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From: <ja...@op...> - 2004-05-02 05:48:18
|
Hey All,
I'm concerned that my previous attempt to explain the BioAssay
hierarchy was less than succesful, so I thought I would take a moment
to go into more detail, and provide an example.
First, there are two seperate levels to describing hybridizations in
MAGE - the BioAssay level and the BioAssayData level. The Data is,
well, the data - this can be either a matrix of number (as is the case
with MeasuredBioAssayData and DerivedBioAssayData) or images (for
PhysicalBioAssayData). The BioAssay level describes the annotions
*about* that data - where it came from, how it was prepared, who
prepared it, etc.
So lets start with the life cycle of a hybridization:
1) A chip is hybridized to a sample - in MAGE this is a LabeledExtract
being hybridized to an Array. This event creates a PhysicalBioAssay
(PBA), the PBA is scanned to produce images and these are the
PhysicalBioAssayData (PBA Data).
2) Now the images are run through a FeatureExtraction Software program
(FE Software) which produces a data matrix - this data matrix is
the MeasuredBioAssayData (MBA Data) - and to store the annotations
we create a thing called the MeasuredBioAssay (MBA). The MBA
doesn't represent anything 'real' - it is just a container that we
use to store annotations of the data matrix produce by the FE
Software.
3) Now this MBA Data matrix is processed in some fashion,
e.g. averaging of replicate values, it will produce a new data
matrix. This a data matrix solely derived from a mathematical
manipulation of other data, so it is called DerivedBioAssayData
(DBA Data), and like MBA Data we create a thingy called a
DerivedBioAssay (DBA) to associate annotations of the data matrix.
To be as clear as possible, the data level has the real data, and the
BioAssay level contains the annotations of the data.
So to use a simple example, we have an experiment in which we are
testing the effect of adding a drug to the growth medium, so we will
have two samples the control and the sample with the drug, and we will
use three replicates.
This creates three PhysicalBioAssay's:
1) PBA1:
* chip1
* control-sample
* exp-sample
2) PBA2:
* chip2
* control-sample
* exp-sample
3) PBA3:
* chip3
* control-sample
* exp-sample
After scanning PBA1 produces image1, PBA2 produces image2, PBA3
produces image3. After feature extraction, image1 produces mba-data1,
image2 produces mba-data2, image3 produces mba-data3. We create MBA1,
MBA2, and MBA3 to hold the annotations, i.e. the FE Software
parameters that were used, as well as what PBA each data matrix was
derived from.
So we currently have the following relations:
PBA1 -> MBA1
| |
| \- mba-data1
|
\- image1
PBA2 -> MBA2
| |
| \- mba-data2
|
\- image2
PBA3 -> MBA3
| |
| \- mba-data3
|
\- image3
This diagram means that MBA3 was derived from PBA3, and MBA3 is
associated with mba-data3, and the PBA3 produced MBA3, and is
associated with image3.
Now we want to average all spot values across each of our replicates,
this produces a single data matrix dba-data1. We create a
DerivedBioAssay DBA1 to contain the annotations for this data matrix.
Now we have the following relations:
PBA1 -> MBA1 -------\
| | \
| \- mba-data1 \
| \
\- image1 \
\
PBA2 -> MBA2 ---------------> DBA1
| | / |
| \- mba-data2 / \- dba-data1
| /
\- image2 /
/
PBA3 -> MBA3 ------/
| |
| \- mba-data3
|
\- image3
So DBA1 is derived from MBA1, MBA2, and MBA3 and is associated with
dba-data1.
Finally, a die-swap correction is done to dba-data1 to produce a new
data matrix dba-data2. We create DBA2 to hold the annotations. This
gives us our final diagram:
PBA1 -> MBA1 -------\
| | \
| \- mba-data1 \
| \
\- image1 \
\
PBA2 -> MBA2 ---------------> DBA1 ---------> DBA2
| | / | |
| \- mba-data2 / \- dba-data1 \- dba-data2
| /
\- image2 /
/
PBA3 -> MBA3 ------/
| |
| \- mba-data3
|
\- image3
DBA2 is derived from DBA1 and contains dba-data2.
In MAGE the relationships always go backwards meaning that you can ask
given any BioAssay, what are the progenitor BioAssay's that it was
derived from - I've followed that Genex.
