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2602?size=60x60 Es Jose Enrique Ruiz
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Blob Sample VOTable from SDSS DR7 Catalog II/294 in Vizier

Created: 2013-04-12 16:21:10

Credits: User Jose Enrique Ruiz

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This VOTable is used in workflow snippets provided in AstroTaverna starter pack

File type: Trident (Package)

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2602?size=60x60 Es Jose Enrique Ruiz
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Blob Sample VOTable from 2MASS Catalog

Created: 2013-04-12 16:16:40

Credits: User Jose Enrique Ruiz

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This VOTable is used in workflow snippets provided in AstroTaverna starter pack

File type: Trident (Package)

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4450?size=60x60 In Drkrish...
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Blob SILDENAFIL CITRATE (Viagra) IN ITS POLYMORPHIC FORMS

Created: 2013-04-08 05:17:04

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 AN IMPROVED PROCESS FOR THE PREPARATION OF SILDENAFIL CITRATE (Viagra) IN ITS POLYMORPHIC FORM The present invention provides an improved process for preparation of 1-[[3-(6,7-dihydro-1-methyl-7-oxo-3-propyl-1H –pyrazolo[4,3-d]pyrimidin-5-yl)-4-ethoxyphenyl]sulphonyl]-4methypiperazine citrate (Sildenafil Citrate) ofPolymorphic form I)

File type: Adobe PDF

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9?size=60x60 Gb Stian Soiland-Reyes
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Blob Workflow run: Pav2Svg using ChemSpider VoID

Created: 2013-04-05 09:28:31

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Taverna provenance of workflow run on PAV2SVG using the ChemSpider VoID descriptor as input. See Pack 418.

File type: ZIP archive

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9?size=60x60 Gb Stian Soiland-Reyes
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Blob Visualization of ChemSpider VoiD provenance

Created: 2013-04-05 09:23:22 | Last updated: 2013-04-05 10:40:18

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

SVG visualization of the PAV provenance from the ChemSpider VoID descriptor example. See Pack 418.Note that this file has been made with PROV Toolbox 0.1.2 as 0.1.3 does not show shortened labels as here.

File type: image/svg+xml

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1780?size=60x60 Gb Donal Fellows
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Blob Characterisation Component

Created: 2013-04-04 12:37:26 | Last updated: 2014-04-01 10:57:41

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A SCAPE component for characterisation

File type: Taverna Component Profile

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1780?size=60x60 Gb Donal Fellows
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Blob Migration Action Component

Created: 2013-04-04 10:44:50 | Last updated: 2014-04-01 10:52:53

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A SCAPE component for migration actions

File type: Taverna Component Profile

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9?size=60x60 Gb Stian Soiland-Reyes
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Blob adfsadf

Created: 2013-01-30 14:15:24

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 asdf

File type: Trident (Package)

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30?size=60x60 Nl Marco Roos
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Blob The Hypothesis for the wf4ever Demo Pack 2013

Created: 2013-01-30 14:06:43 | Last updated: 2013-01-30 14:07:25

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The hypothesis for the Demo pack created for the wf4ever demo in 2013. It is not intended for real use.

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71?size=60x60 Nl Katy Wolstencroft
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Blob Cranfield Msc Intro to Taverna

Created: 2013-01-09 16:43:00

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial give a brief introduction to designing and running workflows in Taverna, using a variety of different types of services and reusing workflows from myExperiment

File type: PowerPoint presentation

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3232?size=60x60 Tn kmezhoud
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Blob Interactive Proteomics Data Enrishment Tutorial

Created: 2013-01-09 10:48:37

Credits: User kmezhoud

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial describes the main steps used to construct an enriched network from a list of genes with their expression values. The network includes the fold change, the False discovery rate (FDR), the gene expression correlation, the most often involved biological processes, and the most likely corresponding diseases. All the main steps are illustrated by screen shots. The “Tools & Data” section lists all the tools and data required. The “Data computing” s...

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2602?size=60x60 Es Jose Enrique Ruiz
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Blob Calculation of Luminosity Profiles for a Sample of G...

Created: 2013-01-05 16:57:08

Credits: User Jose Enrique Ruiz

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document describes the "Luminosity Profiles" Research Object

File type: Adobe PDF

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2602?size=60x60 Es Jose Enrique Ruiz
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Blob Extraction of Properties from a Sample of Galaxies

Created: 2013-01-05 16:54:48 | Last updated: 2013-01-05 16:57:46

Credits: User Jose Enrique Ruiz

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document describes the "Galaxies Sample Selection" Research Object

File type: Adobe PDF

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2602?size=60x60 Es Jose Enrique Ruiz
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Blob D5.3v2 Calculation of Luminosity Profiles for a Samp...

Created: 2013-01-05 16:45:48 | Last updated: 2013-01-05 16:48:45

Credits: User Jose Enrique Ruiz

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document describes the development of the second Golden Exemplar proposed in Work Package 5: Workflow Astronomy Preservation, and provides discussion about user-driven issues risen in this process and related with general objectives of the Wf4Ever project. The document pertains to the assembly of two Research Objects (RO) packing the digital experiment undertaken for the extraction of a sample of galaxies based on environmental criteria and the calculation of luminosi...

