Difference between revisions of "Donaldson Group"

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== Research Interests ==
 
== Research Interests ==
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Our interests include computer modelling of biological processes, especially those related to cell signaling. Modelling requires access to a variety of data that needs to be collected or generated. These activities include data warehousing, data mining, prediction of protein-protein interactions and biological text-mining.
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Our primary interests include protein interaction data consolidation, text mining and data mining especially with respect to diseases.  
  
 
Our recent work on a consolidated protein interaction database can be found at http://irefindex.uio.no/ .
 
Our recent work on a consolidated protein interaction database can be found at http://irefindex.uio.no/ .
  
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Email: ian.oslo@gmail.com
  
 
== Projects ==
 
== Projects ==
  
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</imagemap> || [[iRefIndex|'''iRefIndex''']] [[iRefIndex|http://irefindex.uio.no/]]<br/> iRefIndex (interaction Reference Index) provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.
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=== [[iRefIndex | iRefIndex, iRefWeb, iRefScape, iRefR]] ===
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[[iRefIndex|http://irefindex.uio.no/]]<br/> iRefIndex (interaction Reference Index) provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.
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iRefIndex is available via a number of interfaces: in MITAB tab-delimited text (iRefIndex), web-site (iRefWeb), Cytoscape plugin (iRefScape) and an R package (iRefR).  
  
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iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.
 
 
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</imagemap> || [[Magrathea|'''Magrathea''']] [[Magrathea|http://magrathea.uio.no/]]<br/> Magrathea is prototype software demostrating the principals of coordinated agent modeling.  
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=== [[Magrathea]] ===
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[[Magrathea|http://magrathea.uio.no/]]<br/> Magrathea is prototype software demonstrating how animations of molecular pathways can be driven automatically using local context of the participant molecules.  
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=== [[The Biolibrarian Proposal]] ===
  
 
The Biolibrarian proposal proposes the creation of new positions at university libraries around the world.  
 
The Biolibrarian proposal proposes the creation of new positions at university libraries around the world.  
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It is envisioned that molecular biologists could meet with a Biolibrarian in the same way that they meet with and use the services of a librarian. The Biolibrarian could help molecular biologist researchers to locate pathways, complexes and interactions that their molecules of interest are involved in.
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These people would act as local biocurators that help local university researchers submit data to relevant biological databases.
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=== [[DiG: Disease groups|DiG: Disease Groups]] ===
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[[DiG:_Disease_groups|http://donaldson.uio.no/wiki/DiG:_Disease_groups]]<br/> The Disease Groups project groups together phenotypically related disease-gene associations found in OMIM's Morbid Map. The resulting map of disease genes may be used to explore relationships between disease genes in the human protein-interactome.
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=== [[Bioscape]] ===
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http://bioscape.uio.no/<br/> Bioscape is our in-house text-mining system used to locate gene and protein mentions in PubMed abstracts.
 
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== Group Members ==
 
== Group Members ==
  
−
* [http://www.biotek.uio.no/research_groups/donaldson_group.html Ian Donaldson]
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* [http://www.biotek.uio.no/english/about/organization/donaldson-group/people/iand/ Ian Donaldson]
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* [http://www.biotek.uio.no/english/about/organization/donaldson-group/people/paulbodd/ Paul Boddie]
 +
 
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== Past Group Members ==
 
* Katerina Michalickova
 
* Katerina Michalickova
−
* Paul Boddie
+
* Hanna Nemchenko
−
* Sabry Razick
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* Sabry Razick: Now in Trondheim at [http://www.ntnu.edu/employees/sabry.razick NTNU].
 
* [[Antonio Mora]]
 
* [[Antonio Mora]]
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* Hanna Nemchenko
 
  
 
==Local Seminar Series==
 
==Local Seminar Series==
  
−
The Biotechnology Centre of Oslo holds a weekly [[Bioseminar|Bioseminar]] on Tuesdays at 3pm in room 10 of Forskningsparken at.
+
The Biotechnology Centre of Oslo holds a weekly [[Bioseminar|Tuesday seminar]] at Forskningsparken, Gaustadalléen 21, Oslo.
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Gaustadalléen 21 (see map [http://www.gulesider.no/kart/map.c?q=Gaustadalleen+21&imgt=MAP&id=a_173374 here]).  
 
  
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The [http://www.bioinformatikk.no/seminars.html Bioinformatics Seminars] are held every Wednesday at 12:15 by the Joint Centre for Bioinformatics in Oslo, located at Gaustadalléen 25 (see map [http://www.gulesider.no/kart/map.c?id=a_173378&q=Gaustadalleen+25 here]).
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The [http://www.ifi.uio.no/research/clsi/seminars.html Computational Life Science seminars] are held every Wednesday at Ole-Johan Dahls hus, located at Gaustadalléen 23D, Oslo (opposite the Forskningsparken main entrance).
  
