My role as a biologist and bioinformatician in e-science is to help increase the usefulness of emerging information technologies for biology, while experimenting with new ways to increase insight into mechanisms related to structure and function of DNA in the cell. I experiment with technologies such as workflow, knowledge extraction from text, semantic web and virtual research environments such as myExperiment.

More information on the blog below (originally uploaded as an example for the 'NBIC on workflows' workshop in Lunteren, the Netherlands, March 2008).

http://www.myexperiment.org/blogs/15

Other contact details:

Also see my web page at the University of Amsterdam: http://home.medewerker.uva.nl/m.roos1

Interests:

Structure/function relationship of DNA in the cell, e-science, automated support for modeling biological mechanisms by knowledge extraction and semantic web technology.

Field/Industry: Biology

Occupation/Role(s): PhD, e-(bio)scientist (biology 'power-user'), biology e-Science liaison for NBIC and e-Science organisations

Organisation(s):

Leiden University Medical Centre
University of Amsterdam
NBIC
OMII-UK / myGrid

Groups that Marco Roos owns

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Marco Roos

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BioRange_NL

Unique name: biorange_nl
Created: Wednesday 01 August 2007 13:03:24 (UTC)

Introduction ------------ BioRange[1] is a Dutch nationwide program for bioinformatics research. It is associated with VL-e[2], an e-science research project that investigates and develops technology to enhance science through general grid-based infrastructure and tools for six diverging applications. Bioinformatics is one of them. Another association is with BioAssist[3], a bioinformatics ...

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Marco Roos

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BioAssist_NL

Unique name: bioassist_nl
Created: Wednesday 01 August 2007 13:05:51 (UTC)

NBIC's BioAssist program BioAssist[1], organised by the Netherlands BioInformatics Centre (NBIC[2]), is a program for support and dissemination of bioinformatics tools and expertise in the Netherlands. It advocates the use of e-science standards such as web services and workflow. It is associated with the projects VL-e[3] and BioRange[4]. Links: http://www.nbic.nl/support/BioAssist...

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AID

Created: Wednesday 07 November 2007 18:45:12 (UTC)

Adaptive Information Disclosure (http://adaptivedisclosure.org) Collaboration within the Dutch Virtual Laboratory e-Science project (http://www.vl-e.nl)

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Marco Roos

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Text mining network

Created: Monday 12 November 2007 23:01:26 (UTC)

The Text mining network on myExperiment.org The text mining network on myExperiment.org is a network of users of text mining workflows and services developers of text mining workflows developers of text mining services Goals (general) increase the efficacy of the field a place for users/developers to find text mining resources and experts derive text mining...

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Marco Roos

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NBIConWorkflows

Created: Tuesday 22 January 2008 17:46:11 (UTC)

Group for scientists associated with NBIC (Netherlands BioInformatics Centre) to discuss anything about (Taverna) workflows. New members are kindly requested to provide some information about their (future) interest in (Taverna) workflows in their profile description or in a seperate file with a reference in their profile description.

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nbiconworkflows

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Marco Roos

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VL-e

Created: Wednesday 23 January 2008 15:17:17 (UTC)

Group of researchers of the Virtual Laboratory e-Science (VL-e) project in the Netherlands. This is a large nation wide e-science research project funded by BSIK grants from the Dutch ministry of Economic Affairs. Its activities range from Grid infrastructure, to middleware, to (six) applications. The projects BioRange and BioAssist (also groups here) are tightly associated with VL-e.

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VL-e

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Marco Roos

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AID_myGrid_collaboration

Created: Tuesday 29 January 2008 13:52:50 (UTC)

A group to share preliminary scientific material in support of scientific collaboration between AID in Amsterdam (plus close friends) and myGrid (plus close friends).

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Marco Roos

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e-science support team for NBIC

Unique name: eScienceSupportTeam4NBIC
Created: Sunday 16 March 2008 22:23:11 (UTC)

This group brings together scientists with expertise in both (medical) bioinformatics and e-science. The members can give advice to bioinformaticians who want to adopt an 'e-science approach'. They want to share their expertise and experience for the application of technologies such as workflow, web/biomoby services, grid, semantic web, etcetera. The group was founded in particular for the Du...

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Marco Roos

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e-(bio)science tool group

Created: Tuesday 03 June 2008 09:46:58 (UTC)

Group for sharing bioinformatics tools that can enhance life science research.

