[base] wrongly aligned spot images

have, cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] ___ The BASE general discussion mailing list

[base] filtering/analysis tips please

would help me figure out how to write one. cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

[base] refreshing in BASE 2

users is very useful however!) -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Take

[base] bioassays inheriting sample annotations in BASE 2

to edit all the bioassays in one go using the GUI. Does anyone have any experience with this? Are there some docs on this I didn't read? The default behaviour in BASE 1 (to propagate the sample annotations through to the bioassays) seemed sensible to me. cheers, Bob. -- Bob MacCallum

[base] JEP extra value calculator

@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

Re: [base] Offline files

=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides

Re: [base] Offline files

___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone

Re: [base] Offline files

PROTECTED] [mailto:basedb-users- [EMAIL PROTECTED] On Behalf Of Bob MacCallum Sent: 29 November 2006 18:36 To: BASE ML Subject: Re: [base] Offline files It looks like I let the cat out of the bag on this one... Some discussion among the community would be good to establish

Re: [base] Offline files

] [mailto:basedb-users- [EMAIL PROTECTED] On Behalf Of Bob MacCallum Sent: 29 November 2006 18:36 To: BASE ML Subject: Re: [base] Offline files It looks like I let the cat out of the bag on this one... Some discussion among the community would be good to establish what we

Re: [base] Questions on Reporter IDs

data, samples, experiment info as usual to BASE 2) perform any reporter or assay merging required to match processed data's shape using existing plugins 3) add processed data using new plugin (would this create an ExtraValue?) -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups

Re: [base] Reporter ID issue

___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial

[base] multi-experiment processed data summaries

discussion page unless you say otherwise). If you'd rather edit the wiki, just let me know and I'll fix an account for you. thanks a lot! cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone

[base] tab2mage/annotation questions

date)? Thanks for reading this far! cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

Re: [base] affymetrix

thanks to Dominic, Philippe Nicklas for the informative replies. I'll take the external ontology thing off-list with the EBI guys and we'll report back as necessary. Nicklas Nordborg writes: Bob MacCallum wrote: Emmanuel Courcelle wrote: Hello Trying to use BASE

[base] small gui feature suggestion

choice of default protocols and other menu items (project defaults or recently used) seems to be working well for me. Thanks. cheers, Bob -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone

Re: [base] inherited annotations GUI suggestion

mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL

[base] thoughts on data xfer between BASE2 instances

of the base1-2 migrator, including analysis steps 3. using batch loaders, load data from scratch on live server (and re-run analysis steps) any more ideas/thoughts? much appreciated! cheers, Bob -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell

Re: [base] Base1PluginExecuter parameter xml

. /Johan 11 sep 2007 kl. 16.58 skrev Bob MacCallum: Hi, I was trying to find out if base1's hierarchical clustering would run under base2 - and got to the point where I need to provide parameter settings as XML. I could spend an hour figuring this out

Re: [base] Base1PluginExecuter parameter xml

the plugin page in Base1 you will find an export link with each plugin. Use that file to configure the Base1PluginExecuter. /Johan 11 sep 2007 kl. 16.58 skrev Bob MacCallum: Hi, I was trying to find out if base1's hierarchical clustering would run under

Re: [base] Base1PluginExecuter parameter xml

you will find an export link with each plugin. Use that file to configure the Base1PluginExecuter. /Johan 11 sep 2007 kl. 16.58 skrev Bob MacCallum: Hi, I was trying to find out if base1's hierarchical clustering would run under

Re: [base] problems with my trashcan

http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides

[base] BASE 2.4.4 released. Please read, important performance issue fixed in this release.

discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email

[base] multiple/compound experimental factors in BASE

not be treated in this manner? I can't think of a scenario off the top of my head. cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

[base] execution of plugin stalled

with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

[base] labeled extract amounts

Hello BASEers If I add two labeled extracts to a hyb (e.g. two colour array), there is only one box for the used amount. Does this mean that hyb'ing different amounts for each channel is not possible (in BASE)? many thanks, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides

[base] analysis table already exists

: 910.3 MB -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Check out the new

[base] how to save filter presets?