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3377?size=60x60 Gb Jon Giddy
Project Biovel
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Blob Matrix Population Modelling documentation

Created: 2012-11-05 16:32:34 | Last updated: 2012-11-07 09:01:58

Credits: User Jon Giddy User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document describes the Matrix Population Modelling workflow, and includes a tutorial on its use.

File type: Adobe PDF

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Demographic data Gentiana pneumonanthe 1987-1988 fro...

Created: 2012-11-05 09:47:37 | Last updated: 2013-08-13 12:06:34

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow Matrix Population Model construction and analysis v20

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of one year demographic data of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population (http://www.myexperiment.org/workflows/3276.html) or Matrix Population Model construction and analysi...

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Avatar Cherian Mathew
Project Biovel
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Blob Data Refinement Workflow Documentaion

Created: 2012-11-02 17:42:05 | Last updated: 2012-11-07 08:47:24

Credits: User Cherian Mathew

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 This document provides comprehensive information about the Data Refinement Workflow.

File type: Adobe PDF

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Avatar Cherian Mathew
Project Biovel
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Blob Sample Input for Data Refinement Workflow

Created: 2012-11-02 16:10:54 | Last updated: 2012-11-07 08:48:11

Credits: User Cherian Mathew

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 This file is a sample input file for the Data Refinement Workflow. It is also the input file used in the tutorial section of the documentation.

File type: Plain text

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Demographic data Gentiana pneumonanthe 1987-1991 fr...

Created: 2012-11-02 12:37:19 | Last updated: 2014-07-04 12:31:17

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow Matrix Population Model construction and analysis v20

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This is a .txt file of four years demographic data of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population (http://www.myexperiment.org/workflows/3276.html) or Matrix Population Model construction and analysis v...

File type: Plain text

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3377?size=60x60 Gb Jon Giddy
Project Biovel
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Blob Demographic data Gentiana pneumonanthe 1987-1988 fro...

Created: 2012-11-02 10:59:24 | Last updated: 2012-11-07 08:56:00

Credits: User Jon Giddy User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Small example file to allow users to run population modelling workflow  

File type: Plain text

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3400?size=60x60 Gb Khalid Belhajjame
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Blob Semantic Annotation of Web Services (Feta)

Created: 2012-10-26 09:45:01

Credits: User Khalid Belhajjame

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains the semantic annotations of web services using Feta.

File type: ZIP archive

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3424?size=60x60 De jhermes
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Blob Governmental Statements (Merkel)

Created: 2012-09-19 14:50:30

Credits: User jhermes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A corpus of all governmental statements from chancellor Merkel.

File type: ZIP archive

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Avatar Adamhen...
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Blob family tree

Created: 2012-09-17 21:49:40

Credits: User Adamhenshall

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 attempt at mapping levels of Pearl Ogden's family tree.

File type: Trident (Package)

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3489?size=60x60 Gb Helen Hulme
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Blob Agenda of Bonn tutorial

Created: 2012-09-14 09:51:22

Credits: User Helen Hulme User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the list of presentations and workshop items from the Bonn tutorial 2012. The presentations (and many of the workflows and datafiles) for this are in the pack: "Pack for Bonn2012" http://www.myexperiment.org/packs/330

File type: Word document

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3489?size=60x60 Gb Helen Hulme
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Blob Assignment Data - suggested SNPs

Created: 2012-09-05 07:20:29 | Last updated: 2012-09-05 07:22:16

Credits: User Helen Hulme

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Here are some SNPs you can use for the assignment on day 3 of the Bonn 2012 Taverna course. The assignment is about SNP annotation and analysis If you would prefer to use some others that you are working with, fine. This data is a column of dbSNP identifiers  

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3489?size=60x60 Gb Helen Hulme
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Blob Bonn Taverna Presentation - Case Studies

Created: 2012-09-04 10:17:41 | Last updated: 2012-09-04 13:45:55

Credits: User Helen Hulme User Katy Wolstencroft User Paul Fisher User Shoaib Sufi User Mcornell User Robert Haines

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Presentation comparing and contrasting Taverna workbench use on two case studies: 1. African Sleeping Sickness (Trypanosomiasis) Wellcome Trust Project 2. NHS / TSB SNP annotation pipeline

File type: PowerPoint 2007 presentation

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71?size=60x60 Nl Katy Wolstencroft
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Blob Bonn Tutorial REST services

Created: 2012-09-03 19:34:12

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a brief introduction to using REST servicces through Taverna

File type: PowerPoint presentation

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71?size=60x60 Nl Katy Wolstencroft
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Blob Bonn Tutorial Different Service Types

Created: 2012-09-03 19:32:32

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Thie tutorial introduces you to using different types of services with Taverna - e.g. asynchronous, biomart and soaplab

File type: PowerPoint presentation

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3655?size=60x60 Nl Magnus Palmblad
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Blob rt3.c

Created: 2012-09-03 10:36:54 | Last updated: 2012-09-03 10:42:13

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Linear retention time prediction training rt, version 3.0 with improved command-line interface and format options.

