Nl User: Marco Roos

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Name: Marco Roos

Joined: Saturday 21 July 2007 @ 10:43:23 (BST)

Last seen: Saturday 13 March 2010 @ 15:59:16 (GMT)

Email (public): roos [at] science.uva.nl

Website: http://home.medewerker.uva.nl/m.roos1

Location: Amsterdam, Netherlands

54 Friends

14 Groups (admin)

13 Groups (member)

2 Blogs

9 Packs

3 Files

26 Workflows

0 Favourites

Marco Roos has been credited 29 times

Marco Roos has an average rating of:

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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:

If for some reason I am not available, please contact my colleague Scott Marshall (marshall@science.uva.nl)

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): Post-doc, e-(bio)scientist (biology 'power-user'), PAL for OMII-UK, BioAssist core group member

Organisation(s):

University of Amsterdam
NBIC
OMII-UK

 

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File

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Blob New run.sh for Taverna 2 (in case of problems with nighlty build)

Created: 28/05/09 @ 09:25:03 | Last updated: 28/05/09 @ 09:25:04

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This may help solve problems with T2 snapshot.

File type: Trident (Package)

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 8 times | Downloaded: 7 times

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Blob From biologist to web service to Taverna to myExperiment to biologist

Created: 21/03/08 @ 19:00:24 | Last updated: 23/03/08 @ 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

Rating: 1.0 / 5 (1 rating) | Comments: 1 | Viewed: 125 times | Downloaded: 139 times

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Workflow

Taverna 1

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Workflow Analysing workflows (v3)

Created: 13/02/09 @ 09:12:58 | Last updated: 06/05/09 @ 08:50:31

Credits: User Wassinki User Pieter Neerincx User Katy Wolstencroft User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Analysing_workflows
This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site The amount of services used The amount of local processors used The amount of scripting tasks The amount of sub workflows Furthermore it classifies the local services based on their intended function. The workflow has two inputs: ...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 109 times | Downloaded: 32 times

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Workflow

Taverna 1

Original Uploader

Workflow BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v11)

Created: 29/02/08 @ 01:34:47 | Last updated: 28/05/09 @ 12:21:06

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_proteindiscovery_filteronhumanuniprot_perdoc_html
This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...

Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow

Taverna 1

Original Uploader

Workflow Demo_DiseaseDiscovery_byHumanUniprot_scaffold (v1)

Created: 10/12/07 @ 23:10:00

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Demo_diseasediscovery_byhumanuniprot_scaffold_28715_1
This workflow finds disease relevant to the query string via the following steps: A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene)...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow

Taverna 1

Original Uploader

Workflow Retrieve_documents_MR1 (v1)

Created: 10/12/07 @ 22:17:00

Credits: User Marco Roos User Edgar Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieve_documents_mr1_16960_1
This workflow applies the search web service from the AIDA toolbox. Comments: This search service is based on lucene defaults; it may be necessary to optimize the querystring to adopt the behaviour to what is most relevant in a particular domain (e.g. for medline prioritizing based on publication date is useful). Lucene favours shorter sentences, which may be bad for subsequent information extraction.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow

Taverna 1

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Workflow Retrieve_bio_documents (v2)

Created: 10/12/07 @ 22:15:54 | Last updated: 10/12/07 @ 22:45:49

Credits: User Marco Roos User Edgar Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieve_bio_documents_524_2
This workflow retrieves relevant documents, based on a query optimized by adding a string to the original query that will rank the search output according to the most recent years. The added string adds years with priorities (most recent is highest); it starts at 2007.

Rating: 4.5 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 2 | Citations: 0

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Workflow

Taverna 1

Original Uploader

Workflow Lucene_bioquery_optimizer_MR1 (v1)

Created: 10/12/07 @ 22:14:26

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Lucene_bioquery_optimizer_mr1_7699_1
This workflow does four things: it retrieves documents relevant for the query string it discovers entities in those documents, these are considered relevant entities it filters proteins from those entities (on the tag protein_molecule) it removes all terms from the list produced by 3 (query terms temporarily considered proteins) ToDo Replace step 4 by the following procedure: 1. remove the query terms from the output of NER (probably by a regexp matching on what is inside the tag, ...

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Workflow

Taverna 1

Original Uploader

Workflow Link_protein_to_OMIM_disease (v1)

Created: 10/12/07 @ 22:13:35

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Link_protein_to_omim_disease_31835_1
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Workflow

Taverna 1

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Workflow Flatten_and_make_unique (v1)

Created: 10/12/07 @ 22:12:01

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Flatten_and_make_unique_9537_1
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Workflow

Taverna 1

Original Uploader

Workflow Extract_proteins (v2)

Created: 10/12/07 @ 22:10:51 | Last updated: 10/12/07 @ 22:30:53

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extract_proteins_31269_2
This workflow filters protein_molecule-labeled terms from an input string(list). The result is a tagged list of proteins (disregarding false positives in the input). Internal information: This workflow is a copy of 'filter_protein_molecule_MR3' used for the NBIC poster (now in Archive).

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow

Taverna 1

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Workflow Discover_entities (v2)

Created: 10/12/07 @ 21:48:34 | Last updated: 10/12/07 @ 22:54:42

Credits: User Marco Roos User Sophia katrenko Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Discover_entities_29989_2
This workflow contains the 'Named Entity Recognize' web service from the AIDA toolbox, created by Sophia Katrenko. It can be used to discover entities of a certain type (determined by 'learned_model') in documents provided in a lucene output format. Known issues: The output of NErecognize contains concepts with / characters, breaking the xml. For post-processing its results it is better to use string manipulation than xml manipulations. The output is per document, which means entities will ...