Hi, Could someone just point me roughly in the direction of how to save an analysis filter preset? I can't seem to figure it out myself... many thanks, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College

Re: [base] analysis table already exists

if we see duplication again and can recreate the conditions. In the meantime, all seems OK again. cheers, Bob. /Nicklas Bob MacCallum wrote: Dear BASE team, I just got the following error while creating a root bioassayset for a small test experiment. My hunch

Re: [base] analysis table already exists

test server. For production purposes we could figure out some way of maintaining different versions of base.config (with jobqueue.internal.enabled = false) for all but the main web instance. cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell

Re: [base] how to save filter presets?

Thanks for this. The column restriction formula type seems to work for me here. Nicklas Nordborg writes: Bob MacCallum wrote: Hi, Could someone just point me roughly in the direction of how to save an analysis filter preset? I can't seem to figure it out myself

[base] annotation-based analysis filters

did). many thanks, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Check out

[base] reporter lists

into BioMart. I could export a MEV or BASEfile but this would be overkill. Also, can reporter lists be used in filter expressions in BASE2? many thanks, Bob -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone

Re: [base] base-2.3.2 and exporting basefiles - the last line of the bioassay set is absent

/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone

Re: [base] Base1PluginExecutor

unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

[base] BASE2 backups

was designed for. A more incremental approach to backing up the db would be useful when we are in the tens/hundreds of gigs. Maybe a slave mysql server? Could that work reliably between two distant sites? Any ideas? cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups

[base] small administrator's wishlist

browsed (or would mysqldump --lock-tables achieve basically the same thing?) cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

Re: [base] BASE2 backups

Nicklas Nordborg writes: Bob MacCallum wrote: deleted in BASE. I doubt these would interfere with the running of BASE however. A small program could be written to delete any files that are not known about by the db (unless there is already something to do

Re: [base] raw data files with hyb name in column headings

excellent, thanks, will try that. Nicklas Nordborg writes: Bob MacCallum wrote: Hi, I'm trying to import some ChipSkipper data into BASE2.6. While configuring the raw data importer I see that the files all have different column headings, incorporating the hybridisation

[base] annotating other users' items as administrator

of these items? many thanks, Bob -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Check out

Re: [base] annotating other users' items as administrator

to provide a shared directory for all users to read it has to be under /home/ and of course have Everyone read/use permissions.) I'm running 2.6.2pre (==2.6.1) on a pretty standard system. cheers, Bob Nicklas Nordborg writes: Bob MacCallum wrote: Hi all, I'm having difficulty getting

[base] upgrading BASE without restarting tomcat

know better? Any nuggets of wisdom gladly received on the ticket page or mailing list. cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

Re: [base] upgrading BASE without restarting tomcat

independently of each other. Maybe this helps you? I can give you more information on how to setup this if you think it helps you. Cheers, Jari Bob MacCallum wrote: I just opened a feature suggestion ticket on the subject of being able to upgrade base without

[base] 2 bugs

@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

Re: [base] upgrading BASE without restarting tomcat

exposed outside of the server. I do not think the firewall interferes with these ports (need to be checked). Jari Bob MacCallum wrote: Thanks Jari. That might be an option, although we don't have many ports open to the outside world (only 80 and 8080) and would like

Re: [base] BASE2 backups

(removed,owned by others) could work on everything at once. While we are on the subject of a GUI wish-list: would a File-New-Biosource/Sample/Extract... menu be of use to anyone? At the moment one must go to the list page and then the New... button. cheers, Bob. Bob MacCallum writes: I

[base] annotation importer suggestion

, this would save a lot of GUI work (prior to the MAGE-TAB importer being completed) I could imagine project defaults would be suitable for some of the item attributes, otherwise they could be empty of course. many thanks, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups

Re: [base] PermGen space error

://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase

[base] annotations not always updated

annotations by showing them as columns in the list view, and I always press the refresh button after the plugin has finished (like you do with the analysis pipeline). cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology

[base] bulk annotation removal

it seems to leave the existing annotations untouched. Is there a special NULL value I can put in the input file? cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL

[base] lowess normalisation

always fine in BASE1. You can look for yourself with the guest login at http://fungen.vectorbase.org/base2 Experiment Male vs. female (Koutsos et al., 2007) is a good small example. I don't see a recent ticket on this (I have not upgraded in a few months). cheers, Bob. -- Bob MacCallum