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71?size=60x60 Nl Katy Wolstencroft
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Blob Bonn Taverna Shims

Created: 2012-08-30 14:18:06

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial provides an introduction to finding, using and designing Shim services for Taverna workflows

File type: PowerPoint presentation

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71?size=60x60 Nl Katy Wolstencroft
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Blob Bonn Taverna WF Engine

Created: 2012-08-30 14:15:51

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial provides an introduction to using the advanced features of the Taverna workflow engine, such as iterations, looping etc

File type: PowerPoint presentation

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71?size=60x60 Nl Katy Wolstencroft
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Blob Bonn Taverna Intro Tutorial

Created: 2012-08-30 14:11:55

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial provides an introduction to designing, combining and sharing workflows with Taverna and myExperiment

File type: PowerPoint presentation

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1253?size=60x60 Gb Anja Le Blanc
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Blob HELIO Service List for Taverna 2.4

Created: 2012-08-30 09:45:06

Credits: User Anja Le Blanc

License: BSD License

Import HELIO SOAP web services from this file. This works for Taverna 2.4. Pervious service lists cause problems while importing them.

File type: XML

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71?size=60x60 Nl Katy Wolstencroft
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Blob Bozeman Tutorial

Created: 2012-08-22 09:59:37

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to designing and using Taverna workflows and myExperiment. It was created for the workshop "Making Sense of Biological Systems:Using Knowledge Mining to Improve and Validate Models of Living Systems", at Montana State University Aug 2012

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Blob STUDY OF QUANTIFICATION OF IMPURITIES AND RELATED SU...

Created: 2012-08-13 16:46:39

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

    Bulk drug during its production process, after its scale up, it is necessary to analyse for the presence of any impurities or related substances in it. This is to ensure the impurities and related substances are within their limits as per ICH Guidelines. The impurities and related substances are defined as; Impurity: Any component present in the drug substance or drug product which is not the desired product, a product-related substance, or excipient including buffer com...

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3400?size=60x60 Gb Khalid Belhajjame
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Blob Execution traces copied from the vistrails console ...

Created: 2012-08-06 11:00:38

Credits: User Khalid Belhajjame

License: Creative Commons Attribution-Share Alike 3.0 Unported License

  This is the execution trace as it appeared in the Vistrailsworkbench of the workflow that retrieves the pathways associated with given kegg gene identifier.

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3400?size=60x60 Gb Khalid Belhajjame
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Blob Provenance traces of the Gene To Pathway Taverna Wor...

Created: 2012-08-06 10:58:38

Credits: User Khalid Belhajjame

License: Creative Commons Attribution-Share Alike 3.0 Unported License

  This is the provenance trace in Janus of the Tavrerna workflow that retrieves the pathways associated with given kegg gene identifier.

File type: RDF data

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3400?size=60x60 Gb Khalid Belhajjame
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Blob Provenance traces of the Gene To Pathway Taverna Wor...

Created: 2012-08-06 10:57:37

Credits: User Khalid Belhajjame

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 This is the provenance trace in provo of the Tavrerna workflow that retrieves the pathways associated with given kegg gene identifier.

File type: ZIP archive

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3813?size=60x60 Program...
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Blob Combined workflow from my master work

Created: 2012-08-03 11:13:35

Credits: User Programmerva

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Here is two workflows is combined to one workflow. One part of this workflows is taken from MyExperiment.

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Avatar Cherian Mathew
Project Biovel
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Blob Data Refinement Workflow Utility Jar (Current Version)

Created: 2012-07-26 14:56:42 | Last updated: 2012-11-07 08:48:49

Credits: User Cherian Mathew

License: Creative Commons Attribution-Share Alike 3.0 Unported License

   jar which includes all utility classes with functionality used in the Data Refeinement workflow

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Blob Process for the preparation of amorphous atorvastati...

Created: 2012-07-24 12:07:03

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Atorvastatin calcium is a drug compound that is used as a lipid-lowering agent, fortreating hypercholesterolemia. The compound has the chemical name[R-(R*,R*)]-2-(4-fluorophenyl)-3,ö-dihydroxy-5-(1-methylethyl)-3-phenyl-4-{(phenylamino)carbonyl}-1H-pyrolle-1-hepatonic acid, calcium salt (2:1) trihydrate. Pharmaceutical productscontaining crystalline atorvastatin calcium trihydrate are sold using the trademarkLIPITOR.

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Blob Novel polymorph of 5-cyanopthalide high purity inter...

Created: 2012-07-24 12:02:16

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The present invention relates to obtaining a new polymorph of 5-Cyanophthalide in highly pure form (99.5 to 99.99%), which is an intermediate used forthe synthesis of citalopram& escitalopram both of which are potent antidepressant drugs.Moreover this new polymorph of 5-cyanophthalide does not contain impurities liketerephthalic acid & diphthalide derivatives.        

