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345?size=60x60 Nl Wassinki
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Blob Installing java certificates for services using SSL

Created: 2008-10-15 09:05:44 | Last updated: 2009-02-16 07:37:39

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This jar file, designed by sun microsystems, helps you to install certificates for java to access services using a secure socket. The complete documentation of this small java tool, including its source, can be found at: http://blogs.sun.com/andreas/entry/no_more_unable_to_find In this document, I will explain how to create a keystore holding the certificate required to access services provided by www.bioinformatics.nl . To install the certificate for www.bioinformatics.nl, do the follow...

File type: Java archive

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30?size=60x60 Nl Marco Roos
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Blob From biologist to web service to Taverna to myExperi...

Created: 2008-03-21 19:00:12 | Last updated: 2008-03-23 10:39:27

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A movie to show the principle of the round trip from a biology question via pieces of code wrapped as web services and combined into a workflow (computational experiment) in Taverna, via uploading to myExperiment and back to the biologist through myExperiment's run facility. NB: at the time of uploading this movie the runner-option was in test-phase. It is important to note that the workflow combines the work of various scientists with different expertise and some at remote locations around ...

File type: AVI video

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396?size=60x60 Gb Franck Tanoh
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Blob Taverna tutorial

Created: 2008-03-03 11:05:24 | Last updated: 2008-03-03 11:20:45

Credits: User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A step by step guide on how to build workflows in Taverna. This tutorial is designed for any background. i welcome your comments and suggestions.

File type: PowerPoint presentation

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76?size=60x60 Gb Paul Dobson
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Blob Smiles Search of ChemSpider

Created: 2008-02-27 16:21:30 | Last updated: 2012-01-12 21:12:15

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A Pipeline Pilot protocol to search ChemSpider by structure (smiles string) to illustrate use of the ChemSpider wsdl

File type: XML

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3947?size=60x60 Gb Don Cruickshank
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Blob Viking boat

Created: 2007-11-07 11:46:06 | Last updated: 2008-02-06 12:02:05

Credits: User Don Cruickshank

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

This boat is alongside the largest remaining section of Southampton's city wall, next to the Grand Harbour hotel. The sand and blue coloured stone sections on the ground represent the original beach and waterline before the land was reclaimed.

File type: Progressive JPEG image

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1217?size=60x60 Gb Alan Williams
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Blob Example XSLT file

Created: 2008-09-26 12:13:31

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

XSLT file to be used for example workflows

File type: Binary data

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1217?size=60x60 Gb Alan Williams
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Blob Example XML file

Created: 2008-09-26 12:12:41

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

XML file to be used for example workflows

File type: XML

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71?size=60x60 Nl Katy Wolstencroft
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Blob The Data Playground: An Intuitive Workflow Specifica...

Created: 2008-06-02 14:46:40

Credits: User Katy Wolstencroft User Andrew Gibson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a copy of the paper we wrote for the 3rd International Conference on e-Science and Grid Computing 2007 (http://www.escience2007.org/index.asp). It won the Best Paper award!  

File type: Adobe PDF

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Avatar Nl Bas Vroling
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Blob Using Taverna and webservices as tools to revive a d...

Created: 2008-04-20 17:04:40

Credits: User Bas Vroling

License: Creative Commons Attribution 3.0 Unported License

In this report a short description is given on how webservices were used as supporting tools for reviving an outdated database containging biological data.

File type: Adobe PDF

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396?size=60x60 Gb Franck Tanoh
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Blob Taverna tutorial

Created: 2008-03-03 11:15:00 | Last updated: 2008-03-03 11:16:11

Credits: User Franck Tanoh User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A step by step guide on how to build workflows in Taverna.  Biology oriented but  should be ok with other background with a 'tiny'  Biology knowledge.  I welcome your comments and suggestions.

File type: PowerPoint presentation

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298?size=60x60 Us Andrea Wiggins
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Blob Output from FLOSS Communication Centralization Workflow

Created: 2008-02-10 01:56:29 | Last updated: 2008-06-09 21:53:03

Credits: User Andrea Wiggins User Crowston User James Howison

Attributions: Workflow FLOSS Communication Centralization Plot, Exponentially Weighted

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This example shows the communication dynamics in the Gaim project's "users helping users" forum.

File type: PNG image

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Avatar Gb Yuwei Lin
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Blob Introduction to NCeSS Data Mining Pilot Project

Created: 2007-11-22 15:51:42

Credits: User Yuwei Lin

License: Creative Commons Attribution-Share Alike 3.0 Unported License

These slides created by Jon Gibson for his presentation at the 3rd e-Social Science Conference at Ann Arbor (USA) summarise the progress of the NCeSS Data Mining Pilot Project. Two social scientific datasets are used: European Work and Employment Survey, and English Longitudinal Study of Aging.

File type: Adobe PDF

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Avatar Us Lance A. Schell
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Blob Experiment One: Vapor Pressure of Liquids [Lab Report]

Created: 2009-03-23 22:50:57

Credits: User Lance A. Schell

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document is the report for the vapor pressure of liquids laboratory experiment.

