 Einar Ryeng
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e5cd8a8077
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Started on a function to enhance gene lists by using GO similarities.
Not in a usable state.
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2007-06-22 15:37:22 +00:00 |
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Einar Ryeng
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68cc583d2c
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Added common_dimensions(ds) that lists common dimensions between two
datasets.
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2007-06-22 15:35:45 +00:00 |
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Einar Ryeng
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ff8833a22c
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Added read functions for the medium and large smokers sets.
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2007-06-21 10:28:10 +00:00 |
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Einar Ryeng
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d6298a2d99
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Ensures that the GO is only loaded once.
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2007-06-21 10:26:35 +00:00 |
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Einar Ryeng
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ff2c42902f
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Commented out some log lines that just cluttered the log.
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2007-06-21 10:25:17 +00:00 |
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Einar Ryeng
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2eb3d71a5d
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Moved data/smokers-med to data/smokers-medium.
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2007-05-16 15:35:25 +00:00 |
 Arnar Flatberg
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91032d729e
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Some more smoker data
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2007-05-16 11:45:43 +00:00 |
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Einar Ryeng
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7bdfdea23b
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Added -d option to get all identifiers along a single dimension.
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2007-05-16 10:30:54 +00:00 |
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Einar Ryeng
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c7bfefe358
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Fixed resnik distances.
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2007-05-15 18:16:07 +00:00 |
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Einar Ryeng
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335efe231a
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go-gene-matrix takes a GO vs. GO distance matrix and a gene-go-mapping file
and makes a gene vs. go distance matrix based on the shortest distances found
between each gene and go term.
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2007-05-15 18:15:51 +00:00 |
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Einar Ryeng
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1ab558248c
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Piping information through dataset -i works. Added names of planned features
to the dataset script.
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2007-05-09 21:52:59 +00:00 |
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Einar Ryeng
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7272eb63d2
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Working on a script to query datasets without starting fluents.
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2007-05-09 17:41:50 +00:00 |
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Arnar Flatberg
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ebe7621817
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some biocondoctur utilities
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2007-05-06 13:51:06 +00:00 |
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Einar Ryeng
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f1301be67a
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go-distance update.
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2007-04-26 18:54:34 +00:00 |
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Arnar Flatberg
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a0faed2614
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Forgot some ...
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2007-04-24 17:21:40 +00:00 |
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Arnar Flatberg
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34ae426c86
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Added correlation plot and moved colorbar to plots
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2007-04-24 17:17:31 +00:00 |
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Arnar Flatberg
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90bb25eb55
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added default mappable to None
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2007-04-24 17:16:34 +00:00 |
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Arnar Flatberg
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31ac569c3e
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Added colorbar shortcut
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2007-04-24 17:04:29 +00:00 |
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Einar Ryeng
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fefaffb2e3
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go-distance seems to be able to calculate resnik now. Not asserted with
calculations by hand.
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2007-04-04 19:08:50 +00:00 |
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Einar Ryeng
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28f0f53e8a
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go-distance script soon calculating resnik distances.
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2007-04-03 13:08:48 +00:00 |
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Einar Ryeng
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a5c3a1f154
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A couple of extra lines of code in a script.
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2007-03-27 13:02:22 +00:00 |
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Einar Ryeng
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728c334e8a
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ontology distance script now accumulates annotations correctly.
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2007-03-26 23:15:14 +00:00 |
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Einar Ryeng
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11eb3306b9
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Works a bit better.
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2007-03-26 17:18:26 +00:00 |
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Arnar Flatberg
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947cf8385f
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Annotations on yeast from Stanford mdb.
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2007-03-23 20:51:04 +00:00 |
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Einar Ryeng
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0904a59310
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Gene ontolgy distance script in C. Will hopefully speed up calculations when
finished.
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2007-03-23 13:25:07 +00:00 |
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Arnar Flatberg
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6f19fe1b4b
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Resnick distance matrix
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2007-03-16 17:05:46 +00:00 |
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Einar Ryeng
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0eff457910
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Added biological process info to the small smokers example, and a README file to
explain the dataset, at least the non-trivial parts.
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2007-03-15 23:57:35 +00:00 |
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Einar Ryeng
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3dc1867be4
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Added entrez-go-mapping that maps entrez IDs to GO terms based on a file of the form:
affy_id ::: geneid_1 /// geneid_2 ::: go(bp) ::: go(cc) ::: go(mf)
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2007-03-15 23:47:24 +00:00 |
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Einar Ryeng
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6fe4ff3c59
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Added scripts folder for small but useful scripts.
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2007-03-15 12:46:41 +00:00 |
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Arnar Flatberg
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b02773b4e6
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pls loading plot now have correct name
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2007-03-15 10:38:52 +00:00 |
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Arnar Flatberg
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dbe49b366d
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added import of networkx
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2007-03-15 10:38:05 +00:00 |
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Einar Ryeng
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f6696dfacc
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Added gobrowser to smalltest workflow.
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2007-03-14 21:08:56 +00:00 |
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Einar Ryeng
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1c48315a0f
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Added debug output.
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2007-03-14 17:26:40 +00:00 |
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Arnar Flatberg
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438a268b1d
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Inserted visible header sort
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2007-03-14 16:34:50 +00:00 |
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Arnar Flatberg
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3d2492578e
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whitespace
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2007-03-14 16:33:54 +00:00 |
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Arnar Flatberg
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3bd21ab089
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metric support
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2007-03-14 16:33:16 +00:00 |
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Arnar Flatberg
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48047f1395
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Moved lots of stuff back to sandbox
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2007-03-14 16:32:49 +00:00 |
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Arnar Flatberg
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7f1f639ee7
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Updates on metric, whitespace
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2007-03-14 16:31:25 +00:00 |
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Arnar Flatberg
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22f6e3284c
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whitespace
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2007-03-14 16:30:18 +00:00 |
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Arnar Flatberg
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818dc0b2b0
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added a logger for constructor calls
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2007-03-14 16:27:23 +00:00 |
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Arnar Flatberg
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212da78933
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correct comp update
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2007-03-14 16:17:21 +00:00 |
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Arnar Flatberg
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00dd3e8d9d
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added validation on identifiers input
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2007-03-14 16:06:16 +00:00 |
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Arnar Flatberg
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51435d9fdc
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Fixed dataset type to network
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2007-03-14 10:27:08 +00:00 |
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Arnar Flatberg
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ac447546a2
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Annotation file for dim: gene_id
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2007-03-14 10:26:11 +00:00 |
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Arnar Flatberg
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a9981779a6
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network of articles
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2007-03-14 10:25:35 +00:00 |
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Arnar Flatberg
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9cbefb5705
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in write_ftsv: adjusted so it splits specifically on tab, whitespace allowed in annotations
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2007-03-14 10:24:49 +00:00 |
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Arnar Flatberg
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6cbf6d0689
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Initial commit of small example test workflow
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2007-03-13 15:24:20 +00:00 |
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Einar Ryeng
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6b2737efb9
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Added a line.
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2007-03-09 14:33:09 +00:00 |
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Einar Ryeng
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f61bc353a9
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Typofix
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2007-03-09 14:30:40 +00:00 |
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Arnar Flatberg
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5be2f1faf6
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Initial import of Iris data
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2007-03-04 21:00:39 +00:00 |