[base] lowess normalisation

the base1 plugin. many thanks, Bob. Bob MacCallum writes: Has anyone had problems with the Lowess analysis plugin? To me it looks like it is overcorrecting. Where a M/A plot is largely below the zero line before normalisation, it ends up largely above it afterwards. I'm using

Re: [base] lowess normalisation

Bob MacCallum wrote: I've done some more tests on the lowess problem. Please refer from now on to our development server: http://base.vectorbase.org:8080/base2dev/ Experiment: Male vs. female (Koutsos et al., 2007) I ran the base1 lowess plugin and got a very different

[base] Agilent reporter import problem

___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology

[base] BASE 2.8 has been released

=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology

[base] replacing import files

the select file to import dialogue. At the moment it doesn't seem possible and I have to interrupt my work flow to go to the file browser to perform the replacement, then go back to the list view. This has been bugging me for a while! many thanks, Bob. -- Bob MacCallum | VectorBase Developer

Re: [base] replacing import files

nice workaround, hadn't thought of that. thanks! Nicklas Nordborg writes: Bob MacCallum wrote: Now that the GUI is maturing nicely (I love the auto-configure button for setting the file parser column mappings, select all button for bioassays, column filters and more), I would like

[base] batch import/edit experiment items

, change names, import data again.) Is there a technical reason, or did you not think there was a valid reason for anyone to use it? cheers, Bob. Bob MacCallum writes: I've just loaded a 60-hyb Affy experiment on our production server using the new import plugins. Everything worked fine

Re: [base] batch import/edit experiment items

real benefit for importing experiments. There is no technical limitation. /Nicklas Bob MacCallum wrote: Hello, I was wondering why there is not an Experiment item importer, just like all the other new importers? I was hoping to use it to create a bunch

[base] hibernate connection pool size

(or perhaps webservices clients) on your BASE instance you might find this is the explanation behind the site hanging for your users. cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945

[base] high-throughput transcriptome sequencing data

for 3a (and 3b?) but that's not difficult. Is it possible to go with 3a, but also attach the sequence file to the raw bioassay (or scan?) - something like keeping tiff files for scans? Just for documentation purposes. Any thoughts from the community or developers? cheers, Bob. -- Bob MacCallum

Re: [base] high-throughput transcriptome sequencing data

Hi again, I saved you the trouble of cutting and pasting to make a new ticket: Handling short read transcript sequence data http://base.thep.lu.se/ticket/1153 Is there any way for me to subscribe to this ticket (get email updates when changed)? cheers, Bob. -- Bob MacCallum | VectorBase

[base] raw bioassay listing workaround request

anyone know a workaround? many thanks, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED

[base] Sharing

://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Bob MacCallum

[base] project defaults and ticket #1112

to add the protocols to the bulk import text file(s), but I was hoping not to have to do this. regards, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email r.maccal

Re: [base] project defaults and ticket #1112

will go away, right? (Because this other BASE instance doesn't need to run jobs.) So actually the default protocols work perfectly from the bulk import plugins. Sorry for any trouble! Nicklas Nordborg writes: Bob MacCallum wrote: As an admin user, I created a new project, set

[base] summary of how the new core batch importers can be used for importing whole experiments

/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Bob MacCallum | VectorBase Developer

Re: [base] Experiment overview loads very slowly

-requ...@lists.sourceforge.net -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email r.maccal...@imperial.ac.uk

[base] GUI suggestion: next/prev item in list

I don't know if it's easy to implement, but somehow the GUI would know that it had come from a list view and display the buttons: [first |] [previous ] [next ] [last |] Many mail readers do this kind of thing. It would be much appreciated if you could add this to BASE. Any thoughts? -- Bob

Re: [base] GUI suggestion: next/prev item in list

Another idea might be to use Javascript to highlight the just-edited-with-shift-click list entry somehow. That would make it easier to process a list in this way without missing an entry. Nicklas Nordborg writes: Bob MacCallum wrote: It's not possible to show inherited annotations in list

[base] Querying annotations

of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Bob MacCallum

Re: [base] Querying annotations

unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email r.maccal...@imperial.ac.uk

[base] Data truncation: Data too long

-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email

[base] Odd scientific number behaviour

Help, can anyone explain? In BASE 2.12.2pre I'm getting the following exception thrown, despite the issue being addressed way back in 2.4 http://base.thep.lu.se/changeset/3703 http://base.thep.lu.se/ticket/743 net.sf.basedb.core.BaseException: For input string: 1.10E+03 on line 11 in file