File type: Word 2007 document

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345?size=60x60 Nl Wassinki
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Blob Test Input for Mapping oligonucleotides to an assembly

Created: 2008-12-11 12:06:36 | Last updated: 2008-12-11 12:21:53

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a small test set to quickly test the workflow. This test set can be run on almost any computer and takes 5 minutes approximately.

File type: XML

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345?size=60x60 Nl Wassinki
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Blob Input for Mapping oligonucleotides to an assembly

Created: 2008-12-11 12:04:22 | Last updated: 2008-12-11 12:21:40

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The complete input set for "Mapping oligonucleotides to an assembly" When this set is used, the whole workflow run takes about 6 hours on a 3 GHz Linux computer with 24 Gig RAM!

File type: XML

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97?size=60x60 Be Antoon Goderis
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Blob Workflow re-use and discovery in bioinformatics

Created: 2008-10-03 16:34:45

Credits: User Antoon Goderis

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

Antoon Goderis, PhD thesis, University of Manchester, 2008.

File type: Adobe PDF

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537?size=60x60 Nl Thomask...
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Blob Example protein list for wikipathways workflow

Created: 2008-09-16 11:40:24

Credits: User Thomaskelder

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is an example protein list that can be used as input to this workflow.

File type: Plain text

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255?size=60x60 Hong Chang Bum
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Blob pdf file test

Created: 2007-11-16 00:31:00

Credits: User Hong Chang Bum

License: Creative Commons Attribution-Share Alike 3.0 Unported License

pdf file test

File type: Unknown

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Avatar Richard Marchese Robinson
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Blob NanoPUZZLES ISA-TAB-Nano Templates

Created: 2015-03-27 14:29:30 | Last updated: 2015-12-18 15:59:53

Credits: User Richard Marchese Robinson

License: Creative Commons Attribution 3.0 Unported License

The files hosted here are Excel-based templates for the creation of ISA-TAB-Nano datasets [https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano] which were developed within the context of the NanoPUZZLES EU project [http://www.nanopuzzles.eu/]. (Up to date information on ISA-TAB-Nano can be found here: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano ISA-TAB-Nano is a derivative of ISA-TAB, for which further information may be found here: http://www.isa-tools.org/format/specification/)The resea...

File type: application/x-zip-compressed

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Integral Projection Model documentation

Created: 2013-08-13 13:22:56 | Last updated: 2014-07-04 12:20:25

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

Attributions: Workflow Integral Projection Model for Demographic Modelling v34 Blob Demographic data Cryptantha flava

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Integral Projection Model Workflow provides an environment for create an integral projection model and to calculate its population growth, structure, sensitivities and elasticities analyses, age-specific metrics, etc.Create an IPM with no density dependence and perform several analyses on it.Analyses:Lambda (λ).Sensitivity analysis.Elasticity analysis.Parameters ...

File type: Adobe PDF

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Avatar booiiing
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Blob EPR-Solver

Created: 2009-06-05 16:46:06 | Last updated: 2009-06-05 18:10:35

Credits: User booiiing

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This little perl-script automatically probes all assignments (g1, g2, g3) to (gx, gy, gz) (including negated values) in EPR/ESR (electron paramagnetic resonance / electron spin resonance) and tests them for several conditions. In the end, it gives you the assignements, as well as Eg, E1, E2, V/Delta and a, b, c. It is published under the terms of the GNU General Public Licence. Thus uploading is allowed for everyone to make it easier to contribute.

File type: Trident (Package)

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3791?size=60x60 Gb David De Roure
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Blob The impact of workflow tools on data-centric research

Created: 2009-05-05 23:59:48

Credits: User David De Roure User Carole Goble

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

final draft article for Tony Hey and Kristin Tolle's book "Data Intensive Computing: The Fourth Paradigm of Scientific Discovery"

File type: Adobe PDF

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3791?size=60x60 Gb David De Roure
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Blob Word file for myExperiment CCPE paper

Created: 2009-04-10 13:40:18 | Last updated: 2009-04-21 15:01:57

Credits: Network-member CCPE eScience 2008 special issue myExperiment paper co-authors

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Note this is not in any aprticular CCPE template as they only provide a LaTeX template

File type: Word document

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76?size=60x60 Gb Paul Dobson
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Blob ONDEX Graph from the Yeast Jamboree SBML

Created: 2009-02-10 10:51:58 | Last updated: 2009-02-10 12:48:52

Credits: User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

File type: GNU Zip Archive

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411?size=60x60 Gb Dfmac
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Blob London Roadshow PPT

Created: 2009-01-29 13:56:35

Credits: User Dfmac

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 David Fergusson's presentation for London Roadshow

File type: PowerPoint presentation

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460?size=60x60 Gb Will
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Blob Seeding cells protocol for OMERO.editor

Created: 2008-09-15 14:46:28 | Last updated: 2008-10-07 13:09:38

Credits: User Will

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 A simple demo protocol for OMERO.editor.  You can download OMERO.editor (as part of OMERO clients) from here.

