Nathan Dunn

edit sequence error

5

[Annotations.gff3.gz](https://github.com/GMOD/Apollo/files/3065740/Annotations.gff3.gz) [Cam_Hsc_genes_v1_UTRs-Hsc_scaff001-1..6046013.gff3.gz](https://github.com/GMOD/Apollo/files/3065749/Cam_Hsc_genes_v1_UTRs-Hsc_scaff001-1.6046013.gff3.gz) From GenSas / Jodi Huffman > A GenSAS user reported this, and I am pretty sure it’s an Apollo error, but I just don’t know how to explain...

provide warnings for missing start / stop codon

1

From @strumpfe - provide warnings for missing start / stop codon similar to what we do for non-canonical splice sites, and potentially with a slightly different icon - give a...

translated sequence panel should indicate stop codons with '*' explicitly

3

from @strumpfe > Another potential suggestion for the Sequence panel, though one that usually divides opinion, is should the peptide translation include the stop codon? The use case is that...

integrate react app within Apollo with assemble

2

Integrate react is easy for doing the build: ` yarn build && rm -rf /Users/nathandunn/repositories/APOLLO/nathanApolloMaster/web-app/jb2 && cp -r build /Users/nathandunn/repositories/APOLLO/nathanApolloMaster/web-app/jb2` then go to: http://localhost:8080/apollo/jb2/ Using this as a template (Grails...

User has admin organism permissions, but not global admin permissions. It also can not see groups, as well. 

indicate stop codon in sequence when CDS is being color for phase

2

in draggable HTMLFeatures, indicate stop codon in phase with an orange or yellow line (or asterisk) if in phase stop codon present. Note: #1852 , https://github.com/GMOD/Apollo3Server/issues/76 , and https://github.com/GMOD/Apollo3Server/issues/75

Expected: - if a user an admin for an organism the organism panel is show, but not the user and group panel Actual: - user and group panels are shown,...

Provide support for regulatory sites such as transcription binding sites, promoters

11

This will be done similar to #524 (and is dependent on it) . . . at least initially. We need visualizations for it later that imply a different relationship, as...

From #1991 / #2176 unfixed - [ ] fix organism filter in lookup - [ ] add to side-panel for transcripts and other types - [ ] upload script should...

Feature: create indexes within a track database for JBrowse tracks without sufficient indexes

1

What we want to do here is emulate the behavior we get for NCList backed GFF3 (json) tracks or objects with a combined density track. The major reasons behind this...