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 64 times | Downloaded: 31 times

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Workflow

Taverna 1

Original Uploader

Workflow TestIteratorStrategy_withCloning (v2)

Created: 29/11/07 @ 15:35:49 | Last updated: 29/11/07 @ 15:40:30

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Testiteratorstrategy_withcloning_21054_2
This workflow implements a strategy for this problem: > I would like to perform an iteration including a dot product between > a list and a list of lists; example: > Input: > > [1] (1) > [A,B,C] (2) > [[a,b],[c,d],[e,f]] (3) > > Desired output: > > [1Aa, 1Ab, 1Bc, 1Bd, 1Ce, 1Cf] In this implementation a java beanshell is used to clone the items in list 2 as many times per item as there are items in the sublists of list 3. The iteration stra...

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow

Taverna 1

Original Uploader

Workflow CloneItemsInList (v1)

Created: 29/11/07 @ 15:34:53

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Cloneitemsinlist_10203_1
Utility workflow that clones an item copy_number times. You can use this to work around standard iteration strategies, e.g. in combination with the CountListItems workflow. Workflow examples: TestIterationStrategy_withClones. For an alternative approach see TestIterationStrategy_withNesting. Example I/O: input: A copy_number: 3 result: [A,A,A] input: [A,B,C] copy_number: 3 result: [[A,A,A][B,B,B][C,C,C]] input: [A,B,C] copy_number: [3,2] result: [[[A,A,A],[A,A]][[B,B,B],[B,B]],[[C,C,C],...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow

Taverna 1

Original Uploader

Workflow TestIteratorStrategy_withNesting (v1)

Created: 29/11/07 @ 15:31:33

Credits: User Marco Roos User Tomoinn

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Testiteratorstrategy_withnesting_29185_1
Implementation of the iteration workaround by Tom Oin conform the Q&A below. The nested workflow 'NestedProcessor' is called that to conform to Tom's explanation. For an alternative solution using a java beanshell to clone list items see 'TestIteratorStrategy_withCloning. This workflow implements the following Q&A: Marco Roos wrote: > Dear Taverna user, > > Issue 1: Complex iteration > > I would like to perform an iteration including a dot product between > a list and a list of li...

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Workflow

Taverna 1

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Workflow TestIterator (v1)

Created: 28/11/07 @ 15:28:44

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Testiterator_22554_1
Workflow to experiment with list iteration strategies. Look at metadata of nested workflow 'Concatenate' to see the current iteration strategy.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow

Taverna 1

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Workflow BioAID_Discover_proteins_from_text_plus_synonyms (v1)

Created: 15/11/07 @ 09:40:24

Credits: User Marco Roos User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_discover_proteins_from_text_plus_synonyms_16131
This workflow discovers proteins from plain text and adds synonyms using Martijn Schuemie's proteins synonym service. Proteins are discovered with the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

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Workflow

Taverna 1

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Workflow Discover_proteins_from_text (v2)

Created: 15/11/07 @ 08:58:00 | Last updated: 15/11/07 @ 09:12:34

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Discover_proteins_from_text_18980_2
This workflow discovers proteins from plain text. It is built around the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

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Workflow

Taverna 1

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Workflow DiscoverProteinLink (v2)

Created: 03/10/07 @ 18:36:12 | Last updated: 15/11/07 @ 09:02:44

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Discoverproteinlink_6189
COMPETITION: For friends only: If you find any two topics that return true positives with this workflow I will buy you a bottle of wine (or equivalent). Terms: if we confirm that the protein was indeed never mentioned together with both input topics in one article, we will publish this together. ---- This workflow implements Swanson's prinicple with services from the AIDA toolbox. It tries to find proteins that link two topics, while they never mentioned together with both topics in ...

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Workflow

Taverna 1

Original Uploader

Workflow BioAID_DiseaseDiscovery (v3)

Created: 12/11/07 @ 22:39:04 | Last updated: 15/12/08 @ 20:47:51

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_diseasediscoveryworkflow_070904_1__1_
This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Rating: 4.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 0

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Workflow

Taverna 1

Original Uploader

Workflow BioAID_protein_discovery (v1)

Created: 14/11/07 @ 12:46:33 | Last updated: 15/11/07 @ 09:01:13

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_protein_discovery_1051
This workflow finds proteins relevant to the query string via the following steps: A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned) Discover proteins: extract proteins discovered in the set of relevant abstracts. Services by...

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Workflow

Taverna 1

Original Uploader

Workflow BioAID_ProteinToDiseases (v1)

Created: 14/11/07 @ 12:47:57 | Last updated: 15/11/07 @ 09:00:44

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bioaid_proteintodiseases_16160
This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms). This workflow finds diseases relevant to the query string via the following steps: A user query: a single protein name Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) Retrieve documents: finds relevant documents (abstract+title) based on query Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link proteins ...

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Workflow

Taverna 1

Original Uploader

Workflow ProteinSynonymsToQuery (v2)

Created: 03/10/07 @ 18:36:10 | Last updated: 13/11/07 @ 23:47:41

Credits: User Marco Roos User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Proteinsynonymstoquery_26040
This workflow uses Martijn Schuemie's protein synonym service to produce synonyms and a new query string from the input query term. The service is limited to proteins, enzymes and genes. An input query that is a boolean string will be split and processed, but the boolean logic of the input query will be lost. Workflow URL: http://rdf.adaptivedisclosure.org/~marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml

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Workflow

Taverna 1

Original Uploader

Workflow BioAID_EnirchBioModelWithProteinsFromText (v7)

Created: 22/08/08 @ 11:00:51 | Last updated: 16/05/09 @ 01:13:19

Credits: User Marco Roos User Sophia katrenko User Andrew Gibson User M. Scott Marshall User Willem van Hage User Edgar User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Roosetal_paper14_swat4ls_figure_06
This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string i...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0

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