3 shared items | 0 announcements

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Marco Roos

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Semantic_BioAID_collaboration

Created: Friday 22 August 2008 10:49:27 (UTC)

Group for collaboration of Andy, Scott, and Marco.

5 shared items | 1 announcements

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Marco Roos

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NBIC BioWise PhD student course - Manageme...

Unique name: BioWiseInformationManagement2009
Created: Saturday 23 May 2009 13:58:01 (UTC)

Group in support of the course 'Management of Life Science Information', 25/5-21/6 2009, organized for the Netherlands BioInformatics Centre (NBIC) as part of the BioWise programme.

4 shared items | 0 announcements

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Marco Roos

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CWA working group 2.1 - Content Capture

Unique name: CWA_ContentCapture
Created: Tuesday 01 September 2009 13:06:04 (UTC)

Concept Web Alliance working group on content capture CWA wants to help disclose experiment-derived knowledge from within the scientific community via concepts and relations between concepts, stored as concept-relation-concept triples that together form a 'nano-publication'. A nano-publication contains a single 'unit of though', and minimal provenance about who made it, where it was stated, ho...

1 shared item | 1 announcements

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Marco Roos

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CWA users

Unique name: CWA_Users
Created: Tuesday 01 September 2009 16:35:48 (UTC)

Group for (potential) users of the Concept Web. See below for information on CWA taken from the Concept Web Alliance Blog. Also see other CWA groups here on myExperiment. Please request to join this group if you are (i) a scientist working in application fields such as life science, (ii) interested in computer support for sharing knowledge between (computational) experiments and between scie...

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Marco Roos

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BioSemantics Privileged Users @ Human Gene...

Unique name: LeidenBioSemanticsUsers
Created: Wednesday 23 September 2009 01:10:24 (UTC)

Group of colleagues at the Human Genetics Department of the Leiden University Medical Centre and closely collaborating groups who are interested to be prime users of new developments in BioSemantics and e-Science, and in return are willing to provide feedback and suggestions. See http://biosemantics.org for more information about the BioSemantics collaboration in the Netherlands.

15 shared items | 1 announcements

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Marco Roos

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BioSemantics

Unique name: biosemantics
Created: Thursday 30 June 2011 13:06:48 (UTC)

Group for members of the BioSemantics group and their close collaborators.BiosemanticsWith the explosion of information in the biomolecular field, there is a dire need for information technology that assists in retrieving, extracting, and relating information and knowledge in the biomedical literature and databases. Biosemantics researchers and developers develop, evaluate, and apply such techn...

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Marco Roos

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NBIC Life Science Information Management 2013

Created: Tuesday 18 June 2013 15:51:17 (UTC)

myExperiment group for the NBIC course for Managing Life Science Information, LUMC, Leiden, 2013

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Other Groups that Marco Roos belongs to

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Ian Dunlop

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Open PHACTS

Unique name: openphacts
Created: Friday 21 June 2013 13:19:22 (UTC)

To reduce the barriers to drug discovery in industry, academia and for small businesses, the Open PHACTS consortium is building the Open PHACTS Discovery Platform. This will be freely available, integrating pharmacological data from a variety of information resources and providing tools and services to question this integrated data to support pharmacological research.

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David De Roure

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Wf4Ever

Unique name: wf4ever
Created: Sunday 06 February 2011 18:22:05 (UTC)

Wf4Ever aims at providing the methods and tools required to ensure the long-term preservation of scientific workflows in order to support the scientific discovery process and the development of new scientific assets. See http://www.wf4ever-project.org/

42 shared items | 0 announcements

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Katy Wolstencroft

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NBIC-Amsterdam

Created: Friday 14 October 2011 12:27:54 (UTC)

This is the group where you can find tutorial exercises, workflows and related material about using Taverna in the NBIC course on Managing Life Science Data

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Paul Fisher

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Next Generation Sequencing

Unique name: NextGenSeq
Created: Monday 23 November 2009 11:20:47 (UTC)

This group is for people wishing to contribute / find out more about 'Next Generation Sequencing' technology and data. Please feel free to join this group and add any workflows you think others may benefit from.

