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- 16:01, 25 March 2009 Biobanking (hist) [4,540 bytes] Marcvandriel (Talk | contribs) (New page: Genetic association analyses are often compromised by missing genotypic data. However several imputation methods are available to overcome this in some way. Below an overview of some of th...)
- 18:55, 15 March 2009 BioWiseInformationManagement2009 (hist) [16,316 bytes] Mroos (Talk | contribs) (New page: =Managing life science information= ===PhD course Managing life science information=== :;Target audience: ''Bioinformatics PhD students'' :;Lecturers: Ammar Benabdelkader, Peter Boncz, A...)
- 09:29, 11 March 2009 NMC DSP metabolomics software (hist) [1,238 bytes] Tabma (Talk | contribs) (New page: This page gives an overview of already available metabolomics (related) software which is publicly available. * [http://mzmine.sourceforge.net/ MZmine 2] - MZmine 2 is an open-source proj...)
- 17:47, 25 February 2009 OMSSA (hist) [333 bytes] Pieterb (Talk | contribs) (New page: '''OMSSA''' stands for ''Open Mass Spectrometry Search Algorithm''. For the metabolomics platform, SARA builds an OMSSA web-application (-portal). == Manual == This manual is incomplete. ...)
- 16:09, 18 December 2008 Packaging HOWTO (hist) [7,095 bytes] Pieterb (Talk | contribs) (New page: This HOWTO explains how to create your own software packages for use on the Grid. It uses the hmmer package as an example. == Compiling hmmer == Create a directory where you will compile ...)
- 09:52, 17 December 2008 Ibidas code style (hist) [451 bytes] Jjbot (Talk | contribs) (New page: To make the code more readable we need to adhere to some coding standards. For now we will assume that the coding standards mentioned in [http://www.python.org/dev/peps/pep-0008/ Python PE...)
- 16:57, 8 December 2008 Ibidas imports (hist) [2,290 bytes] Jjbot (Talk | contribs) (New page: * Gene Ontology (GO) obo file http://www.geneontology.org/GO.downloads.ontology.shtml GO Download)
- 14:12, 8 December 2008 Python SOAP libraries (hist) [1,015 bytes] Jjbot (Talk | contribs) (New page: Currently multiple libraries for Python exists which try to implement SOAP. Unfortunately, most of them are not maintained anymore. ==ZSI== ==SOAPpy== No longer maintained. ==SOAPlib=...)
- 13:57, 8 December 2008 Ibidas design ideas (hist) [1,403 bytes] Jjbot (Talk | contribs) (New page: ==Updating the SQL abstraction layer== More info will follow soon.)
- 17:49, 3 December 2008 Functional Genomics: who is who (hist) [689 bytes] Jjbot (Talk | contribs) (New page: People involved in the BA1 project. ==Jan Bot== Location: TU Delft Function: Scientific programmer Works on: Ibidas E-mail: j[-dot-]j.bot[-at-]tudelft(.nl) Tel nr: 015 27 83418) originally created as "BA1 who is who"
- 13:50, 2 December 2008 KCSmart (hist) [437 bytes] Mgjansen (Talk | contribs) (New page: [http://www.dutchgrid.nl/events/tutorial08/agenda/tut08_UseCase_BioMed.ppt])
- 10:54, 24 November 2008 Ibidas (hist) [6,573 bytes] Jjbot (Talk | contribs) (New page: <big>'''Ibidas'''</big> is aimed to be an integration platform for various sorts of biological data. We hope that by providing a very minimal but flexible database scheme we're able to sto...)
- 11:36, 15 November 2008 Service Oriented Architecture (hist) [39,262 bytes] Rholland (Talk | contribs) (New page: = MyProxyWebService = A TavernaGrid project has been created in https://gforge.nbic.nl/projects/tavernagrid/ GForge. Inside the subversion repository you will find MyProxyWebService....)
- 15:31, 29 October 2008 TavernaGrid (hist) [27,487 bytes] Pieterb (Talk | contribs) (Unfinished)
- 15:16, 1 October 2008 BioAssist Scientific Programmers (hist) [919 bytes] Marcvandriel (Talk | contribs) (New page: Proteomics *Alexandros Georgiou *Henk van den Toorn *I. Ahmad *Martijn Dijkstra Metabolomics *Malick Heuvel *Tjeerd Abma *Mark Fiers (left september 1st 2008) *Egon Willighagen (left sept...)
- 14:37, 1 October 2008 BioAssist programme committee (hist) [1,445 bytes] Marcvandriel (Talk | contribs) (New page: The task of the BioAssist programme committee is to inform each other about choices with respect to tools and databases, standardizations etc, within the different support platforms to ens...) originally created as "BioAssist programme commitee"
- 14:35, 1 October 2008 BioAssist structure (hist) [15,131 bytes] Marcvandriel (Talk | contribs) (New page: __TOC__ ==Mission statement== The BioAssist programme focuses on the use e-Bioscience approaches to provide flexible and sustainable bioinformatics support: “generic solutions to generi...)