Notice that an MBA can only be derived from a *single* PBA (this is
until someone complains to the MAGE group that they want to combine
images from seperate PBA's into a single FE event). But DBA's are
often created from multiple input sources which can be either DBA's or
MBA's. It's theoretically possible to combine MBA's and DBA's to
produce a single DBA, but I haven't seen it being done yet.
I hope this little example helps. Once we start looking at PBA's there
is actually a lot of complexity that MAGE allows, but I don't want to
go there - in Genex I want to forbid some of the unnecessary
complexity that MAGE provides.
Please help me shape this document into something useful for genex
users - we will need to change it to the perspective of what happens
we the user loads data and does analyses using Genex.
Cheers,
jas.
|
|
From: <ja...@op...> - 2004-05-02 05:16:37
|
Hey all,
It looks like a change I made to the 'Configure' script on 3/23/2004
got lost when recon.pl was split off - I had renamed the 'readonly'
user to 'sessions' because that is the name of the only table that
user has access to. This wasn't obvious because I never use the
hard-coded name of any user in the API - I always use the Perl
Config.pm variable, e.g. $Bio::Genex::Config->{GENEX_TEST_USER}.
But it showed up when I was helping Durga debug her installer problem.
I'm proposing the following changes:
1) Rename recon.pl to Configure - make it the 'official' configuration
tool. It's had enough testing now, I think it's stable.
2) Make the genex administrative user names clearly genex
specific. This is in keeping with the role names, e.g. genex_admin,
genex_user, etc. So instead of 'sessions' make it 'genex_sessions',
etc. This way our administrative users don't conflict with other
potential users.
3) Instead of only a test user that has only USER level priveleges,
add a second user that has CURATOR priveleges as well. This came up
when I was adding the sample data set - I needed a user with
curator priveleges, so I had to give them to the 'test' user.
These changes are relatively minor, but I believe they will make long
term maintenance simpler.
I'm asking this to the list, because it will require a 'make
uninstall' for every installation (the old users will need to be
deleted from the DB).
Cheers,
jas.
|
|
From: SourceForge.net <no...@so...> - 2004-04-30 23:22:34
|
Bugs item #945670, was opened at 2004-04-30 23:22 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945670&group_id=16453 Category: Mason GUI Group: None Status: Open Resolution: None Priority: 8 Submitted By: Harry Mangalam (mangalam) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: mason errors when exporting data Initial Comment: repeated errors when trying to view data on genex2 - from: http://genex2.binf.gmu.edu/genex/mason/login/workspace/workspace.html logged in as test/test try to export anything, get a mason errror: could not find component for path 'class-from-tablename' ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945670&group_id=16453 |
|
From: <jw...@gm...> - 2004-04-30 22:47:50
|
1=2E Executive Decisions=3A I completely agree that neither PBA nor MBA s= hould be modifiable except by the data owner=2C through the curator =96 a= nd we have to decide about cascading effects when this does happen=96 if = one of these is modified what do we do about downstream DBAs=3F It is lik= ely that the results can no longer be verified by applying the specified = protocol to the substituted data matrix=2E It is also likely that if we d= elete them someone will get really pissed off=2E It is also likely that a= dditional users will not want to build more analyses on top of them=2C at= least not without elaborate warnings=2E = More Executive Decisions=3A Users have to be allowed to insert data =96 w= e could limit upload size per user (space above default to be negotiated = with the Administrator or Curator)=2E I would prefer a task-prioritized s= cheduler to a timed scheduler=2C it seems more efficient=2E Is it possibl= e to have a graphical =91current usage=92 widget for users so that you c= an see if a fairly extensive task is in process (so come back later)=3F O= nce we figure it out for ourselves it would also be useful to provide an = estimate of the time some of the more intensive tasks will likely take (e= g loading 20 U133a chips will take 2 hours =96 so come back later)=2E Future Executive Decision=3A I would like to wait to split db and analysi= s functions until we have a demonstrated need=2C and also appropriate res= ources=2E We tried this development path at NCGR and got bogged down in a= rchitecture decisions before we ever had data in the first place (of cour= se=2C there was that Curation Tool=85=2E=2E) 2=2E Comments on Data Loading Workflow skeleton I think medium-sized is a good way to express the assumption about skill = sets =96 there is no reason why a correctly staffed individual lab could = not use it=2C but we are not making self-extracting installing out-of-the= box whee! software=2E I think we seek other funding if we decide there i= s a call for this=2E NIH has particular programs to facilitate exactly th= is=2E For repetitive workflow-another things we really need is to establish = antecedents so that you know what to enter first so you can build on prev= ious entries=2E Also=2C you want to be able to see what already exists=2C= so you can re-enter or modify entries rather than repeat them=2E = On the MAGE vocabulary =96 could we separate into array-associated and= analysis-associated concepts=3F Or object-related=3F The straight alphab= etical list doesn=92t let me see which things are major ideas and which a= re examples that should be in particular controlled vocabularies=2E 3=2E As Jason mentioned=2C you must be able to associate a protocol with = any flavor of BioAssay=2E Question =96 where are we storing the PBA images=3F If someone wants to load MBAs for which we don=92t have images=2C how is = the original referenced=3F A URL=2C a citation=3F Is it optional or requi= red to reference this=3F Cheers=2C Jennifer |
