myExperiment

Uploader

Wassinki

View

Download

Installing java certificates for services using SSL

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

Credits: 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

Comments: 1 | Viewed: 1757 times | Downloaded: 1485 times

Tags:

Uploader

Marco Roos

View

Download

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: Marco Roos Martijn Schuemie AID 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

Comments: 1 | Viewed: 490 times | Downloaded: 381 times

Tags:

Uploader

Franck Tanoh

View

Download

Taverna tutorial

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

Credits: Franck Tanoh 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

Tags:

Uploader

Paul Dobson

View

Download

Smiles Search of ChemSpider

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

Credits: 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

Comments: 0 | Viewed: 533 times | Downloaded: 242 times

Tags:

Uploader

Don Cruickshank

View

Viking boat

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

Credits: 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

Comments: 0 | Viewed: 260 times | Downloaded: 1 time

Tags:

boat

Uploader

Alan Williams

View

Download

Example XSLT file

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

Credits: 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

This File has no tags!

Uploader

Alan Williams

View

Download

Example XML file

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

Credits: 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

This File has no tags!

Uploader

Katy Wolstencroft

View

Download

The Data Playground: An Intuitive Workflow Specifica...

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

Credits: Katy Wolstencroft 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

Comments: 0 | Viewed: 232 times | Downloaded: 242 times

Tags:

Uploader

Bas Vroling

View

Download

Using Taverna and webservices as tools to revive a d...

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

Credits: 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

This File has no tags!

Uploader

Franck Tanoh

View

Download

Taverna tutorial

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

Credits: Franck Tanoh 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

Comments: 0 | Viewed: 227 times | Downloaded: 300 times

Tags:

Uploader

Andrea Wiggins

View

Download

Output from FLOSS Communication Centralization Workflow

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

Credits: Andrea Wiggins Crowston James Howison

Attributions: 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: 254 times | Downloaded: 123 times

Tags:

Uploader

Yuwei Lin

View

Introduction to NCeSS Data Mining Pilot Project

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

Credits: 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

Comments: 1 | Viewed: 190 times | Downloaded: 0 times

Tags:

Uploader

Lance A. Schell

View

Download

Experiment One: Vapor Pressure of Liquids [Lab Report]

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

Credits: 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

Comments: 0 | Viewed: 111 times | Downloaded: 593 times

This File has no tags!

Uploader

Wassinki

View

Download

Test Input for Mapping oligonucleotides to an assembly

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

Credits: 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

Comments: 0 | Viewed: 814 times | Downloaded: 51 times

Tags:

oligonucleotides

Uploader

Wassinki

View

Download

Input for Mapping oligonucleotides to an assembly

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

Credits: 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

Comments: 0 | Viewed: 100 times | Downloaded: 35 times

This File has no tags!

Uploader

Antoon Goderis

View

Download

Workflow re-use and discovery in bioinformatics

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

Credits: 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

This File has no tags!

Uploader

Thomask...

View

Download

Example protein list for wikipathways workflow

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

Credits: 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

This File has no tags!

Uploader

Hong Chang Bum

View

pdf file test

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

Credits: 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

This File has no tags!

Uploader

Richard Marchese Robinson

View

Download

NanoPUZZLES ISA-TAB-Nano Templates

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

Credits: 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

Comments: 0 | Viewed: 282 times | Downloaded: 56 times

Tags:

Uploader

Maria Paula Balcazar-Vargas

Project

View

Download

Integral Projection Model documentation

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

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Integral Projection Model for Demographic Modelling v34 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

Comments: 0 | Viewed: 200 times | Downloaded: 124 times

Tags:

Uploader

booiiing

View

Download

EPR-Solver

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

Credits: 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)

Comments: 0 | Viewed: 71 times | Downloaded: 117 times

Tags:

Uploader

David De Roure

View

Download

The impact of workflow tools on data-centric research

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

Credits: David De Roure Carole Goble

Attributions: 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

Comments: 0 | Viewed: 107 times | Downloaded: 118 times

This File has no tags!

Uploader

David De Roure

View

Download

Word file for myExperiment CCPE paper

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

Credits: 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

Comments: 0 | Viewed: 75 times | Downloaded: 153 times

This File has no tags!

Uploader

Paul Dobson

View

Download

ONDEX Graph from the Yeast Jamboree SBML

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

Credits: 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

Comments: 0 | Viewed: 619 times | Downloaded: 57 times

Tags:

Uploader

Dfmac

View

Download

London Roadshow PPT

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

Credits: Dfmac

License: Creative Commons Attribution-Share Alike 3.0 Unported License

David Fergusson's presentation for London Roadshow

File type: PowerPoint presentation

Comments: 0 | Viewed: 78 times | Downloaded: 223 times

Tags:

Files