 
==Courses==
 
==Courses==
  
−
Ian Donaldson is organizing this year's Molecular Biotechnology Course at the Biotechnology Centre of Oslo. You can find the MNBTS 9000 course web page [http://www.biotek.uio.no/MNBTS/ here] and the latest schedule [[MNBTS_9000_(2008)|here]].
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=== [[Bioinformatics_course|Bioinformatics for molecular biology]] ===
  
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Introductory Perl is taught by Antonio Mora and Ian Donaldson as part of the [http://www.uio.no/studier/emner/matnat/molbio/MBV3070/ MBV3070] course.
+
A new, two-week, intensive bioinformatics course that covers various aspects of bioinformatics analyses for molecular biology. Statistics, multiple hypothesis testing, microarray analysis, sequence alignments, working with protein structures, protein interaction networks and more.  See the [[Bioinformatics course|course page]] for schedule information along with all material used in the course. The course is composed of lectures and practical tutorials.  
 +
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Antonio Mora and Ian Donaldson also hold the "Applied readings in mathematics, computer science and biology" course every second Autumn term.  See [http://www.uio.no/studier/emner/matnat/molbio/MBV-INF4410/ MBV-INF4410].
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Introductory Perl is taught by Antonio Mora and Ian Donaldson as part of the [http://www.uio.no/studier/emner/matnat/molbio/MBV3070/ MBV3070] course.  The slides for these lectures are available here at [[MBV3070|Perl lectures for MBV3070]].
 +
<!--Antonio Mora and Ian Donaldson also hold the "Applied readings in mathematics, computer science and biology" course every second Autumn term.  See [http://www.uio.no/studier/emner/matnat/molbio/MBV-INF4410/ MBV-INF4410].
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-->
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Ian Donaldson is organizing this year's Molecular Biotechnology Course at the Biotechnology Centre of Oslo. You can find the MBV9100 course web page [https://www.biotek.uio.no/events/courses_workshops/2011/MBV9100BTS.html here] and the latest schedule [[MBV9100|here]].
  
−
 
 
==Contact==
 
==Contact==
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ian.donaldson at biotek.uio.no
 
−
 
  
−
==Editing help==
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ian.oslo at gmail.com
−
[http://meta.wikimedia.org/wiki/Help:Help Editing Help]
 

Latest revision as of 16:05, 15 November 2012


The Donaldson Group at the Biotechnology Centre of Oslo

BiO-logo-liten-pms-border.png

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Research Interests

Our primary interests include protein interaction data consolidation, text mining and data mining especially with respect to diseases.

Our recent work on a consolidated protein interaction database can be found at http://irefindex.uio.no/ .

Email: ian.oslo@gmail.com

Projects

iRefIndex logo.png

iRefIndex, iRefWeb, iRefScape, iRefR

http://irefindex.uio.no/
iRefIndex (interaction Reference Index) provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.

iRefIndex is available via a number of interfaces: in MITAB tab-delimited text (iRefIndex), web-site (iRefWeb), Cytoscape plugin (iRefScape) and an R package (iRefR).

Magrathea logo.png

Magrathea

http://magrathea.uio.no/
Magrathea is prototype software demonstrating how animations of molecular pathways can be driven automatically using local context of the participant molecules.

ancientlibraryalex.jpg

The Biolibrarian Proposal

The Biolibrarian proposal proposes the creation of new positions at university libraries around the world. These people would act as local biocurators that help local university researchers submit data to relevant biological databases.

Vitruvian man.jpg

DiG: Disease Groups

http://donaldson.uio.no/wiki/DiG:_Disease_groups
The Disease Groups project groups together phenotypically related disease-gene associations found in OMIM's Morbid Map. The resulting map of disease genes may be used to explore relationships between disease genes in the human protein-interactome.

Bioscape logo.gif

Bioscape

http://bioscape.uio.no/
Bioscape is our in-house text-mining system used to locate gene and protein mentions in PubMed abstracts.

Group Members

Past Group Members

  • Katerina Michalickova
  • Hanna Nemchenko
  • Sabry Razick: Now in Trondheim at NTNU.
  • Antonio Mora

Local Seminar Series

The Biotechnology Centre of Oslo holds a weekly Tuesday seminar at Forskningsparken, Gaustadalléen 21, Oslo.

The Computational Life Science seminars are held every Wednesday at Ole-Johan Dahls hus, located at Gaustadalléen 23D, Oslo (opposite the Forskningsparken main entrance).

Courses

Bioinfo course logo.jpg

Bioinformatics for molecular biology

A new, two-week, intensive bioinformatics course that covers various aspects of bioinformatics analyses for molecular biology. Statistics, multiple hypothesis testing, microarray analysis, sequence alignments, working with protein structures, protein interaction networks and more. See the course page for schedule information along with all material used in the course. The course is composed of lectures and practical tutorials.

Introductory Perl is taught by Antonio Mora and Ian Donaldson as part of the MBV3070 course. The slides for these lectures are available here at Perl lectures for MBV3070.

Ian Donaldson is organizing this year's Molecular Biotechnology Course at the Biotechnology Centre of Oslo. You can find the MBV9100 course web page here and the latest schedule here.

Contact

ian.oslo at gmail.com

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