|
From: <jw...@gm...> - 2004-04-30 22:47:50
|
More things to discuss (Mark Knopfler providing the backbeat) 1. DefaultSpot concentration units : This seems like a manufacturing specification, if I understand it correctly. If this is about what is on the array surface doesn't this have to be a density of probe molecules per surface area or effective volume? We could allow a mass or molar concentration deposited for cDNA arrays. I think this should be a drop-down list. And should this be optional? And should there be an uncertainty associated with it? Is there a PBAConcentrationUnit (for the PhysicalBioassay, which might be cpm, fluorescent units or concentration again)? By relating the spot concentration and the extracted signal intensity, you could get an efficiency, such as those of who used radioactivity used to determine. 2. Array manufacture - is the date the manufacture date associated with the lot number? And it seems like the lot number should go in here, because it is sometimes possible to buy an older array design from a manufacturer that is being superceded by a newer design. 3.bioThingie: maybe we could say 'source of solution-phase material being queried by the array; expected to be cell-derived, labeled nucleic acid in gene expression experiments' ? 4. FactorValues for PBA: you can check out what Array Express does for this. It is mildly irritating because everyone thinks of things differently. I had certain experiments I had read about (time series through developmental stages) and I had to go to the arrays to figure out what the factor had been called in order to call up the whole set. Luckily at this point they don't have that many experiments. It is a quick way to browse for certain types of experiments if you call them by the same name as the curator. I expect we will need synonyms, and it should be a controlled vocabulary. For example, the factor I was looking for got listed as a time series rather than a developmental series, but in this case they are not distinguishable, so I would want to allow either to be used as the factor. Cheers, Jennifer |
|
From: <jw...@gm...> - 2004-04-30 22:47:49
|
Hi Harry, I like the definitions. I am working on a graphical representation to show order of events and optional/mandatory with precedence for filling them in; this is really useful for seeing if we came to the same conclusion. Also trying to keep up with dev list messages, so my responses may hop around quite a bit. Hi Jason, Should the Measured BioAssay be required to reference an image? Your explanation says it OFTEN uses images, referenced through PBA, but this seems fuzzy. How are we going to discriminate the Derived Bioassay from the Measured BioAssay unless we impose this constraint? Or alternatively, when would we want to call something an MBA that did not reference an image? Cheers, Jennifer |
|
From: <ja...@op...> - 2004-04-30 17:54:31
|
Harry Mangalam <hj...@ta...> writes: > YTH (Yeah, That Helps) :) Thanks. I'll mod and continue. I'll go > thru the MAGE glossary and perhaps convert a bit more to English, but > yeah, let's definitely include that in our docs or link to it if it > has a home base. It's in [HX]ML somewhere so we can link to the > right entry? Sadly, MS Word. The text only is what I tore out of the 133 page submission document. Cheers, jas. |
|
From: SourceForge.net <no...@so...> - 2004-04-30 17:04:43
|
Bugs item #945446, was opened at 2004-04-30 17:04 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945446&group_id=16453 Category: Mason GUI Group: None Status: Open Resolution: None Priority: 8 Submitted By: Harry Mangalam (mangalam) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Insert -> FactorValues for PBA -> ERROR Initial Comment: From: http://bodi.tacgi.com/genex/mason/login/annotate/annotate.html hitting the Insert -> FactorValues for PBA I get: ERROR: Page: edit/pba-factorvalue-insert.html not found on top of a table that shows the experiments that I've entered. did this work..? hjm ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945446&group_id=16453 |
|
From: SourceForge.net <no...@so...> - 2004-04-30 16:54:01
|
Bugs item #848007, was opened at 2003-11-23 23:06 Message generated for change (Comment added) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848007&group_id=16453 Category: Installer Group: Genex-2 Status: Open Resolution: None >Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) >Summary: fix scratch views with lookup table security permissions Initial Comment: need mechanism to create scratch views with lookup table security permissions based on dba_fk. ---------------------------------------------------------------------- >Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 10:54 Message: Logged In: YES user_id=85550 This is true, the proper GRANT's are not being run, but even with permission, users not in the security group are allowed to edit data. This is a bad security hole, bump priority to max. ---------------------------------------------------------------------- Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 10:44 Message: Logged In: YES user_id=85550 The mechanism exists, but views are not being given the proper GRANT, so members of genex_user are beig refused. Bumped priority to get fixed pre-beta ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848007&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:44:32
|