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Rob Hooft

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BioAssist II Taskforce for e-science

Unique name: e
Created: Saturday 24 October 2009 11:20:06 (UTC)

Taskforce of BioAssist, part of NBIC II in The Netherlands, that is responsible for developing e-science tools and workflows

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Erik Schultes

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CWA working group 2.9: triple browser / re...

Unique name: ConceptWebReasoning
Created: Saturday 15 August 2009 06:01:22 (UTC)

The Triple Browser & Reasoning (TBR) Working Group of the Concept Web Alliance confronts the major challenges associated with efficiently searching and 'creatively' reasoning with massive quantities of concept triples. In the immediate time frame, members of the of the TBR will focus on (1) formulating precise definitions of how the Concept Web should in principle (and might in ...

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Barend

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MyExperiment, WikiPeople and VIVO

Created: Monday 17 August 2009 13:15:03 (UTC)

12.00 Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-style-parent:"";...

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Barend

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Concept Web Alliance (general)

Unique name: CWA
Created: Monday 27 July 2009 12:48:15 (UTC)

This group aims to connect all people actively interested or participating in the new initiative, the Concept Web Alliance.(CWA) the Aim of the CWA is: “To enable an open collaborative environment to jointly address the challenges associated with high volume scholarly and professional data production, storage, interoperability and analyses for knowledge discovery.“ The 'Magnet Gro...

4 shared items | 2 announcements

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Jacintha Valk

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NBICommons office

Created: Tuesday 18 August 2009 09:11:18 (UTC)

This group is for NBICommons employees and invited partners to keep track of a common agenda and running projects.

1 shared item | 2 announcements

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Barend

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BioAssist II Taskforce for BioBanking Plat...

Created: Friday 31 July 2009 11:53:06 (UTC)

This group has been set up to exchange ideas, documents, workflows and news about the BioBanking Platform of NBIC in the The Netherlands. However, international members of the Concept Web Alliance or the BBMRI initiatives are very welcome to join. It will keep you updated on all technical developments regarding data harmonization and other aspects of BioBanking. Colleagues involved in the P3G ...

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Latest announcement:: Visit Paris to discuss WikiPedia Scholar with Segolene and Denis

Owner

David De Roure

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HCLS - Semantic Web for Health Care and Li...

Unique name: hcls
Created: Friday 01 May 2009 17:12:56 (UTC)

The mission of the Semantic Web for Health Care and Life Sciences Interest Group (HCLSIG) is to develop, advocate for, and support the use of Semantic Web technologies for biological science, translational medicine and health care. These domains stand to gain tremendous benefit by adoption of Semantic Web technologies, as they depend on the interoperability of information from many domains and ...

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semantic web

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Pieter Neerincx

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myExperimentBeanshellCollection

Unique name: myExperimentBeanshellCollection
Created: Thursday 06 March 2008 11:41:29 (UTC)

Group for development, curation and maintenance of collections of generic Beanshell processors. Join this group if you have some cool Beanshells that you want to share! Please add your Beanshells to the myExperimentBeanshellCollection workflow and don't create new workflows for this purpose. (It's not fun to load dozens of workflows manually to load a fragmented collection of Beanshells.) If t...

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Franck Tanoh

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Bio web service annotation

Created: Thursday 07 February 2008 13:56:13 (UTC)

To discuss annotation of biological web services. How can we help biologists and bioinformaticians find and use the web services they are looking for ???

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Mark Borkum

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Mark's Project

Created: Saturday 21 July 2007 19:32:46 (UTC)

This project provides tools and applications which utilise the myExperiment Mashup API (maintained by Don Cruickshank) iGoogle Gadgets Workflow Trading Card - this gadget is great for blogs! show your workflow to world using a customisable trading card (you can set the colour scheme and everything!!) Workflows RSS Feed - stay up to date with the latest workflows and most rece...

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M. Scott Marshall

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Amsterdam

Unique name: amsterdam
Created: Saturday 21 July 2007 08:27:16 (UTC)

Amsterdam ========= Eventually members of the VL-e project could log in here. At the moment, Amsterdam is overrepresented from NL and is handy for Marco and Scott to share workflows.

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Katy Wolstencroft

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workshop

Created: Friday 27 July 2007 15:17:45 (UTC)

Introduction ------------ This is the initial project page. You can edit this page like a wiki using [Markdown syntax][1] or by adding html. [1]: http://daringfireball.net/projects/markdown/syntax

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