- 09:39, 1 October 2008 Presentations (hist) [203 bytes] Mgjansen (Talk | contribs) (New page: = Presentations = Here you can find presentations given in one of the BioAssist meetings. Please feel free to add your own. * mgjansen-190909.pptx)
- 14:45, 23 September 2008 Small Grid Tools (hist) [1,874 bytes] Jjbot (Talk | contribs) (New page: One of the most frequent and annoying tasks on the grid is checking running jobs. This is done using the glite-wms-job-status command which, due to its multi-line output per job entry, is ...)
- 13:53, 4 September 2008 Next Generation Sequencing (hist) [3,713 bytes] Marcvandriel (Talk | contribs) (New page: __TOC__ ==Vendors== [http://www.illumina.com/ Illumina] [http://www.pacificbiosciences.com Pacific BioSciences] [http://www.roche-applied-science.com/ Roche] [http://www.helicosbio.com...) originally created as "High throughput sequencing"
- 11:18, 27 August 2008 NBIC myExperiment wish wiki (hist) [3,161 bytes] Mroos (Talk | contribs) (New page: = NBIC wish-list for myExperiment and BioCatalogue = :''We regularly have meetings for identifying, prioritising and planning our myExperiment developments. We have input from a number o...)
- 14:08, 5 August 2008 User:Toorn101 (hist) [198 bytes] Toorn101 (Talk | contribs) (New page: == Henk van den Toorn == Working at the Biomolecular Mass Spectrometry and Proteomics Group at the Utrecht University. Contact: e-mail: [mailto:h.w.p.vandentoorn@uu.nl] phone: +31 30 2...) originally created as "Henkvandentoorn"
- 10:38, 28 July 2008 Metware BigMet (hist) [1,947 bytes] Tabma (Talk | contribs) (New page: '''BigMet''' contains the ontology (SKOS based) and the database design (SQL based). == SKOS ontology == [http://en.wikipedia.org/wiki/SKOS SKOS] is a W3C standard for Simplified Knowled...)
- 08:52, 28 July 2008 Metware MetWeb (hist) [287 bytes] Tabma (Talk | contribs) (New page: '''MetWeb''' is the GUI on top of the datawarehouse. MetWeb will be a [http://en.wikipedia.org/wiki/JavaServer_Faces JSF] (JavaServer Faces) application. This means JSF renders all the HTM...)
- 12:54, 24 July 2008 Metware developers (hist) [9,268 bytes] Tabma (Talk | contribs) (New page: This page is intended to contain information for developers on the Metware project. == SVN == To check out the latest version of the Metware code, use: <pre>svn co https://metware.svn.s...)
- 15:19, 3 July 2008 Gforge (hist) [308 bytes] Mgjansen (Talk | contribs) (New page: There is a gforge page available at https://gforge.nbic.nl Logging in You can create an account and login. Changing laguage options Go to "my page" and "account maintenance". Language...)
- 18:12, 22 May 2008 QuickBlast (hist) [6,654 bytes] Pieterb (Talk | contribs) (Initial version)
- 15:16, 23 April 2008 E-science (hist) [1,315 bytes] Marcvandriel (Talk | contribs) (New page: __TOC__ == Demo e-science technologies == [http://www.myexperiment.org/files/28 This movie] shows one way of how e-Science technologies can be applied to perform BioInformatics. It encom...)
- 14:31, 14 April 2008 VBrowser (hist) [2,254 bytes] Pieterb (Talk | contribs) (New page: The '''vBrowser''' is a tool that allows you to browse Grid resources (both computational and storage) with an "Explorer-like" browser. It was developed by Piter de Boer from the Universit...)
- 11:47, 14 April 2008 GridSite (hist) [2,950 bytes] Pieterb (Talk | contribs) (Initial version)
- 14:02, 11 April 2008 REST.inc (hist) [16,391 bytes] Pieterb (Talk | contribs) (New page: REST.php was programmed by User:Pieterb. It aids in developing RESTful applications with PHP. It can be downloaded here. <pre><?php /*·***************************...) originally created as "REST.php"
- 20:41, 8 April 2008 Representational State Transfer (hist) [58 bytes] Pieterb (Talk | contribs) (New page: Category:Todo)
- 20:23, 8 April 2008 ToPoS (hist) [2,823 bytes] Pieterb (Talk | contribs) (New page: The '''Token Pool Server (ToPoS)''' is a very simple pilot job framework for BioAssist. {{Todo}})
- 17:24, 8 April 2008 Virtual laboratory for e-science (hist) [815 bytes] Pieterb (Talk | contribs) (New page: The exceptional increase in computing power, storage capacity and network bandwidth of the past decades forms the basis of a digital revolution, which has only just started. Also the chang...)
