Difference between revisions of "Donaldson Research"

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== Research Interests ==
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==About Donaldson Research==
  
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Our primary interests include protein interaction data consolidation, text mining and data mining especially with respect to diseases.  
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I am a bioinformatician based in Oslo, Norway.  A number of open source projects developed in my group at the University of Oslo will continue to be supported and developed on this site.
  
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Our recent work on a consolidated protein interaction database can be found at http://irefindex.org/.
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If you are interested in collaborative projects or consulting services involving these resources, please contact me at the address below.
  
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Email: ian.oslo@gmail.com
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Ian Donaldson
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ian.oslo@gmail.com
  
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== Projects ==
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== Projects being maintained by Donaldson Research ==
  
 
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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).  
 
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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=== [[Magrathea]] ===
 
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[[Magrathea]]<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]] ===
 
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The Biolibrarian proposal proposes the creation of new positions at university libraries around the world.
 
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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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=== [[Bioscape]] ===
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<br/> Bioscape is our in-house text-mining system used to locate gene and protein mentions in PubMed abstracts.
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=== [[Donaldson Group | Past Projects]] ===
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Access to past projects including Magrathea, BioScape and past courses in Bioinformatics can be found on the old [[Donaldson Group]] page.
 
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== Group Members ==
 
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* Ian Donaldson
 
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* Paul Boddie
 
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== Past Group Members ==
 
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* Katerina Michalickova
 
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* Hanna Nemchenko
 
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* Sabry Razick: Now in Trondheim at [http://www.ntnu.edu/employees/sabry.razick NTNU].
 
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* [[Antonio Mora]]
 
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==Local Seminar Series==
 
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The [http://www.mn.uio.no/ifi/english/research/networks/clsi/seminars/ Computational Life Science seminars]
 
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==Links to Past Courses==
 
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=== [[Bioinformatics_course|Bioinformatics for molecular biology]] ===
 
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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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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]].
 
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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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==Contact==
 
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ian.oslo at gmail.com
 

Revision as of 18:33, 27 November 2012


About Donaldson Research

I am a bioinformatician based in Oslo, Norway. A number of open source projects developed in my group at the University of Oslo will continue to be supported and developed on this site.

If you are interested in collaborative projects or consulting services involving these resources, please contact me at the address below.

Ian Donaldson ian.oslo@gmail.com


Projects being maintained by Donaldson Research

iRefIndex logo.png

iRefIndex, iRefWeb, iRefScape, iRefR

http://irefindex.org/
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).

Vitruvian man.jpg

DiG: Disease Groups

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.

Past Projects

Access to past projects including Magrathea, BioScape and past courses in Bioinformatics can be found on the old Donaldson Group page.

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