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Blob Enantioselective method of synthesizing methylphenid...

Created: 2012-07-24 11:51:52

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Process for the preparation of enantioselective method of making methylphenidate and derivatives . The method involves use of a rhodium catalyst, and selectively produces the D-enantiomer of the methylphenidate derivative in excess of the L-enantiomer . Furthermore, the method selectively produces the threo-diastereomer in excess of the erythro-diastereomer. The method is thus suitable for synthesis of D-threo-methylphenidate (the biologically active form of this compound) and derivatives &...

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Blob Quality Assurance and GMP and ICH

Created: 2012-07-24 11:46:03

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Quality Assurance is a planned and systematic approach to generate enough confidence in the quality of the product and processes in the long run as per the specifications." In this biog you will find post related to ICH, GMP and Quality related matters.

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Blob GLIBENCLAMIDE Complexes ( Complexes of Mg,Cr,Ni,Zn a...

Created: 2012-07-24 11:33:50 | Last updated: 2012-07-24 11:33:51

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The N-acetyl derivative of β-phenethylamine is reacted with chlorosulfonic acid to form the para sulfonyl chloride derivative. This is then subjected to ammonolysis, followed by base-catalyzed removal of the acetamide. This is then acylated with 2-methoxy-5-chlorobenzoic acid chloride to give the amide intermediate. This is then reacted with cyclohexyl isocyanate to yield the sulfonylurea glibenclamide

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Blob HOW TO START ANALYTICAL METHOD DEVELOPMENT

Created: 2012-07-24 11:28:31

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 A bulk drug during its production process, after its scale up, it is necessary to analyse for the presence of any impurities or related substances in it. This is to ensure the impurities and related substances are within their limits as per ICH Guidelines.The impurities and related substances are defined as; Impurity: Any component present in the drug substance or drug product which is not the desired product, a product-related substance, or excipient including buffer components. I...

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Blob DEFINITION “IMPURITY”

Created: 2012-07-24 11:18:54

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Impurities are normally generated during the formation of Active PharmaceuticalIngredients and their intermediates. Chances of their generation during Drug Productsformation are less as formulation is a physical blending process. Care is taken that theseexcipients do not react with each other to produce the degradants. They may consist oforganic and inorganic, and define levels at which impurities/degradants should beidentified.ICH Q3A covers drug substances and Q3B covers drug products. Th...

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Blob Improved process for preparing L-phenylephrine hydro...

Created: 2012-07-24 11:12:15

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The present invention relates to an improved process for preparing L-phenylephrinehydrochloride on an industrial scale    

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Blob PROCESS FOR PREPARATIN OF VITAMIN-C-Dr.krishnasarma ...

Created: 2012-07-24 11:03:13

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Ascorbic acid (vitamin C) is a water-soluble vitamin. It occurs as a white or slightly yellowcrystal or powder with a slight acidic taste. It is an antiscorbutic product. On exposure to light, itgradually darkens. In the dry state, it is reasonably stable in air, but in solution it rapidlyoxidizes. Ascorbic acid (vitamin c) is freely soluble in water; sparingly soluble in alcohol;insoluble in chloroform, in ether, and in benzene. The chemical name of ascorbic acid (vitaminc) is L-ascorbic a...

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Blob Industrial process for preparation of Levetiracetam....

Created: 2012-07-24 10:59:51

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

         Levetiracetam belongs to the class of compounds used in the treatment of epilepsy so it.has huge demand in market and it is worth to develop the product.

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Blob solid-state forms of celecoxib andAN IMPROVED PROCE...

Created: 2012-07-24 10:54:47

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

          The present application provides an improved process for the preparation  of          4-[5-(4-methylphenyl)-3- (trifluoromethyl)-1H-pyrazol-1-yl] benzenesulfonamide           (Celecoxib) and its purification and crystallisation to produce polymorph .  

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Blob A Primer on Intellectual Property Rights-Dr.krishnas...

Created: 2012-07-24 10:39:44

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

  nTypes of Intellectual Property   nWhat is a Patent , its requirements & specification   nPatent claims   nCriteria for claiming inventors   nTypes of patents   nInfringement & validity of patent   nIndian patent scenario   nPatent Cooperation Treaty (PCT)   nDifferences in patent Laws   nPatent Resources  

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Blob Using A Dynamic Bayesian Network-based Model for Inf...

Created: 2012-07-24 04:51:56

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Largely due to the technological advances in bioinformatics, researchers are now garnering interests in inferring gene regulatory networks (GRNs) from gene expression data which is otherwise unfeasible in the past. This is because of the need of researchers to uncover the potentially vast information and understand the dynamic behavior of the GRNs. In this regard, dynamic Bayesian network (DBN) has been broadly utilized for the inference of GRNs thanks to its ability to handle time-seri...

