replicates into one data
set.
Do people normally do this type of analysis with plugins or external software?
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phon
Hi again,
Now that the festive season is well and truly over, I wonder if
anyone can help me out with my question (see below).
many thanks!
Bob.
Bob MacCallum writes:
>
> Hi all,
>
> I've been looking at the demo of BASE 1.2 at Lund and I can't figure out one
>
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
---
This SF.net email is sponsored by: Splunk Inc. Do you g
is well and truly over, I wonder if
> > anyone can help me out with my question (see below).
> >
> > many thanks!
> > Bob.
> >
> > Bob MacCallum writes:
> > >
> > > Hi all,
> > >
> > >
.x similar
functionality?
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
---
This SF.Ne
" allow customised reporter and
raw data columns? I guess it does, and if not, modifying the migrate program
can't be too hard.
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
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 | Imper
ion code and 1.2.20 (BASE
1.2.17) is required/supported.
it was just a case of slightly out-dated documentation.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Ema
>
> ---
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat certifications in
> the hosting industry. Fanatical Support. Click to learn mo
to share?
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
---
All the advantages of L
will send the code.
comments on your experience with SSL/HTTPS still gratefully received.
Bob MacCallum writes:
>
> Hi,
>
> As usual I have two topics...
>
> I was looking into baseftpd and running it through an SSH tunnel (as
> suggested
> in the BASE inst
of (0,0) but that caused an out-of-bounds
error in the spot extractor.
thanks for any advice you might have,
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL
spond
to each other - no surprise that the spots didn't line up!
sorry to those who wasted energy reading my mail and this one!
cheers,
Bob.
Bob MacCallum writes:
>
> Hi,
>
> Has anyone had trouble creating the jpeg spot images from GenePix files? All
> the software
even does the JPEG
spot image extraction. The GUI looks and feels like BASE - except that you
have to enter your username/password again (to authorise the robot). If
anyone is interested I can send the scripts - I'll need to add a bit more
documentation though, and note that it has onl
specified sample annotation), I would be very grateful. Installing such a
plugin would help me figure out how to write one.
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology
t; > Bob.
> >
> >
>
>
> -
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions
which the array was intended.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
-
Tak
.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
-
Using Tomcat but need to do more? Need to
being able to log into multiple BASE sessions as different users is very
useful however!)
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College Londo
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 MacC
php?page=join.php&p=sourceforge&CID=DEVDEV
> ___
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> basedb-users@lists.sourceforge.net
> unsubscribe: send a mail with subject "unsubscribe" to
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Bob MacCal
ou'll get the chance to share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> ___
> The BASE general discussion mai
s your responsibility to scan the
> email
> and the attachments (if any).
>
>
> -
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'l
er
> Bioinformatics Specialist
> Genetics Programme
> The Scottish Crop Research Institute
> Invergowrie
> Dundee
> DD2 5DA
> Scotland, UK
> Telephone +44(0)1382 562731 ext. 2309
> Fax +44(0)1382 562426
> http://www.scri.sari.ac.uk/MichaBayer.htm
> =
>
>
InteractivePlugin, AutoDetectingImporter
> >>> {
> >>> private static final Set guiContexts =
> >>> Collections.singleton(new GuiContext(Item.EXPERIMENT,
> >>> GuiContext.Type.ITEM));
> >>>
> >>>
> >>> then I'll get an import tab created in
if(isset($i_login) && $i_login != "")
+ if(!$loggedIn && isset($i_login) && $i_login != "")
{
if($curSession->attemptLogin($i_login,
$i_password, $_SERVER["REMOTE_ADDR"]))
meanwhile I co
genepix ratios
are no longer valid.
I haven't loaded any data in our BASE2 test server yet (data migrated from
BASE1 only) - so I have a general question: what is the strategy for loading
dye swaps in BASE2, is it the same as BASE1?
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kaf
clarification
> a) BASE (1) imports dye swap experiments with different importers so that
> the experimental/control data always ends up in channel 1/channel 2.
and therefore the original ch1/ch2 calculations are no longer any use
--
Bob MacCallum | VectorBase Developer | K
t can
> do that.
This is something of interest here too. What would the general workflow be?
Would it be like this?
1) upload raw data, samples, experiment info as usual to BASE
2) perform any reporter or assay merging required to match processed data's
"shape" using
#x27;ll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> ___________
> The BASE general discussion mailing list
&g
to the list most welcome (I'll post them on the wiki's
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
___
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> unsubscribe: send a mail with subject "unsubscribe" to
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Bob MacCallum | VectorBase Developer | Kafatos/Christop
Regardless, I'm quite convinced a report/visualisation tool of this
> kind implemented in a general fashion would find many uses in the
> BASE community. We'll take a closer look at it to give you some
> creative feedback.
Thanks - that will be appreciated.
Developer
3 23 100 96 0 298
294 57 64 67 24 100 98 0 0.538 0.557
0.526 0.538 1.599 0.549 0.730 80 590 360 358 -0.893
126 234 128 230 0
However in BASE1 it was possible to impo
ata and I guess there is more to find before the problems
> disappear.
Haha, all we have is non-perfect data ;-)
I just found a minor bug with the web interface while importing raw data:
http://base.thep.lu.se/ticket/57
a separate anatomy ontology, so that it goes into
tab2mage correctly (or perhaps MAGE-TAB at a later date)?
Thanks for reading this far!
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell
> http://lev.thep.lu.se/trac/baseplugins/browser/tags/se/lu/thep/affymetrix-0.6/README
> for details.
could someone point me to these .csv files please?
