Web-apollo-meeting-2011-3-15
Contents
3/15/2011: Suzi, Gregg, Ed, and Nomi
Progress Report
- WebApollo year 1 progress report submitted. Thanks to all who
contributed to it.
Hardware
- What hardware do we need for a WebApollo server?
- One server (Linux or OSX). (Budget?)
- Server itself doesn’t need to be too studly–mostly we need a lot of
storage.
- Four 3-terabyte drives (or at least 8 terabytes to start with)
- Need space to double every year (but hopefully that will be constant
cost/year as price of memory drops)
- Server speed is not a huge issue. The client side (how much data a
browser can handle) will be the limiting factor.
- Seth says we have space on campus and the networking we need.
- Action items:
- AI: Suzi will check on time constraint (when does this grant year
end? April 30?) and hardware budget
- AI: Seth will get a price quote
- AI: Seth and/or Ed will do the ordering
- AI: Ed will get Tomcat up on the server
- AI: Gregg will deal with the rsync
- Backups and server use by outside groups
- Need to back up user data (though not the UCSC data, which we can
always get again).
- Larger groups may set up their own servers, but we need to be a
server for smaller groups that want to use WebApollo.
- Would we have to set limits about how much data users could save on
our server?
- Seth proposed buying a server with the following (which we can afford
with our current hardware budget):
- 2x 4 core
- 6GB RAM
- 7x 2TB hd (RAID 6 + one hot spare = 8TB)
- 1x 120MB SSD boot disk
- 3U profile, 12 hd slots
- 4x Gb ethernet (for bonding on two interfaces)
- Gregg said: “Seth and I talked briefly in person on Tuesday, and he
convinced me that it makes sense to spend the money for enough hard
drives to set up RAID 6 for the UCSC data. And I agree to allow for
future expansion we should go ahead with a 4U 16 slot box.”
- I believe the server has now been ordered?
JBrowse issues
- JBrowse currently only supports two-level feature hierarchy.
- Mitch wants to do a JSON approach that allows arbitrary levels of
features, and also different kinds of features at the same level
(possibly with different fields).
- Gregg and Mitch have talked about details of this approach, sounds
like it’ll provide what we need
- Mitch may be able to implement this in the next several months
- If Mitch doesn’t get to it before we need it, Gregg can implement
What does WebApollo need to provide?
- We looked at old Apollo to see what it has so we could decide what
WebApollo needs.
- Authentication service with read/write privileges (records who made
the annotation)
- Sequence window (old Apollo)–view as cDNA, AA, etc., and can
copy&paste or save to a file
- Suzi notes that it’s really annoying when web apps pop up extra
windows
- Gregg says what he’d want is a menu item, Copy to Clipboard
- Alignment viewer
- (Exon Detail Editor–don’t want)
- Show start/stop codons (when you’ve zoomed in enough to see
bases)–calculate on the fly on client. (Would need to show which
strand they were on.)
- Stuff that’s in Apollo’s Annotation Information Editor–what do we
need?
- Ability to rename annotations
- Add/edit comments
- Synonyms
- Dbxrefs (JBrowse already provides this?)
- Ability to paste in new exon boundaries (?) (Maybe this doesn’t
belong in the Annotation Info Editor)
- Little pieces of info, some of which are calculated automatically
(e.g., missing start/stop codons)
- Ontology terms? (Old Apollo doesn’t really have this, except via the
dbxref, which has a checkbox for “is from an ontology”.)
- Gregg suggests that this panel could pull out as a slider, or it
could be brought up by a right-menu option. We don’t want it
around taking up space unless it’s requested. We don’t want it to
pop up as a separate window.
- Ability to create de novo annotation (Apollo offers a right-menu
option to choose annotation type)–types should be a subset of the
Sequence Ontology, but you should also be able to create your own new
annotation type.
- Time-stamp annotations
- Let user set an anchor? (Keep a point centered even when zooming in
and out.)
- Should we offer zoomed-in and zoomed-out views (vertically) in the
same screen? Suzi says yes. Can have two vertical scrollbars. Can zoom
the two views independently.
- Splice view (like in IGB)–show all the exons (plus a bit
of the introns) and leave out the boring empty intron stretches.
- Annotation editing operations:
Discussed commonality between editing operations
- Interval algebra
- Add exon, extend exon, merge exons, create transcript, merge
transcripts can all be considered union operations on
exon/transcript intervals
- Delete exon, shorten exon, split exon, delete transcript, split
transcript can all be considered intersect (or alternatively XOR or
NOT) operations on exon/transcript intervals
- Not exactly sure what this implies for user interface, but hopefully
thinking about this will help simplify the GUI
Undo/Redo
- Discussed global undo vs. per-annotation undo
- Implementing undo/redo as ancestor/descendant traversal
- Handling splits and merges – implies multiple ancestors, multiple
descendants
- UI for undo/redo – back/forward, select from version list, or both
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