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Blob Aspartate Biosynthesis Pathway Simulation Using an I...

Created: 2012-07-24 04:49:23

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 An improved Differential Evolution algorithm (IDE) is proposed in this paper. It is aimed at enhancing its efficiency in estimating the relevant kinetic parameters for metabolic pathway data to simulate aspartate biosynthesis pathway for plant model Arabidopsis. Metabolic pathway data are anticipated to be of vital help in the development of effectual tools in parameter estimation and kinetic modeling platforms. However, a number of computation algorithms face difficulty, produces low a...

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Blob Gene Knockout Strategies Identification by Using a H...

Created: 2012-07-24 04:48:16

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 By optimizing microbial strains it is possible to improve product yield or improve growth characteristics. Microbial strains can be optimized through genetic engineering. It is proven that through genetic engineering it is able to obtain the desirable phenotypes. However, it is difficult to predict the effects of genetic modifications on the resulting phenotype due to the complexity of the networks. Optimization algorithms are implemented in previous works in order to identify the effec...

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Blob Parameter Estimation for Simulation of Glycolysis Pa...

Created: 2012-07-24 04:46:49

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 An improved differential evolution (DE) algorithm is proposed in this paper to optimize its performance in estimating the germane parameters for metabolic pathway data to simulate glycolysis pathway for Saccharomyces cerevisiae. This study presents an improved algorithm of parameter sensitivity test into the process of DE algorithm. The result of the improved algorithm is testifying to be supreme to the others estimation algorithms. The outcomes from this study promote estimating ...

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Blob Identifying Metabolic Pathway within Microarray Gene...

Created: 2012-07-24 04:45:28

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Extracting metabolic pathway that dictates a specific biological response is currently one of the important disciplines in metabolic system biology research. Previous methods have successfully identified those pathways but without concerning the genetic effect and relationship of the genes, the underlying structure is not precisely represented and cannot be justified to be significant biologically. In this article, probabilistic models capable of identifying the significant pathwa...

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Blob Random Forest for Gene Selection and Microarray Data...

Created: 2012-07-24 04:44:00

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 A random forest method has been selected to perform both gene selection and classification of the microarray data. The goal of this research is to develop and improve the random forest gene selection method. Hence, improved gene selection method using random forest has been proposed to obtain the smallest subset of genes as well as biggest subset of genes prior to classification. In this research, ten datasets that consists of different classes are used, which are Adenocarcinoma, ...

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Blob Optimized Local Protein Structure with Support Vecto...

Created: 2012-07-24 04:21:20

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. Living cells are controlled by proteins and genes that interact through complex molecular pathways to achieve a specific function. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. Therefore, determination of protein structure is fundamental ...

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Blob Prediction of Protein Residue Contact Using Support ...

Created: 2012-07-24 04:19:46

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Prediction of protein residue contact is one of the important twodimensional prediction tasks in protein structure prediction. The residue contact map of protein contains information which represents three-dimensional conformation of protein. However the accuracy of the prediction is dependent on the type of protein information used to distinguish between contacts or noncontacts. According to CASP (Critical Assessment of Techniques of Protein Structure Prediction) the accuracy of ...

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Blob eScience-WF-Motifs-Consolidated-DataSet

Created: 2012-07-18 23:58:01

Credits: User pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The spreadsheet containing data consolidated by domain. Also contains al the charts that are generated over consolidated data.

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Blob eSCience-WF-Motifs-Wings-DataSet

Created: 2012-07-18 23:56:30

Credits: User pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

  The Dataset containing Wings workflows that are manually analyzed for the detection of motifs

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Blob eScience-WF-Motifs-Taverna-DataSet

Created: 2012-07-18 23:55:17

Credits: User pinarpink

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The Dataset containing Taverna workflows that are manually analyzed for the detection of motifs

File type: Excel workbook

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Blob A Test File

Created: 2012-07-10 23:30:05

Credits: User Jreeves

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Testing

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3400?size=60x60 Gb Khalid Belhajjame
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Blob Janus Provenance trace of a Gene_To_Pathway Taverna ...

Created: 2012-07-10 08:13:07

Credits: User Khalid Belhajjame

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the Janus provenance traces produced by the Taverna workflow in http://www.myexperiment.org/workflows/3001.html?version=1

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3400?size=60x60 Gb Khalid Belhajjame
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Blob OPM Provenance trace of a Gene_To_Pathway Taverna wo...

Created: 2012-07-10 08:11:43

Credits: User Khalid Belhajjame

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The following file is the OPM provenance produced by the execution of the workflow in http://www.myexperiment.org/workflows/3001.html?version=1

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Blob Log file of the execution of a Vistrails workflow

Created: 2012-07-10 08:08:14

Credits: User Khalid Belhajjame

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the log file obtained by executing the Vistrails workflow in http://www.myexperiment.org/workflows/3003.html?version=1

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Blob Metabolic Pathway Extraction Using Combined Probabil...