I've downloaded the xxx_libraryfile.zip (containing a .cdf file amongst
others) but no .csv file. Do you get this from NetAffx online
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
The sensible 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
the last step is the important one
(for analysis).
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
---
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files, directories, jobs). Now I believe our guest user is truly
read-only.
The "multi-user account" option is invaluable here (it stops the user changing
the password).
hope that helps someone...
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Divis
it all out myself
(have pimped my BASE1 enough already) - so if anyone can send some diffs,
that would be great.
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Em
of migrator program - in the style 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/Chris
2. some kind of migrator program - in the style of the base1->2
> > migrator,
> >including analysis steps
> >
> > 3. using batch loaders, load data from scratch on live server (and
> > re-run
> >analysis steps)
>
re requested to preserve this
> confidentiality and you must not use, disclose, copy, print or rely on this
> e-mail in any way. Please notify [EMAIL PROTECTED] quoting the
> name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable p
tate somehow. Could someone help me at least clear the error?
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College Lo
Problem temporarily solved!
"clear filter" in the view/presets menu clears the problem
(although I had previously cleared all the filters manually)
I forgot to mention that the error appears in a big red box
above the list table.
Bob MacCallum writes:
>
> Hi,
>
> I
can work with the PNGs and assorted text files.
many thanks,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +44
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,
> >>
>
of from a
> base1 plugin configuration file. From 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:
>
> >
&g
lution like that in Base2.
> >
> >
> > When you configure Base1 plugins you should always start of from a
> > base1 plugin configuration file. From the plugin page in Base1 you
> > will find an export link with each plugin. Use that file to configure
> > t
rosoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
> ___
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> unsubscribe: send a ma
pping through log files to find problems? Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
> ___
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(0)1382 562731 ext. 2309
> Fax +44(0)1382 562426
> http://www.scri.ac.uk/staff/michabayer
> ==
>
>
> > -Original Message-
> > From: [EMAIL PROTECTED] [mailto:basedb-users-
> > [EMAIL PROTECTED] On Behalf Of Bob MacCallum
s to find problems? Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
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> basedb
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SF.net email is sponsored by: Splunk Inc.
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Bob MacCallum |
d you ever have two or more experimental factors that should 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 | Imper
> The BASE general discussion mailing list
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k Inc.
> Still grepping through log files to find problems? Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
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> The BASE gener
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 Deve
p
Memory Total: 474.6 MB
Free: 238.2 MB
Max: 910.3 MB
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
---
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 Co
ot only one result - no more duplication!
On starting one tomcat and BASE-related webapp again I still don't get
duplication.
I'll post back here again if we see duplication again and can recreate the
conditions. In the meantime, all seems OK again.
cheers,
Bob.
>
> /Nickla
stance, as this
saves a lot of hassle when upgrading BASE on our 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 |
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 ca
ld make lots of reporter lists and do this (although I never actually
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]
---
paste/upload them 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
lists.sourceforge.net
> > unsubscribe: send a mail with subject "unsubscribe" to
> > [EMAIL PROTECTED]
> >
>
> -
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express
Ah yes, I see this appears (in the expression builder) after I have made a
reporter list. Thanks.
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> >
> > Also, can reporter lists be used in filter expressions in BASE2?
>
> Yes. They should show up in the expression
__
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--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Mo
orkload than svn 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/
ample), then backups could be made while
people still 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 Lon
rosoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
> ___
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> basedb-users@lists.sourceforge.net
> unsubscribe: send a ma
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 t
ow if this works in BASE2.
Has anyone else run into this type of problem?
cheers,
Bob.
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL
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
>
,
Bob.
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > Thanks for all the ideas on this.
> >
> > re: userfiles/db sync, would this work..?
> >
> > backup:
> >
> > 1. mysqldump to date-stamp-named files
> > 2. rsync -arv /data/base2/file
o take ownership 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]
--
as a workaround. Note/tip: if you need 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:
&g
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
and update
> BASE servers 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 suggest
239;13503038;w?http://sf.net/marketplace___
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> basedb-users@lists.sourceforge.net
> unsubscribe: send a mail with subject "unsubscribe" to
> [EMAIL PROTECTED]
--
Bob MacCallu
through
> different port numbers that isn't 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 a
e an optional flattened view in the
Files browser. Then the filters (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 th
biosources, 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/Chr
iver com.mysql.jdbc.Driver (version 5.0)
Java runtimeJava(TM) SE Runtime Environment (1.6.0-b105), Sun Microsystems
Inc.
Operating systemLinux amd64 2.6.16.54-0.2.5-smp
Memory Total: 108.4 MB
Free: 22.6 MB
Max: 910.3 MB
--
Bob MacCallum | VectorBase Developer | Kafatos/Chri
_________
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> unsubscribe: send a mail with subject "unsubscribe" to
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ng event. There's still time to save $100.
> Use priority code J8TL2D2.
> http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___
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> basedb-users@lists.sourceforge.ne
://poi.apache.org/).
--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
-
This SF.net email is
y use anyway: verify
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 a
ut file 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 +
were 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.
our analysis
over to use 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 end
; Thank you for reporting this issue to us.
>
>
> Jari
>
>
> 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/base2de
lameness
> and boredom. Vote Now at http://www.sourceforge.net/community/cca08
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> unsubscrib
nged so if
> you have created configurations for the previous sample file you need to
> update the configurations. The changes are from Array design and down to
> rawbioassays.
>
>
> Jari
>
>
> Bob MacCallum wrote:
> > Dear Nicklas et al.,
> &g
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