflow takes as input a pepXML file from PeptideProphet, applied RTCalc and outputs a filtered list of peptides based on the retention time Z-scores.

Created: 2014-02-06 | Last updated: 2014-02-06

Credits: Magnus Palmblad Sonja Holl

Taverna 2

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Artur Kulmukhametov

PhotoHawk - SSIM (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using SSIM metric (http://purl.org/DP/quality/measures#15).

Created: 2014-02-05

Credits: Artur Kulmukhametov

Taverna 2

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Artur Kulmukhametov

PhotoHawk - AE (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using AE metric (http://purl.org/DP/quality/measures#4).

Created: 2014-02-05

Credits: Artur Kulmukhametov

Taverna 2

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Artur Kulmukhametov

PhotoHawk - MAE (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using MAE metric (http://purl.org/DP/quality/measures#5).

Created: 2014-02-05

Credits: Artur Kulmukhametov

Taverna 2

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Artur Kulmukhametov

PhotoHawk - MSE (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using MSE metric (http://purl.org/DP/quality/measures#6).

Created: 2014-02-05

Credits: Artur Kulmukhametov

Taverna 2

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Artur Kulmukhametov

PhotoHawk - PAE (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using PAE metric (http://purl.org/DP/quality/measures#7).

Created: 2014-02-05

Credits: Artur Kulmukhametov

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