File type: XML data

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3947?size=60x60 Gb Don Cruickshank
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Blob White noise

Created: 2007-11-22 15:31:12 | Last updated: 2009-07-08 16:57:59

License: GNU General Public License (GPL) 2.0

Perfect for headphones in a busy environment.

File type: Binary data

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4144?size=60x60 De Alexey Mints
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Blob Tools to split spatial N-dimensional data in cells o...

Created: 2016-10-19 09:31:56 | Last updated: 2018-06-29 09:12:04

Credits: User Alexey Mints

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Documentation to follow later

File type: text/x-python

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4144?size=60x60 De Alexey Mints
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Blob Multiplot

Created: 2014-10-05 11:04:30 | Last updated: 2018-03-12 15:20:56

Credits: User Alexey Mints

License: Creative Commons Attribution-Share Alike 3.0 Unported License

usage: multiplot.py [-h] [-x XCOLUMN] [-y COLUMNS] [-f FILES] [-o OUTPUT]                    [-s STYLE] [-xl XLABEL] [-yl YLABEL] [--log LOG]                    [-ltitles LEGENDTITLES] [-m MARKER] [-d DELIMITER]                    [--skip-header SKIP_HEADER] [-lp LEGEND_POSITION]Background calculatoroptional arguments:  -h, --help   &n...

File type: text/x-python

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Demographic data Cryptantha flava

Created: 2013-08-13 10:13:10 | Last updated: 2014-07-04 12:30:08

Credits: User Robcito

Attributions: Workflow Integral Projection Model for Demographic Modelling v34

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .csv file of one year demographic data of the species: Cryptantha flava, collected and published by Roberto Salguero-Gómez (University of Queensland).This file allow users to run Integral Projection Model workflow. http://www.myexperiment.org/workflows/3687.html Each row represents one observation of an organism in the population at one census time t with the following column names:size: size of individuals in census time tsizeNext: size of individual...

File type: Excel workbook

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4450?size=60x60 In Drkrish...
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Blob Industrial process for OXICONAZOLE Dr Krishnasarma P...

Created: 2012-07-24 11:38:44 | Last updated: 2013-06-21 09:49:15

Credits: User Drkrishnasarmapathy

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Industrial process for OXICONAZOLE Dr Krishnasarma PathyOxiconazole inhibits ergosterol biosynthesis, which is required forcytoplasmic membrane integrity of fungi. It acts to destabilize the fungal cyctochromeP450 51 enzyme (also known as Lanosterol 14-alpha demethylase). This is vital in thecell membrance structure of the fungus. Its inhibition leads to cell lysis. Oxiconazole hasalso been shown in inhibit DNA synthesis and suppress intracellular concentrations ofATP. Like other imidazole an...

File type: Adobe PDF

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688?size=60x60 Us M. Kirsh
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Blob The Path of Knowledge ; The Knowledge of Path - New ...

Created: 2010-03-31 05:35:36

Credits: User M. Kirsh

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

Abstract   An unwitnessible silence is suggested to accompany all change. Conceptual paradox involving mind and matter, contrasting mind as an enduring state of the becoming of energy into a state of matter, and matter as the constantly becoming environment, is tested against criteria of witnessibility with respect to criteria for the existence of entities and phenomenon for consistency to capture an acceptably reasoned description, from a modern perspective, of cultural evolution....

File type: Adobe PDF

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469?size=60x60 Gb Paolo
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Blob EDBT Provenance talk presentation - PFD version

Created: 2010-03-26 14:01:00 | Last updated: 2010-03-26 14:02:09

Credits: User Paolo

License: Creative Commons Attribution-Share Alike 3.0 Unported License

PDF version -- see related pack for Native Keynote link to paper link to conference proceedings  

File type: application/unknown

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Avatar Architpuri
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Blob test

Created: 2010-03-08 14:43:10

Credits: User Architpuri

License: Creative Commons Attribution-Share Alike 3.0 Unported License

test

File type: Plain text

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688?size=60x60 Us M. Kirsh
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Blob THE PATH OF KNOWLEDGE : KNOWLEDGE OF THE PATH

Created: 2010-02-22 00:21:43

Credits: User M. Kirsh

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

Abstract       The philosophies of Parmenides, Socrates, Aristotle, the science of Einstein is discussed with respect to a division of the empirical and abstracted as they refer to the universe and universals. Methodologies of the natural and anthropological sciences are contrasted  in order to discuss validity in the representation of nature. A physical model for the evolution of knowledge is presented that distinguishes both the conceptual and physical in terms of...