Created: 2012-07-04 06:59:13

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Extracting metabolic pathway from microarray gene expression data that dictates a specific biological response is currently one of the important disciplines in system biology research. However due to the complexity of the global metabolic network and the importance to maintain the biological structure, this has become a greater challenge. Previous methods have successfully identified those pathways but without concerning the genetic effect and relationship of the genes, representation o...

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Blob Protein secondary structure prediction using optimal...

Created: 2012-07-04 06:55:38

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. The importance of understanding protein structure has fueled the development of protein structure databases and prediction tools. The main objective of this research is to optimize local protein str...

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Blob test

Created: 2012-07-03 09:19:43 | Last updated: 2013-05-16 01:56:36

Credits: User Cs88dn

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 1111

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3559?size=60x60 Ie Eoghan Barry
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Blob Sample Dataset

Created: 2012-06-17 14:45:21

Credits: User Eoghan Barry

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

Dummy file for usability testing

File type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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2615?size=60x60 Hr Ninoaf
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Blob Dataset for workflow: "TextualAttributeExtraction fo...

Created: 2012-06-03 19:47:32 | Last updated: 2012-06-04 08:37:05

Credits: User Ninoaf

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 This dataset is used as an input in the workflow: http://www.myexperiment.org/workflows/2932.html   This dataset is taken from "VideoLectures.Net Recommender System Challenge" Cite as: N. Antulov-Fantulin, M. Bošnjak, T. Šmuc, M. Jermol, M. Žnidaršič, M. Grčar, P. Keše, N. Lavrač, ECML/PKDD 2011 - Discovery challenge: "VideoLectures.Net Recommender System Challenge", http://lis.irb.hr/challenge/ and   N. Antulov-F...

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71?size=60x60 Nl Katy Wolstencroft
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Blob Getting Started with Taverna - an NGS tutorial

Created: 2012-05-23 14:53:24 | Last updated: 2012-05-30 08:48:19

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to using Taverna, using an example from Chip-Seq analysis

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3840?size=60x60 Hr Matej Mihelčić
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Blob MovieLens data for hybrid recommenders

Created: 2012-05-17 11:04:57 | Last updated: 2012-05-17 11:06:10

Credits: User tomS

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 This is MovieLens data set containing user,item, ratings and item attributes enabling hybrid recommendation system testing. 

File type: Trident (Package)

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Blob Prediction of Protein Residue Contact Using Support ...

Created: 2012-05-11 02:44:49

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Prediction of protein residue contact is one of the important two-dimensional prediction tasks in protein structure prediction. The residue contact map of protein contains information which represents three-dimensional conformation of protein. However the accuracy of the prediction is dependent on the type of protein information used to distinguish between contacts or noncontacts. According to CASP (Critical Assessment of Techniques of Protein Structure Prediction) the accuracy o...

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Blob Predicting Protein Secondary Structure with Neural N...

Created: 2012-05-11 02:34:20

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Protein secondary structure prediction has benefited largely from the improvements in machine learning techniques. A novel neural network classifier based on the Dempster-Shafer theory has been introduced by Denoeux. It demonstrated favourable performance in some artificial and real world problems when compared against methods such as Support Vector Machines and Kernel Fisher Discriminants. However, it has not been used for protein secondary structure prediction. In this work, we examin...

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Blob Pathway-Based Microarray Analysis for Defining Stati...

Created: 2012-05-11 02:33:00

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 In this reiew, we have discussed about approaches in pathway based microarray analysis. Commonly, there are two approaches in pathway based analysis, Enrichment Score and Supervised Machine Learning. These pathway based approaches usually aim to statistically define significant pathways that related to phenotypes of interest. Firstly we discussed an overview of pathway based microarray analysis and its general flow processes in scoring the pathways, the methods applied in both a...

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Blob Parameter Estimation for Simulation of Glycolysis Pa...

Created: 2012-05-11 02:28:43 | Last updated: 2012-05-11 02:28:44

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 An improved differential evolution (DE) algorithm is proposed in this paper to optimize its performance in estimating the germane parameters for metabolic pathway data which is used to simulate glycolysis pathway for Satcharomyces cerevisiae. This study presents an improved algorithm of parameter sensitivity test into the process of DE algorithm. The result of the improved algorithm is testified to be better than the other estimation algorithms. The outcomes from this study promot...

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Blob Optimized Local Protein Structure with Support Vecto...

Created: 2012-05-11 02:27:24

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Protein includes many substances, such as enzymes, hormones and antibodies that are necessary for the organisms. Living cells are controlled by proteins and genes that interact 1fo1sngh complex molecular pathways to achieve a specific function. These proteins have different shapes and structures which distinct them from each other. By having unique structures, only proteins able to carried out their function efficiently. Therefore, determination of protein structure is fundamental...

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Blob One-Class Classifier to Predict Protein-Protein Inte...

Created: 2012-05-11 02:25:30

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Protein-protein interactions are important in a wide range of biological processes. The development of drugs that target such interactions is a very active research field. Hence predicting protein-protein interactions represent an important challenge in bioinformatics research. Machine learning techniques have been applied to predict protein-protein interactions. Most of these techniques address this problem as a binary classification problem. While it is easy to get a dataset of...