Bugs item #848007, was opened at 2003-11-23 23:06 Message generated for change (Comment added) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848007&group_id=16453 Category: Installer Group: Genex-2 Status: Open Resolution: None >Priority: 7 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: create scratch views with lookup table security permissions Initial Comment: need mechanism to create scratch views with lookup table security permissions based on dba_fk. ---------------------------------------------------------------------- >Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 10:44 Message: Logged In: YES user_id=85550 The mechanism exists, but views are not being given the proper GRANT, so members of genex_user are beig refused. Bumped priority to get fixed pre-beta ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848007&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:40:31
|
Bugs item #945413, was opened at 2004-04-30 10:40 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945413&group_id=16453 Category: Mason GUI Group: Genex-2 Status: Open Resolution: None Priority: 7 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: table browser is not caching table names properly Initial Comment: Loading either of the browse table pages is *really*slow. We're supposed to be caching the TableDef entries so that we don't need to reload them. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945413&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:37:02
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Bugs item #848003, was opened at 2003-11-23 23:04 Message generated for change (Comment added) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848003&group_id=16453 Category: Installer Group: Genex-2 >Status: Deleted >Resolution: Invalid Priority: 5 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: if groupsec is a PI table, remove INSERT for users Initial Comment: if groupsec is a PI table, then users should not be allowed to INSERT, ---------------------------------------------------------------------- >Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 10:36 Message: Logged In: YES user_id=85550 PI role is gone ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848003&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:36:17
|
Bugs item #848044, was opened at 2003-11-24 00:26 Message generated for change (Comment added) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848044&group_id=16453 Category: DB Schema Group: Genex-2 Status: Open Resolution: None >Priority: 7 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: create default Scratch view with one (data) column Initial Comment: create default Scratch view with one (data) column - Intensity ---------------------------------------------------------------------- >Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 10:36 Message: Logged In: YES user_id=85550 This should be done as part of the installer when the test data set is being created. And it should be populated with a DBA. Bumped priority so that it's fixed pre-beta ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848044&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:33:27
|
Bugs item #848081, was opened at 2003-11-24 00:29 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848081&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Deleted >Resolution: Duplicate Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: pba-factorvalue-insert.html: has bad URL Initial Comment: pba-factorvalue-insert.html: The requested URL /genex2/mason/workspace/experimentset-bioassays.html was not found on this server. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848081&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:32:49
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Bugs item #848086, was opened at 2003-11-24 00:29 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848086&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: URL to the array-design loader is wrong on array-insert.html Initial Comment: URL to the array-design loader is wrong on array-insert.html ---------------------------------------------------------------------- >Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 10:32 Message: Logged In: YES user_id=85550 added a hash of classes which have a -load.html app ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848086&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:31:08
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Bugs item #848099, was opened at 2003-11-24 00:30 Message generated for change (Comment added) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848099&group_id=16453 Category: Mason GUI Group: Genex-2 Status: Open Resolution: None >Priority: 7 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) >Summary: enable mason-edit-class.pl to order columns properly Initial Comment: update mason-edit-class.pl to display a units CV together with it's value input (like read-group/write-group) ---------------------------------------------------------------------- >Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 10:31 Message: Logged In: YES user_id=85550 This should be a more general issue. All columns should at least be ordered as they appear in the schema definition. There may need to be a better method as well. Bumping up priority to get fixed pre-beta ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848099&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:28:18
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Bugs item #895647, was opened at 2004-02-12 04:29 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=895647&group_id=16453 Category: Administrative Apps Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: array-design-insert.pl spits out too many warnings Initial Comment: If the array design file doesn't have zone information there is way too many warnings emitted. This is very confusing to curators. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=895647&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:27:49
|
Bugs item #929859, was opened at 2004-04-05 11:06 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=929859&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Reporter table should not have a provider column Initial Comment: The Biomaterial on the Reporter is physical and can be provided, but the Reporter is just meta data. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=929859&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:24:15