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688?size=60x60 Us M. Kirsh
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Blob Introduction to My Presented Works-Marvin E. Kirsh

Created: 2010-02-15 01:10:45 | Last updated: 2010-02-15 04:40:32

Credits: User M. Kirsh

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

    An introductory  background and stated approach with initial assumptions employed towards the creation of my manuscripts and ideas.  My notions reflect a naturalism,  with a slant oriented from the realism of perception, away from abstracted theory that is given its' only validity from empirical test rather than direct first person witness. I began this project as a graduate student in the biological sciences with a statement from a professor of classical g...

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688?size=60x60 Us M. Kirsh
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Blob Physical Contiguity of "The Concept" : The Concept o...

Created: 2010-02-05 03:37:55 | Last updated: 2010-02-05 19:31:11

Credits: User M. Kirsh

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

Abstract It is an entity of nature,  the human conceiver that emerges ?the concept?. It might be conjectured that in order for  a human  conceiver to conceive a concept of ?the concept?, as a subset of nature, first he must have a concept of nature with which to commence investigation into the nature of ?the  concept?.  Second,  the nature of ?the concept? might be expected to be an emergence from the individuals? concept of nature; in essence to reflect a conce...

File type: Adobe PDF

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688?size=60x60 Us M. Kirsh
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Blob Uniqueness, Self Belonging and Intercourse in Nature...

Created: 2010-01-09 04:42:06

Credits: User M. Kirsh

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

Abstract Biological organization is discussed within a holistic framework . A new orientation is presented of natural processes with  an approach in model construction that is focused strictly on physical form and centered away from abstractions that escape the perceptual senses,  lead towards the postulation of non-verifiable and non-witnessible  entities.  A universal construction composed of first perspective representations of path, witness as unique loci in volumes o...

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688?size=60x60 Us M. Kirsh
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Blob What Happened? Are We Asking or Telling?

Created: 2010-01-02 04:12:38

Credits: User M. Kirsh

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

Abstract      A conceptual parallel is created between studies in anthropology and natural science.  A  space occupied by “the conceptualization”  is argued to not only parallel  symbolically the scientifically conceived value of volume as space, but to have an equal meaning- the spaces of the conceptual ordering of nature as manifestations of energy are held to be paralleling  manifestations of the same energies that mold the environm...

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45?size=60x60 Gb David R Newman
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Blob NeuroHub Presentation to Southampton Neuroscientists

Created: 2009-11-26 11:59:43

Credits: User David R Newman

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This presentation was given on 19th November 2009 to allow the the neuroscientists in Southampton to get an overview of what we NeuroHub intended to do and get feedback to find out what they would and wouldn't find useful.

File type: PowerPoint presentation

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688?size=60x60 Us M. Kirsh
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Blob Anthropology and Parallelism: The Individual as a Un...

Created: 2009-11-15 19:52:10

Credits: User M. Kirsh

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

Abstract It is difficult to define perspective within sets that are self belonging. For example in the study of man­kind, anthropology, both men and their studies fall into the same category that contains the topic out­line. This situation entails a universal quality of uniqueness, an instance of it, to the topic of anthropo­logy that may be viewed in parallel with the topic of nature as the set of unique particulars. Yet one might assent to the notion in the inclusive study of m...

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324?size=60x60 Gb George
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Blob Kegg Gene Identifiers

Created: 2009-11-14 16:29:01

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An example file of a list of Kegg gene identifiers used to test searching the Kegg database.

File type: Plain text

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324?size=60x60 Gb George
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Blob Pubmed Identifiers

Created: 2009-11-14 16:23:47

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A list of example pubmed identifers to use when testing abstract retrieval and text-mining workflows

File type: Plain text

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Avatar Gb Andrea
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Blob Very simple script to fix pathway commons biopax files

Created: 2009-11-04 11:05:46

Credits: User Andrea

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This very simple script (it only replace one type of ID!) will fix BioPAX files coming from PathwayCommons. In this files, rdf:ID is used instead of rdf:about, and since these files contains repetition, this results in an error in strict parsers. This error gets undetected in many system as they disable replicated ID checking for performance, but it's still a problem in some.

File type: application/x-perl

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4399?size=60x60 Gb Paul Fisher
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Blob KEGG Compounds to Inchi strings

Created: 2009-11-02 16:15:39 | Last updated: 2009-11-02 16:15:57

Credits: User Paul Fisher User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG compounds which are reffered to by their Inchi strings.

File type: Chemistry Plan

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728?size=60x60 Nl Barend
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Blob The general plan and guidelines for BioAssist from O...