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Blob Multi-Objective Optimization Using Genetic Algorithm...

Created: 2012-05-11 02:23:50

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Microarray technology has been increasingly used in cancer research because of its potential for measuring expression levels of thousands of genes simultaneously in tissue samples. It is used to collect the information from tissue samples regarding gene expression differences that could be useful for cancer classification. However, this classification task faces many challenges due to availability of a smaller number of samples compared to the huge number of genes, and many of ...

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Blob Intelligent Hybrid Algorithm using Constraint-Based ...

Created: 2012-05-11 02:21:50

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Almost all hospital has its own nurses and still use the old fashion manual way of managing nurse scheduling in daily business. Nurse scheduling problem represents a difficult class of multi-objective optimisation problems consisting of a number of interfering objectives between the hospitals and individual nurses. Nurse scheduling consists of assignment of shifts and holidays to nurses for each day on the time horizon, taking into consideration a variety of conflicting interests or obj...

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Blob Inferring Gene Regulatory Networks from Gene Express...

Created: 2012-05-11 02:20:28

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Enabled by recent advances in bioinformatics, the inference of gene regulatory networks (GRNs) from gene expression data has garnered much interest from researchers. This is due to the need of researchers to understand the dynamic behavior and uncover the vast information lay hidden within the networks. In this regard, dynamic Bayesian network (DBN) is extensively used to infer GRNs due to its ability to handle time-series microarray data and modeling feedback loops. However, the ...

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Blob Identifying Metabolic Pathway within Microarray Gene...

Created: 2012-05-11 02:18:43 | Last updated: 2012-05-11 02:18:44

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Extracting metabolic pathway that dictates a specific biological response is cunently one of the important disciplines in metabolic system biology research. Previous methods have successfirlly identified those pathways but without concerning the genetic effect and relationship of the genes, the underlying structw€ is not precisely represented and cannot be justified to be significant biologically. In this article, probabilistic models capable of identi&ing the significant...

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Blob Identifying Gene Knockout Strategies Using a Hybrid ...

Created: 2012-05-11 02:16:43

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Genome-scale metabolic networks reconstructions from different organisms have become popular in recent years. Genetic engineering is proven to be able to obtain the desirable phenotypes. Optimization algorithms are implemented in previous works to identify the effects of gene knockout on the results. However, the previous works face the problem of falling into local minima. Thus, a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) is proposed in this paper to solve the lo...

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Blob Identifying Gene Knockout Strategies Using a Hybrid ...

Created: 2012-05-11 02:15:08 | Last updated: 2012-05-11 02:15:09

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Genome-scale metabolic networks reconstructions from different organisms have become popular in recent years. Genetic engineering is proven to be able to obtain the desirable phenotypes. Optimization algorithms are implemented in previous works to identify the effects of gene knockout on the results. However, the previous works face the problem of falling into local minima. Thus, a hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) is proposed in this paper to solve the lo...

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Blob Genetic Algorithms Wrapper Approach to Select Inform...

Created: 2012-05-11 02:13:44

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Constantly improving gene expression technology offer the ability to measure the expression levels of thousand of genes in parallel. Gene expression data is expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. Key issues that need to be addressed under such circumstances are the efficient selection of minimum number of genes that contribute to a disease from the thousands of genes measured on microarrays that are inherently noisy. ...

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Blob Feature Selection Method Using Genetic Algorithm for...

Created: 2012-05-11 02:10:56

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Practical pattern classification problems require selection of a subset of attributes or features to represent the patterns to be classified. The feature selection process is very important which selects the informative features for used classification process. This is due to the fact that performance of the classifier is sensitive to the choice of the features used to construct the good classifier from small or high dimension data that are inherently noisy. In this paper, we propose an...

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Blob Distributed Data Partitioning Interface for Homogene...

Created: 2012-05-11 02:09:31

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The effort required to write efficient parallel programmes or to parallelize existing sequential algorithms remains daunting. This is true even for regularly structured problems. Much of the work takes place when partitioning and distributing workloads over processors in a distributed computing environment. To alleviate this task, we present a data parallel interface called Distributed Data Partitioning Interface (DDPI). Its simple interface permits parallel implementation even by users...

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Blob Bioinformatics: A Tool for Bio-Knowledge Generation ...

Created: 2012-05-11 02:08:16

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 With the knowledge-based economy (KBE) emerging as a new paradigm, it becomes important that economic actors acquire new knowledge and technology. This will stimulate innovation and contribute further growth and development. In the knowledge-based economy, it is not tangible capital but intangible and innovations that determine international competitiveness, productivity growth and worker’s status in the labour market. This intangible capital and innovation are supplied by knowled...

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Blob Automation of DNA Computing Readout Method Based on ...

