myExperiment

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Paul Fisher

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Gene Cosine Scores

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

Credits: 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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abstracts
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african trypanosomiasis
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authors
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cosine vector space
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data-driven
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enrichment
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entity recognition
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gene
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geneid
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genes
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mouse
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ncbi
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phenotype
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pubmed
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ranking
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sleeping sickness
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition

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Paul Fisher

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Pathway Cosine Scores from Day7 and Tir1 QTL

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

Credits: 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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abstracts
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african trypanosomiasis
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cosine vector space
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data-driven
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kegg
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Kegg Pathways
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pathway
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pathway-driven
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pathways
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phenotype
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sleeping sickness
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition
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trait

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M. Kirsh

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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: 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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Carol Lushbough

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BioExtract Server Workflow Tutorial

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

Credits: 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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Kimmo Karhu

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Community model and infrastructure for service devel...

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

Credits: 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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Katy Wolstencroft

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EraSysBio Summer School Taverna Tutorial

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

Credits: 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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M. Kirsh

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Apparency and Actuality

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

Credits: 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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,
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acids
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actuality
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and
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apparency
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biological
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biological lock and key
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cancer
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cellnucleushereditymemoryenergy
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classification
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code
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cognition
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cognitive
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complexity
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conversion
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descriptiontimeforceuniversaluracilvelocity
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diseasebalance
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distance
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disturbance
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diversity
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dream symbolism
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earth
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egg
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emergenceauto
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emergenceules
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equation
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evolution
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faces of objects
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for
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frame of reference
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function
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genealogyapparenttransparentproximityrepresentationvisualrepresentationsensory
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genetic
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genetic transmission
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graph of egg
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immune
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in
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language and nature
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lifeparadoxpe3rceptionperspectiveprocessesrandomnessrandomnonrandomparitydnarnanucleicrelationships
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light"
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matter
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natural
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natural balance and pathology
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nature
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nature and ethics
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naturemirrorofoncogenesisorigin
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of
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radiationspeciesstructuresunsunlighttheory
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reproductionsolar
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speciesrelativityrepresentationrepresentationeinsteintheoryselectionselective
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verses

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M. Kirsh

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Induction, Space and Positive Ethics

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

Credits: 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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M. Kirsh

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Genetics Reconstrued From the Mathematics of Einstei...

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

Credits: 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

Comments: 0 | Viewed: 93 times | Downloaded: 52 times

Tags:

accomodation
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actual
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aqpparent
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art and science
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change
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cloninggenetic
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deoxyuridine
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egg
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einstein
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emergence
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environment
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environmental disturbance
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ethicevolutionscience
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euclid
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general science'
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human behavior and history
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invention
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laws
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logic
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macro
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manipulationethicsnatural
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mass
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micro
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nature
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of
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physical science and invention
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proximity
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relativity
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self
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space
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symmetry
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theoryexperimentationcognitionconsciousnessart
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time
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transgenic
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unified theory
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uracil
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video

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Rafael C. Pinto

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Um Reconhecedor de PadrÃµes EspaÃ§o-Temporais Inspir...

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

Credits: 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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Rafael C. Pinto

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A Neocortex Inspired Hierarchical Spatio-Temporal Pa...

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

Credits: 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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Rafael C. Pinto

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LoopSOM: A Robust SOM Variant Using Self-Organizing ...

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

Credits: 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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David R Newman

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myExperiment RDF slides for F2F 15/07/2009

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

Credits: 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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Gerard Schaafsma

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raven.properties file

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

Credits: 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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Marco Roos

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New run.sh for Taverna 2 (in case of problems with n...

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

Credits: 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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Mcleodm

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

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

Credits: Mcleodm

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

File type: Word document

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Wei Tan

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Output of the lymphoma prediction workflow (on Ubunt...

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

Credits: Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

testing on Ubuntu Linux 8.0.4 + Java 1.5_16

File type: XML

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Wei Tan

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Output of the lymphoma prediction workflow

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

Credits: Wei Tan

Attributions: 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).

File type: XML

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Wei Tan

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Input CQL of the lymphoma prediction workflow

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

Credits: Wei Tan

Attributions: 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.

File type: XML

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