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The data download didn't work for reactome. The script looks fine but I can't see the log files so I don't know what happened last time.
tell @rachellyne
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It looks like the GenomeTools GTF parser does not load all attribute key-value pairs into memory like the GFF3 parser does: see https://gist.github.com/standage/6ce111784628155c09b0. Was this a consci…
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find images to overlay in banner on homepage.
@kltm let me know if there are any constraints other than licensing.
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From @JoelRichardson:
> I'm looking at the objects returned by GET /templates, and it looks like the json format is omitting the switchable/optional inputs. For example, looking at FlyMine, the templ…
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@hdietze has added code to Minerva such that:
- generate model can be done blank
- generate model can be done with just a taxon id argument (detected as part of current call)
Both of these are better…
kltm updated
10 years ago
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The pathways for target/compound/publication API calls return error code 500 when the pathway_organism parameter is defined (e.g. with Homo sapiens). It works fine in the general "Pathways: List" call…
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``` shell
(Ivy)@yukke->smith7 >> ../../bin/ivy \
-f $HOME/db/melanogaster/Nascent-Seq/Drosophila_melanogaster/UCSC/dm3/Sequence/WholeGenomeFasta/genome.fa \
-r $HOME/db/melanogaster/Nascent-Seq/iris_…
soh-i updated
10 years ago
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List upload no longer gives the number of items in your list and number of discrepancies. If you click on 'Add' you have no idea if something has happened.
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> java.util.ConcurrentModificationException: ObjectStore error has occurred (in size) - data changed
> at org.intermine.objectstore.query.ResultsBatches.size(ResultsBatches.java:244)
> at org.…
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From @JoelRichardson
The ID changes for every database build so we should not use this in the code generation.
1. go to zen http://www.flymine.org/query/portal.do?class=Gene&externalids=FBgn0004053
…