- 15:09, 8 April 2008 VL-e proof of concept (hist) [579 bytes] Mgjansen (Talk | contribs) (New page: ==The VL-e POC (Proof of Concept environment== VL-e (Virtual Laboratory for the e-sciences) is a Dutch e-science project. See [http://www.vl-e.nl]. In practical terms the POC environment...) originally created as "The VL-e POC"
- 14:59, 8 April 2008 Loading modules (hist) [2,383 bytes] Mgjansen (Talk | contribs) (New page: The module system. The VL-e POC environment is installed in modules. To see which modules are available type in: module avail The output will look something like this <pre> mgjansen$ m...)
- 14:46, 8 April 2008 Using the Grid (hist) [75 bytes] Mgjansen (Talk | contribs) (New page: == Access to the Grid == *How to get a Grid certificate *How to import your Grid certificate in your browser *[[VOMS proxy|Obtainin...)
- 17:51, 7 April 2008 Service-oriented architecture (hist) [1,007 bytes] Pieterb (Talk | contribs) (New page: '''Service Oriented Architecture''' ('''SOA''') is a computer systems architectural style for creating and using business processes, packaged as ''services'', throughout their lifecycle. S...)
- 15:53, 7 April 2008 Web service repository (hist) [2,167 bytes] Pieterb (Talk | contribs) (Written by User:Mroos)
- 10:34, 31 March 2008 DataTransportMeetingAgenda080409 (hist) [20,040 bytes] Mroos (Talk | contribs) (New page: =Data transport meeting, Manchester, April 9, 2009= ==Goals== * A plan for tackling the data transport bottleneck in Taverna 2 * A list of requirements/consequ...)
- 18:44, 28 March 2008 SARA (hist) [845 bytes] Pieterb (Talk | contribs) (New page: '''SARA Computing and Networking Services''' is an advanced ICT service center that supplies —since more than 30 years— a complete package of high performance computing & visualization...)
- 18:28, 28 March 2008 MyExperiment (hist) [207 bytes] Pieterb (Talk | contribs) (New page: '''myExperiment.org''' is a website where you can find, use and share scientific workflows and other research objects, and build communities. See http://www.myexperiment.org/) originally created as "MyExperiment.org"
- 01:04, 25 March 2008 DataTransportDiscussion (hist) [4,892 bytes] Mroos (Talk | contribs) (New page: ===Disclaimer=== This wiki page is a working document. The authors are working on this page. ===Authors=== * Morris Swertz * Scott Marshall * Adam Belloum * Machiel Jansen * Spiros ? * Ma...)
- 09:57, 11 March 2008 Job submission (hist) [4,887 bytes] Mgjansen (Talk | contribs) (New page: This tutorial will take you through the stages of running simple jobs on the Grid. Before continuing, be sure to have a valid proxy. [TODO] link here. '''Simple JDL''' To submit a job t...)
- 12:21, 10 March 2008 BioMoby (hist) [173 bytes] Mgjansen (Talk | contribs) (New page: '''Where do I get information about working with BioMoby?''' This link is useful: http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/)
- 21:45, 5 December 2007 Public key cryptography (hist) [1,111 bytes] Pieterb (Talk | contribs) (New page: The most important thing to know about public key cryptography is that unlike earlier cryptographic systems, it relies not on a single key (a password or a secret "code"), but on two keys....)
- 20:24, 3 December 2007 Subversion (hist) [3,728 bytes] Pieterb (Talk | contribs) (New page: Users of the Life Science Grid have a subversion repository at their disposal. This document explains what subversion is, and where you can find it. == What is Subversion?<ref name="s...)
- 20:18, 3 December 2007 Sara bouwt Life Science Grid (hist) [3,872 bytes] Pieterb (Talk | contribs) (New page: Voor wetenschappers uit de Life Sciences is het van belang om te kunnen beschikken over geavanceerde HPC-faciliteiten. In opdracht van NCF en NBIC plaatst SARA daarom bij universiteiten di...)
- 20:17, 3 December 2007 Sara builds Life Science Grid (hist) [3,542 bytes] Pieterb (Talk | contribs) (New page: Today's Life Scientists need to have advanced HPC facilities at their disposal. For that reason, and commissioned by the NCF and NBIC, SARA places powerful computer clusters at the local s...)
- 20:16, 3 December 2007 Current events (hist) [285 bytes] Pieterb (Talk | contribs) (Copied from LSG wiki)