Created: 2009-10-26 10:15:03

Credits: User Barend

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document has been accepted at the NBIC management team meeting of 22 October 2009, and will serve as ageneral guideline to run the BioAssist program of NBIC. It might be a good idea to read the short document before you contact BioAssist for support in the scope of your 'code' or 'content' interests. Barend Mons

File type: application/x-download

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728?size=60x60 Nl Barend
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Blob nano publication as a way to explain rich triples

Created: 2009-10-23 07:32:36 | Last updated: 2009-10-25 20:38:34

Credits: User Barend User Jan Velterop Network-member Concept Web Alliance (general)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This paper can be used to explain what triples in our context are meant to be and to serve I will present the paper on the semantic web conference workshop 26th of November

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4399?size=60x60 Gb Paul Fisher
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Blob Ondex and Taverna Tutorial

Created: 2009-10-22 13:50:53 | Last updated: 2009-10-22 13:51:51

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

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688?size=60x60 Us M. Kirsh
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Blob Physical Contiguism

Created: 2009-10-18 05:28:32

Credits: User M. Kirsh

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

The topic of physical contiguism is proposed in description to bridge paradoxes of mind and matter.  It seems that in efforts to bridge topics of science and consciousness focus has drifted towards a means to accommodate the mind in physical terms in order to draw correspondances with the more readily studied topic of matter. – i.e. as a topic in brain science. 

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688?size=60x60 Us M. Kirsh
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Blob The Bend : A Speculation on History and Science

Created: 2009-09-20 04:08:33

Credits: User M. Kirsh

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

The age of human civilization is given the name “the bend” based on a re-examination of the emergence of science, science theory content, and history.</font></font>  Civilization, existing over its course, in  darkness to the  nature of its partnership with the elements, oscillates in a romance that alternates between logical explanation, the rational, and illogical as they are  presented to him from the external. Its&rsquo...

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469?size=60x60 Gb Paolo
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Blob GeoClouds workshop talk

Created: 2009-09-18 13:58:14

Credits: User Paolo User David De Roure User Carole Goble User David R Newman

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Indianapolis, IN, Sept 17, 2009 www.dataandsearch.org/dsi/events/geoclouds.html

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469?size=60x60 Gb Paolo
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Blob Provenance DB dump to be used as a reference

Created: 2009-09-10 14:18:23

Credits: User Paolo

License: Creative Commons Attribution-Share Alike 3.0 Unported License

this dump contains the provenance for 2 runs of this workflow: www.myexperiment.org/workflows/908

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688?size=60x60 Us M. Kirsh
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Blob Uniqueness , Self Belonging and Intercourse in Nature

Created: 2009-08-23 07:53:40 | Last updated: 2009-08-23 08:06:11

Credits: User M. Kirsh

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

The world is discussed and framed so that it does not evolve divisions alike  the conceptual division  between Special and General Relativity in which emerged divides are   suggested to be parallel to and emerged from paradoxes of mind-matter, the self and nature.  Of all of the potential properties of the unique Universe, emergence, affinity, self avoidance , etc., self belonging is never a characteristic of unique and energy metabolizing spaces/entities.  ...

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4399?size=60x60 Gb Paul Fisher
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Blob Pathway Term Enrichment Scores

Created: 2009-08-11 14:23:49

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of each pathway identified from day 7 post infection and linked to the Tir1 QTL. With each pathway is a list of terms that are common to both pathway and phenotype corpora. These terms were ranked accoring to their enrichement scores. The higher the score, the more significant the term is in relation to correlating the pathway with the African trypanosomiasis resistance phenotype.

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4399?size=60x60 Gb Paul Fisher
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Blob Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 2009-08-11 14:08:41 | Last updated: 2009-08-11 14:15:58

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains all the abstracts for pathways found to be differentially expressed at day 7 post infection and intersect the Tir1 QTL region, from the African Trypanosomiasis project. Each pathway is listed as ">> [Pathway Name]", together with a PubMed identifier, date, and abstract for each article. Each pathway has been restricted to 500 abstracts, and is given in the date range 31/12/2007 to 01/01/2009. Note, some pathways do not have any abstracts available due to th...

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4399?size=60x60 Gb Paul Fisher
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Blob PubMed Term Counts

Created: 2009-08-11 13:59:35

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in MEDLINE the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype.

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4399?size=60x60 Gb Paul Fisher
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Blob PubMed Abstract Number

Created: 2009-08-11 13:54:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the number of articles available in MEDLINE, through PubMed, at the time of performing these data analyses. The date of identifying these publications was 25/02/2009.

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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Term Counts (in Phenotype Corpus)

Created: 2009-08-11 13:34:42 | Last updated: 2009-08-11 13:58:28

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in the phenotype corpus the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype.

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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Concept Profile - Terms

Created: 2009-08-11 13:05:07 | Last updated: 2009-08-11 13:06:51

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all terms extracted from the phenotype corpus, relating to African trypanosomiasis resistance in the mouse model. These terms were extracted using the following service: http://gopubmed4.biotec.tu-dresden.de/GoPubMedTermGenerationService/services/GoPubMedTermGeneration?wsdl These terms represent the concept profile for the phenotype.

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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Abstracts for Trypanosomiasis Resistance

Created: 2009-08-11 12:45:24

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of published abstracts from MEDLINE, that are related to the African Trypanosomiasis resistance phentoype in the mouse. The term used in the PubMed search was: trypanosom* AND (tolerance OR resistance) . The workflow limited the date of the search using PubMed between 31/12/2005 to 01/01/2009, and was restricted to 500 abstracts.

