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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

File type: application/x-zip

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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

File type: Chemistry Plan

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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.  ...

File type: Adobe PDF

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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.

File type: Plain text

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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.

File type: Plain text

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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.

File type: Plain text

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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.

File type: Excel workbook

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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 ...

File type: Excel workbook

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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 ...

File type: Adobe PDF

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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.

File type: Word 2007 document

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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

File type: PNG image

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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

File type: application/mspowerpoint

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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 ,...

File type: Adobe PDF

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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...

File type: Adobe PDF

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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...

File type: Adobe PDF

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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.

File type: application/vnd.oasis.opendocument.presentation

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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...

File type: Adobe PDF

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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,...

File type: Adobe PDF

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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.

File type: PowerPoint presentation

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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.

File type: Trident (Package)

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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.

File type: Trident (Package)

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