User Story #2603 (closed)
Opened 14 years ago
Closed 10 years ago
EMDB web client
Reported by: | wmoore | Owned by: | wmoore |
---|---|---|---|
Priority: | major | Milestone: | Unscheduled |
Component: | Web | Keywords: | n.a. |
Cc: | Story Points: | n.a. | |
Sprint: | n.a. | Importance: | n.a. |
Total Remaining Time: | 0.0d | Estimated Remaining Time: | n.a. |
Description (last modified by wmoore)
Implement the current functionality and EMDB entries of the EM Data Bank in an OMERO-based web application. Store all metadata for each entry as an emd.xml attached to Project. Also include OpenAstex? Viewer for viewing maps.
For each EMDB entry, store
- Project, named by EMDB-id. E.g. 1006. Attach to Project:
- emd.xml metadata
- pdb structures, if maps have been fitted.
- gif image of structure, for preview
- bit masks (file.bit) in Ingvar's format
- Dataset.
- Image (mrc map)
Use curl script (below) to download data from EMDB.
Use a Python script to populate OMERO with the data.
set -v baseurl="ftp://emdb-beta.emdatabank.org/structures" for ((i=1001; i<1007; i++)) do echo "downloading $i" curl -O "$baseurl/EMD-$i/header/emd-$i.xml" curl -O "$baseurl/EMD-$i/images/$i.gif" curl -O "$baseurl/EMD-$i/map/emd_$i.map.gz" done
Change History (22)
comment:1 Changed 14 years ago by wmoore
- Description modified (diff)
comment:2 Changed 14 years ago by wmoore
comment:3 Changed 14 years ago by wmoore
comment:4 Changed 14 years ago by wmoore
comment:5 Changed 14 years ago by jmoore
- Milestone set to Work in Progress
comment:6 Changed 14 years ago by jmoore
- Milestone changed from Work in Progress to OMERO-Beta4.2.1
comment:7 Changed 14 years ago by wmoore
comment:8 Changed 14 years ago by wmoore
comment:9 Changed 14 years ago by wmoore
comment:10 Changed 14 years ago by jmoore
- Milestone changed from OMERO-Beta4.2.1 to Unscheduled
comment:11 Changed 14 years ago by wmoore
comment:12 Changed 14 years ago by wmoore
comment:13 Changed 14 years ago by wmoore
comment:14 Changed 14 years ago by wmoore
comment:15 Changed 14 years ago by wmoore
comment:16 Changed 14 years ago by wmoore
comment:17 Changed 13 years ago by wmoore
comment:18 Changed 13 years ago by wmoore
comment:19 Changed 13 years ago by wmoore
comment:20 Changed 13 years ago by wmoore
(In [8934/omero]) Adding multiple datasets handling to Ctf_Correction.py script. See #2603
comment:21 Changed 13 years ago by wmoore
(In [8935/omero]) Small fix to Eman_Filters.py See #2603
comment:22 Changed 10 years ago by wmoore
- Resolution set to fixed
- Status changed from new to closed
(In [7716]) Fixed preview gif to use same code as getFile() for EMDB. See #2603