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4399?size=60x60 Gb Paul Fisher
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Blob Gene Cosine Scores

Created: 2009-08-10 16:00:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of genes linked to the resistance to African trypanosomiasis in the mouse. Genes from the Tir1 QTL were used in a search through PubMed. The results were then correlated to the trypanosomiasis resistance phenotype. The higher the score (and ranking) the more related to the phenotype the gene is likely to be. This is based on the co-occurrence of terms within the gene and phentoype corpora.

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4399?size=60x60 Gb Paul Fisher
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Blob Pathway Cosine Scores from Day7 and Tir1 QTL

Created: 2009-08-10 15:55:24

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of all pathways found to be differentially expressed at day 7 post infection in the trypanosomiasis resistance phenotype, which contain genes in the Tir1 QTL. The pathways in this file have been ranked according to the scores obtained after calculating a cosine vector value against the trypanosomiasis resistance phenotype. The higher the score, the more closely linked to a phentype a given pathway is. This allows each pathway to be ranked giving biologists a ...

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688?size=60x60 Us M. Kirsh
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Blob A Plane Economy of Space Surfaces From the Mathemati...

Created: 2009-08-07 19:38:05 | Last updated: 2009-12-21 17:32:25

Credits: User M. Kirsh

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

A perspective on nature is introduced based on a visit to the Plane Geometry of Euclid and reinterpretation of the theory of relativity. Nature is redifined  as a special case of proximity that is different from normally the construed physical proximity presented to perception. The world is considered as a special case in which the Laws of Motion of Newton and Special Relativity of Einstein are hopefuly united into a single frame. The science of genetics is revisited and new theory ...

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484?size=60x60 Us Carol Lushbough
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Blob BioExtract Server Workflow Tutorial

Created: 2009-08-07 16:20:06 | Last updated: 2009-08-07 16:25:46

Credits: User Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial demonstrates how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.

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Avatar Kimmo Karhu
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Blob Community model and infrastructure for service devel...

Created: 2009-08-04 08:46:13

Credits: User Kimmo Karhu

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Community model and infrastructure for service development

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71?size=60x60 Nl Katy Wolstencroft
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Blob EraSysBio Summer School Taverna Tutorial

Created: 2009-07-24 21:54:27

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial is an introduction to Taverna and myExperiment

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688?size=60x60 Us M. Kirsh
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Blob Apparency and Actuality

Created: 2009-07-19 05:24:57 | Last updated: 2009-07-19 05:29:37

Credits: User M. Kirsh

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

  Introduction   This manuscript was prepared before my introduction to theory in mythology.  My understanding of human behavior with regards to social transmision and communications past and present fell nicely into a discussion of the theory of relativity (re : "Einstein andMythology :The Lengthier the Relations in a Myth  the Greater its' Mass").  The discussion here is much bulkier but delves more into facets of biology ,...

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688?size=60x60 Us M. Kirsh
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Blob Induction, Space and Positive Ethics

Created: 2009-07-19 04:08:44 | Last updated: 2009-07-19 04:11:36

Credits: User M. Kirsh

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

One may purport that ones' awareness of space for scientific purposes comes about from a potential awareness of its' absence that is derived from times when ones attention is not focused on it. Yet simply one might extract the notion that space and entailed properties of it are elemental —i.e. conceptually non reducible and that from which all emanates. The words non-ethical induction, entailing the existence of ethical induction, if compared in a corresponding manner (to indivisible sp...

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688?size=60x60 Us M. Kirsh
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Blob Genetics Reconstrued From the Mathematics of Einstei...

Created: 2009-07-18 19:00:59 | Last updated: 2009-12-21 17:36:49

Credits: User M. Kirsh

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

A new perspective of nature is introduced based on a visit to the Plane Geometry of Euclid, The Paralle Postulate and a reinterpretation of the theory of relativity. Nature is redifined  as a special case of proximity that is different from normally construed physical proximity that is presented to perception. The world is considered as a special case in which the Laws of Motion of Newton and Special Relativity of Einstein are hopefuly united into a single frame. The science of...

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671?size=60x60 Br Rafael C. Pinto
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Blob Um Reconhecedor de Padrões Espaço-Temporais Inspir...

Created: 2009-07-16 21:31:35

Credits: User Rafael C. Pinto

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Presentation of the "A Neocortex Inspired Hierarchical Spatio-Temporal Pattern Recognition System" work, in Portuguese.

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671?size=60x60 Br Rafael C. Pinto
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Blob A Neocortex Inspired Hierarchical Spatio-Temporal Pa...

Created: 2009-07-16 21:26:17 | Last updated: 2009-07-18 17:33:41

Credits: User Rafael C. Pinto

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Undergraduate Thesis presented in partial fulfillment of the requirements for the degree of Bachelor of Computer Science. Abstract. Recently, inspired by our neocortex, an architecture for spatio-temporal pattern recognition has been proposed, the MPF (Memory-Prediction Framework). There already exists some attempts to implement it, like the HTM (Hierarchical Temporal Memory) and the HQSOM (Hierarchical Quilted Self-Organizing Map). The HQSOM lacks some parts of the MPF, which in turn ma...