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Bugs item #945131, was opened at 2004-04-30 02:15 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945131&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: bad URL for pba-factorvalue-insert.html Initial Comment: The navbar entry for Insert FactorValue for PBA in the 'Data Annotation' navbox in 'Annotate' tab is wrong - the url-base is edit/ and it should be insert/ ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945131&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:23:30
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Bugs item #932845, was opened at 2004-04-10 10:09 Message generated for change (Comment added) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=932845&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Fix permissions on views Initial Comment: There was a bug in Postgres 7.3 that allowed users to violate the security of a view, but it has been fixed in 7.4, so suddenly users don't have the proper priveleges (they never did). For USER tables, members of genex_user need all permissions on views. For PI tables, members of genex_pi need all perms on views. ---------------------------------------------------------------------- >Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 10:23 Message: Logged In: YES user_id=85550 There is no PI role anymore. USER role has been fixed. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=932845&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:22:20
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Bugs item #945403, was opened at 2004-04-30 10:14 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945403&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: pba-factorvalue-insert.html not providing load URL for EF Initial Comment: If there are no ExperimentalFactor's associated with an Experiment the user is simple given an HTML table header with no entries. The app should detect the lack of entries and prompt the user to enter some and then return as it does when there are no PBA's. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945403&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:14:01
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Bugs item #945403, was opened at 2004-04-30 10:14 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945403&group_id=16453 Category: Mason GUI Group: Genex-2 Status: Open Resolution: None Priority: 5 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: pba-factorvalue-insert.html not providing load URL for EF Initial Comment: If there are no ExperimentalFactor's associated with an Experiment the user is simple given an HTML table header with no entries. The app should detect the lack of entries and prompt the user to enter some and then return as it does when there are no PBA's. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945403&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-04-30 16:10:06
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Bugs item #945399, was opened at 2004-04-30 10:10 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945399&group_id=16453 Category: Administrative Apps Group: Genex-2 Status: Open Resolution: None Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: mbad-insert.pl is not adding the PBA to ExperimentLink Initial Comment: The PhysicalBioAssay entry is being created, but it is not being associated with the experiment ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945399&group_id=16453 |
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From: Harry M. <hj...@ta...> - 2004-04-30 16:09:21
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YTH (Yeah, That Helps) :) Thanks. I'll mod and continue. I'll go thru the
MAGE glossary and perhaps convert a bit more to English, but yeah, let's
definitely include that in our docs or link to it if it has a home base. It's
in [HX]ML somewhere so we can link to the right entry?
hjm
Jason E. Stewart wrote:
> Harry J Mangalam <hj...@ta...> writes:
>
>
>>PBA (should be renamed PhysicalBioAssay)
>> Def: again, I dunno for sure, but it seems that it refers to the general
>>chip line or product ID or expression technology that is used to quantitate
>>the assay or the organzation that provided the dataset.
>>Prerequisites:
>> Measured BioAssay (optional)
>> Data Provider of type Person or Organization (optional)
>> Array (required)
>
>
> The BioAssay's are simply collections of annotations associated with
> actual data (images are the data for PBA and numerical data matrices
> for MBA and DBA).
>
> This is really one of the nicest parts of the MAGE model. Genex-1 only
> had the ArrayMeasurement - it sucked, and it sucked well. This was
> because we attempted to place all data annotation for data matrices in
> a single table - the problem was there were three distinct types of
> data that needed annotation: the physical chip data, 'raw' data fresh
> off the feature extraction program, and derived data which is
> mathematical munging of other data.
>
[deletia]
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
<<plain text preferred>>
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From: SourceForge.net <no...@so...> - 2004-04-30 15:56:31
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Bugs item #942815, was opened at 2004-04-27 00:23 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=942815&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: array-design-load.html should allow user to set name Initial Comment: The ArrayDesign loader currently sets the name using the MAGE identifier specifiec in the XML file. Since there is a unique constraint on the name of an ArrayDesign, the user should be able to over-ride this setting. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=942815&group_id=16453 |
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