Created: 2012-05-11 02:05:16

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Preaiausly, an eutornatian of a DNA mmputing rcodad methd far the HamiJtoni,an Path Prcblen (EPP) hos been implementd bosed on, LightCgcler Sgstem. In this stud,y, a simiJar reoilmrt approach is implemented baseil on DNA Engine Opticon 2 System. The rcadott appmaeh consists of tuo steps: rcnl-time arnplification in vitro us'i,ng TaqMowbaseil rcal-time PCR, followed by on in sili,co phase. The in silico phase consists of a d,ata clwtering algorithm and an information processing to e...

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Blob Applying Filter Approach and Genetic Algorithm Wrapp...

Created: 2012-05-11 02:02:28

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Gene expression microarray data is expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. One problem arising from this data is how to select a small subset of genes from thousands of genes and much fewer samples that are inherently noisy. This research deals with finding a small subset of informative genes from the gene expression data which maximize the classification accuracy and minimize the running time. This paper proposed a mo...

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Blob An Iterative GASVM-Based Method: Gene Selection and ...

Created: 2012-05-11 02:00:37

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Microarray technology has provided biologists with the ability to measure the expression levels of thousands of genes in a single experiment. One of the urgent issues in the use of microarray data is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a disease. This selection process is difficult due to many irrelevant genes, noisy genes, and the availability of the small number of samples compared to the huge number of genes (hi...

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Blob An Improved Binary Particle Swarm Optimisation for G...

Created: 2012-05-11 01:58:19

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The application of microarray data for cancer classification has recently gained in popularity. The main problem that needs to be addressed is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a disease. This selection process is difficult because of the availability of the small number of samples compared to the huge number of genes, many irrelevant genes, and noisy genes. Therefore, this paper proposes an improved binary parti...

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Blob An Image Registration Technique To Enhance PCB Inspe...

Created: 2012-05-11 01:56:19

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 is well k*atm that renl PCB inuge inipieetio* bwal 0n rclerential ap: proaches foces misalignment problems in detecting delects betwecn a template imoge arul a ilefectiae image. Hence, o reliable image registrtion techniqre is needed to aligt, these two irnages per{utly. Henre, a rqistrution trch*irye uhich inaryorvtes affme trcnsformotion anil bi-cubic interynlation has been prcposed. Etperimental rcsults haae shown that this regishation techniqte is suitoble to be employei to obt...

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Blob A Two-Step Binary Particle Swarm Optimization Approa...

Created: 2012-05-11 01:52:33 | Last updated: 2012-05-11 01:52:34

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Manipitetibn of wdre itzing, buffer sizing, and futffer inseriiai atu a few techniques that con be used to i,mproae tfune d,eloy 'in aery lorge su,le intqrction (VLSI) circuit routing- Thi* paper enhances an eri,sting approach, which is based on Particl,e Swarrn Optimization (PSO) fur sofuing rcuting poblem in VLil circaits. A hoo-step Binary Particle Swarm Optimizatdon (BPSO) apprcach, which is based on BPSO, is chosen in thi^s stuily to improue time ilelay through finding the bes...

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Blob A Study of Network-based Approach for Cancer Classif...

Created: 2012-05-11 01:49:20 | Last updated: 2012-05-11 01:49:21

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The advent of high-throughput techniques such as microarray data enabled researchers to elucidate process in a cell that fruitfully useful for pathological and medical. For such opportunities, microarray gene expression data have been explored and applied for various types of studies e.g. gene association, gene classification and construction of gene network. Unfortunately, since gene expression data naturally have a few of samples and thousands of genes, this leads to a biologi...

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Blob A Parallelizing Interface for K-Means Type Clusterin...

Created: 2012-05-11 01:46:24

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The k-means clustering algorithm and neural network batch training becomes computationally intensive when the manipulated data is large. One way to reduce the computational demand of such techniques is to execute them in a concurrent manner. Unfortunately, the effort required to implement these techniques in a distributed computing environment remains daunting. Much of the work takes place when partitioning and distributing workloads over processors in the distributed computing environm...

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Blob A New Hybrid Firefly Algorithm for Complex and Nonli...

Created: 2012-05-11 01:44:17 | Last updated: 2012-05-11 01:44:18

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 Global optimization methods play an important role to solve many real-world problems. However, the implementation of single methods is excessively preventive for high dimensionality and nonlinear problems, especially in term of the accuracy of finding best solutions and convergence speed performance. In recent years, hybrid optimization methods have shown potential achievements to overcome such challenges. In this paper, a new hybrid optimization method called Hybrid Evolutionary ...

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Blob A Hybrid of SVM and SCAD with Group-specific Tuning ...

Created: 2012-05-11 01:39:36

Credits: User Mohd Saberi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 The incorporation of pathway data into the microarray analysis had lead to a new era in advance understanding of biological processes. However, this advancement is limited by the two issues in quality of pathway data. First, the pathway data are usually made from the biological context free, when it comes to a specific cellular process (e.g. lung cancer development), it can be that only several genes within pathways are responsible for the corresponding cellular process. Second, p...

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