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671?size=60x60 Br Rafael C. Pinto
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Blob LoopSOM: A Robust SOM Variant Using Self-Organizing ...

Created: 2009-07-16 21:20:54

Credits: User Rafael C. Pinto

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Paper accepted in the VIII ENIA - Encontro Nacional de Inteligência Artificial. To appear in proceedings of the XXIX CSBC - Congresso da Sociedade Brasileira de Computação. Abstract. This paper introduces feedback connections into a previously proposed model of the simple and complex neurons of the neocortex. The original model considers only feedforward connections between a SOM (Self-Organizing Map) and a RSOM (Recurrent SOM). A variant of the SOM-RSOM pair is proposed,...

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45?size=60x60 Gb David R Newman
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Blob myExperiment RDF slides for F2F 15/07/2009

Created: 2009-07-15 10:16:03 | Last updated: 2009-07-15 10:17:09

Credits: User David R Newman

License: Creative Commons Attribution-Share Alike 3.0 Unported License

These slides are an update from those given at the May 2009 myExperiment hackfest.  In particular and extra slide about linked data has been added.

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626?size=60x60 Nl Gerard Schaafsma
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Blob raven.properties file

Created: 2009-05-28 10:28:47

Credits: User Gerard Schaafsma

License: Creative Commons Attribution-Share Alike 3.0 Unported License

For those having problems starting Taverna 1, please try this. Put this file in de conf directory inside the taverna directory (where the runme.bat is), and restart Taverna.

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30?size=60x60 Nl Marco Roos
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Blob New run.sh for Taverna 2 (in case of problems with n...

Created: 2009-05-28 09:25:03

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This may help solve problems with T2 snapshot.

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Blob Supporting Data for Soils of western Wright Valley, ...

Created: 2009-04-30 22:42:14

Credits: User Mcleodm

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Soil profile descriptions and photographs of soils in western Wright Valley, Antarctica

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510?size=60x60 Us Wei Tan
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Blob Output of the lymphoma prediction workflow (on Ubunt...

Created: 2009-04-23 20:06:51

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

testing on Ubuntu Linux 8.0.4 + Java 1.5_16

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510?size=60x60 Us Wei Tan
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Blob Output of the lymphoma prediction workflow

Created: 2009-04-23 17:37:16 | Last updated: 2011-09-03 21:56:29

Credits: User Wei Tan

Attributions: Workflow Lymphoma type prediction based on microarray data

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Output of the lymphoma prediction workflow at http://www.myexperiment.org/workflows/746?version=1. It shows the lymphoma type prediction results. It contains lymphoma type predictions for 38 samples and there is only one error (on testSample_4).

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510?size=60x60 Us Wei Tan
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Blob Input CQL of the lymphoma prediction workflow

Created: 2009-04-23 17:25:04 | Last updated: 2011-09-03 21:57:43

Credits: User Wei Tan

Attributions: Workflow Lymphoma type prediction based on microarray data

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Input CQL of the lymphoma prediction workflow at http://www.myexperiment.org/workflows/746?version=1. It is only for the purpose of illustration and  NOT needed to run the workflow since the input has already been embedded.

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3791?size=60x60 Gb David De Roure
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Blob PowerPoint figures for CCPE

Created: 2009-04-10 18:55:45 | Last updated: 2009-04-14 08:43:22

Credits: User David De Roure User Carole Goble

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Figures prepared for the submitted paper, not all used.

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4399?size=60x60 Gb Paul Fisher
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Blob Ensembl gene report

Created: 2009-04-08 19:30:15 | Last updated: 2009-08-10 11:05:59

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains all genes identified in the Tir1 QTL region. Each gene is (if available) associated with an Entrez, UniProt, External Gene Id, Affymetrix probeset identifers (mouse_430_A chip), and Ensembl identifers for genes and their transcripts.

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4399?size=60x60 Gb Paul Fisher
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Blob Kegg pathway identifiers

Created: 2009-04-08 19:28:52 | Last updated: 2009-08-10 11:03:00

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG pathway identifiers, derived from a list of Ensembl genes found to be located with a given QTL/chromosomal region in the mouse. These genes are located in the Tir1 QTL.

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4399?size=60x60 Gb Paul Fisher
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Blob Kegg pathway descriptions

Created: 2009-04-08 19:27:55 | Last updated: 2009-08-10 11:29:34

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG pathway descriptions, identified from genes found within the Tir1 QTL region (for African Trypanosomiasis). Each pathway may contain multiple genes from within the QTL region.

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4399?size=60x60 Gb Paul Fisher
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Blob Kegg pathways and genes

Created: 2009-04-08 19:26:26 | Last updated: 2009-08-10 11:41:55

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all genes found within the Tir1 QTL region. These are represented as KEGG gene identifiers. Each gene is listed in tab deliminated format along with all KEGG pathway ids in which the gene is involved. These are given as KEGG pathway identifiers. Each gene may be included in zero or more pathways, with multiple instances of the same pathway being included in the file (due to multiple genes included in a single pathway).