[base] base 3 RNAseq overview

Hi Nicklas et al, I've been scanning the 3.0 alfa documentation and have seen how biomaterials are handled with respect next gen (with the new library type). However, I can't see how raw data and analysis works. Do the concepts of reporters and array designs still apply? I'm happy to install

Re: [base] Project defaults in batch-import and experiment validator

More feedback: I've extensively used the no column-use project default functionality, and I think it's logical to do it that way, but the expression-based enhancement sounds like a good next step forward. On Tue, Oct 25, 2011 at 1:01 PM, Nicklas Nordborg nick...@thep.lu.se wrote: On 2011-10-25

[base] DataQuery.order(...) 2.x API question

Hi all, I'm trying to get a Reporter query from the BASE2.x API which is basically ORDER BY RAND(123) - to get reproducible random order (I can explain *why* in another email if anyone cares to know). I tried this DataQuerynet.sf.basedb.core.data.ReporterData repQuery =

Re: [base] DataQuery.order(...) 2.x API question

PM, Nicklas Nordborg nick...@thep.lu.se wrote: On 2012-10-09 13:11, Bob MacCallum wrote: Hi all, I'm trying to get a Reporter query from the BASE2.x API which is basically ORDER BY RAND(123) - to get reproducible random order (I can explain *why* in another email if anyone cares to know). I

Re: [base] DataQuery.order(...) 2.x API question

this before :-) https://forum.hibernate.org/viewtopic.php?f=1t=994753 I reckon I'll get it to work sooner or later. cheers, Bob. On Tue, Oct 9, 2012 at 2:15 PM, Bob MacCallum r.maccal...@imperial.ac.uk wrote: Hi Nicklas, Thanks very much for the quick reply. I am *so* close to getting this working

[base] array design GTF import - not 9 columns

Hi all, [mods please delete the mail I sent from my gmail account, or add me with that account but with no delivery, thank] Just upgraded from 2-3 and now trying out the NGS feaures. Quick question about GTF import for array designs... When doing array design-import the importer is

Re: [base] array design GTF import - not 9 columns

this, and I can probably fix this for the next (BASE 3.3) release. But for now, the importer will choke on anything that is not a Field line as described by http://www.ensembl.org/info/website/upload/gff.html /Nicklas On 2014-05-23 18:17, Bob MacCallum wrote: Hi all, [mods please delete

[base] Files with FTP locations only

Hi Nicklas et al, Getting up to speed with BASE3 and NGS - so far all seems good - even upgrading our own API code has gone smoother than I expected. Thanks! A possible feature request for general discussion: Would it be possible to have placeholder files in the BASE file system which weren't

Re: [base] Files with FTP locations only

Thanks Nicklas, Sorry I hadn't seen the existing functionality - we will check it all out and get back to you soon! On Tue, Jun 24, 2014 at 12:42 PM, Nicklas Nordborg nicklas.nordb...@med.lu.se wrote: On 2014-06-24 11:55, Bob MacCallum wrote: Hi Nicklas et al, Getting up to speed

[base] BASE3 paper?

Hi Nicklas et al, Will there be a Third generation BASE paper we can cite any time soon? Happy to continue to cite the 2009 paper but I was just wondering! cheers, Bob -- Want excitement? Manually upgrade your production

[base] Annotations columns in Experiment list view

Dear BASE developers, It's really great that Experiments can have annotations now (I know, already for several years...). Would it be possible to add these as configurable columns in Experiment list view? I can add the Trac ticket if you remind me privately of the login info. many thanks, Bob

Re: [base] Annotations columns in Experiment list view

Thanks Nicklas, Most awesome! On Thu, May 12, 2016 at 12:02 PM, Nicklas Nordborg < nicklas.nordb...@med.lu.se> wrote: > On 2016-05-12 12:24, Bob MacCallum wrote: > > Dear BASE developers, > > > > It's really great that Experiments can have annotations now (I know, &g

[base] upgrade error (3.4 to 3.9 - actually schema version 119-120)

Dear BASE guys, I got the error below with updatedb.sh I've had a look at Update.java and I'm afraid the hibernate stuff is outside my comfort zone... Please could you let me any further information you need to diagnose? cheers, Bob [72%]--Creating platforms... [73%]--Creating