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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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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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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

Comments: 4 | Viewed: 494 times | Downloaded: 682 times

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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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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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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

Comments: 0 | Viewed: 178 times | Downloaded: 282 times

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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

Comments: 0 | Viewed: 219 times | Downloaded: 377 times

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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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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

Comments: 0 | Viewed: 166 times | Downloaded: 146 times

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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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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

Comments: 0 | Viewed: 256 times | Downloaded: 126 times

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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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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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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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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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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

Comments: 0 | Viewed: 126 times | Downloaded: 818 times

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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

Comments: 0 | Viewed: 140 times | Downloaded: 49 times

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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

Comments: 0 | Viewed: 85 times | Downloaded: 0 times

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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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Project Biovel

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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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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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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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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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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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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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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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

Comments: 0 | Viewed: 76 times | Downloaded: 0 times

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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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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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Project Biovel

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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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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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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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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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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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...

File type: Adobe PDF

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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...

File type: Adobe PDF

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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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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...

File type: Adobe PDF

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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...

File type: Adobe PDF

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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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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...

File type: Adobe PDF

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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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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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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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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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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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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

File type: application/x-download

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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.

File type: Word document

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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. 

File type: Adobe PDF

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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...

File type: Adobe PDF

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