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4399?size=60x60 Gb Paul Fisher
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Blob Kegg Pathway release

Created: 2009-04-08 19:25:05 | Last updated: 2009-08-10 12:06:18

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the version of the KEGG pathway database used in the analysis of the Tir1 QTL region

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4399?size=60x60 Gb Paul Fisher
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Blob Kegg-Uniprot-Entrez cross-references

Created: 2009-04-08 19:23:53 | Last updated: 2009-08-10 12:08:00

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG gene identifiers, cross-referenced to UniProt and Entrez identifiers. The UniProt and Entrez ids were obtained from BioMart for genes located in the Tir1 QTL region.

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4399?size=60x60 Gb Paul Fisher
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Blob Kegg gene descriptions

Created: 2009-04-08 18:06:23 | Last updated: 2009-08-10 12:10:07

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG gene descriptions, for each KEGG gene identified within the Tir1 QTL region.

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4399?size=60x60 Gb Paul Fisher
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Blob Ensembl database release

Created: 2009-04-08 18:00:35 | Last updated: 2009-08-10 12:12:09

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The release of the Ensembl database used to identify genes in Tir1 QTL region.

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4399?size=60x60 Gb Paul Fisher
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Blob Tir1 QTL - microarray day 7 intersecting pathways

Created: 2009-04-08 17:57:57

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 7 differentially expressed genes

File type: Excel workbook

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4399?size=60x60 Gb Paul Fisher
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Blob Tir1 QTL - Day 3 Microarray intersecting pathways

Created: 2009-04-08 17:56:10

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadhseet contains all of the intersecting pathways between the Tir1 QTL and day 3 differentially expressed genes

File type: Excel workbook

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4399?size=60x60 Gb Paul Fisher
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Blob Re-sequenced Daxx gene info

Created: 2009-04-08 17:53:46 | Last updated: 2009-08-10 12:30:59

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadsheet contains information about the re-sequencing of the daxx gene, identified as a candidate QTg for the African Trypanosomiasis resiatance phenotype. This file is related to the paper: http://www.ncbi.nlm.nih.gov/pubmed/17709344

File type: Excel workbook

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4399?size=60x60 Gb Paul Fisher
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Blob Authors table

Created: 2009-04-08 13:36:10 | Last updated: 2009-08-10 12:37:37

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This table contains a list of articles used to construct a list of issues with regards to the lack of systematic and explicit data analyses conducted in bioinformatcis. Each author list is linked directly to their publication within PubMed.

File type: Excel workbook

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4399?size=60x60 Gb Paul Fisher
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Blob Table of SNP sequenceing results

Created: 2009-04-08 13:29:32

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the results of re-sequencing the Daxx gene

File type: Word document

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4399?size=60x60 Gb Paul Fisher
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Blob Candidate Gene protocol

Created: 2009-04-08 13:27:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This protocol provides details on how to identify candidate genes from the returned workflow results.

File type: Word document

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4399?size=60x60 Gb Paul Fisher
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Blob A Systematic Strategy for Large-Scale Analysis of Ge...

Created: 2009-04-08 13:23:03

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This PDF is my personal copy of the NAR publication.

File type: Adobe PDF

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4174?size=60x60 Ca Francois Belleau
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Blob Murin.owl ontology designed with Ontowiz

Created: 2009-02-17 04:45:12 | Last updated: 2009-02-17 05:00:49

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The ontology of the Murin protocol was designed with Protege Ontowiz tool.

File type: GIF image

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4174?size=60x60 Ca Francois Belleau
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Blob Pubmed rdfiser from Bio2RDF project

Created: 2009-02-11 06:00:37 | Last updated: 2009-02-11 06:32:03

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file is needed to use Pubmed2n3 rdfizer workflow.

File type: XML

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411?size=60x60 Gb Dfmac
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Blob London Roadshow PDF

Created: 2009-01-29 13:58:35

Credits: User Dfmac

License: Creative Commons Attribution-Share Alike 3.0 Unported License

 David Fergusson's presentation as PDF

File type: Adobe PDF

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4387?size=60x60 Fr Glatard
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Blob input file for feat group analysis workflow

Created: 2009-01-28 17:31:10

Credits: User Glatard

License: Creative Commons Attribution-Share Alike 3.0 Unported License

To be used with VBrowser as input of workflow http://www.myexperiment.org/workflows/640

File type: Binary data

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4387?size=60x60 Fr Glatard
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Blob input file for feat individual analysis workflow

Created: 2009-01-28 17:23:01

Credits: User Glatard

License: Creative Commons Attribution-Share Alike 3.0 Unported License

To be used with the VBrowser as inputs of workflow http://www.myexperiment.org/workflows/639

File type: Binary data

Comments: 0 | Viewed: 40 times | Downloaded: 22 times

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