, by Henrik
Bengtsson from Lund) continues to work in BASE 2.0
Thanks
Charles
On 16 janv. 06, at 13:40, Jari Häkkinen wrote:
Hi Angela,
BASE plug-ins ... we are slowly working on getting the web page up
again. Meanwhile we urge those of you who have plug-ins to send them
to us through http
? If I want to run
BASE2.17 under tomcat, what I need to do? Reinstall the BASE, or just
copy the corresponding folds to Tomcat? Any suggestions will be appreciated.
Thanks a lot!
Best Regards,
Longfei
--
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL
line to
share with us, please use the mailing lists or add comments through
http://lev.thep.lu.se/trac/base/ticket/150
Cheers,
Jari
--
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics phone: +46 (0)46
Nicklas Nordborg wrote:
Emmanuel Courcelle wrote:
Hello
Now using Base 2.1...
I am trying to configure the Raw Data importer plugin, to upload and
parse
genepix-type files.
1/ Pb configuring this plugin
--
I click Plugin/Configuration/New
The reporter import button does appear because there is no plug-in
configured for import of reporters. You need to create a configuration
for the Reporter importer plug-in. We have compiled a getting started
document that outlines the first steps with BASE 2,
.
The list of BASE team supported browsers is short:
Firefox production releases 2 or later.
Internet Explorer 7 or later.
Jari
--
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics phone: +46 (0)46
=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]
--
Jari Häkkinen, PhD
Complex Systems Division
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
[EMAIL PROTECTED]
--
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics
PROTECTED]
--
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics phone: +46 (0)46 2229347
Lund University fax: +46 (0)46 2229686
Sölvegatan 14a, SE-223 62 Lund, Sweden http
Ah, even better ;-)
Nicklas Nordborg wrote:
Jari Häkkinen wrote:
Hi all,
Just a thought, I think the best choice to trigger a large import like
this is to create a plug-in instead of adding extra tabs to the file
browser. The plug-in should start by requesting the zip file/directory
Micha Bayer wrote:
Hi Jari,
That sounds perfectly reasonable when you put it like this, but I was put off
going down that route by a post to the list from Nicklas
(http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00228.html)
where he says that it is best to not use a
Jari Häkkinen wrote:
Hi all,
Just a thought, I think the best choice to trigger a large import
like
this is to create a plug-in instead of adding extra tabs to the
file
browser. The plug-in should start by requesting the zip
file/directory
to import. If the zip file
] On Behalf Of Nicklas Nordborg
Sent: 29 November 2006 14:40
To: BASE ML
Subject: Re: [base] Offline files
Jari Häkkinen wrote:
Hi all,
Just a thought, I think the best choice to trigger a large import
like
this is to create a plug
clean.
Jari
Micha Bayer wrote:
-Original Message-
From: [EMAIL PROTECTED] [mailto:basedb-users-
[EMAIL PROTECTED] On Behalf Of Jari Häkkinen
Sent: 30 November 2006 15:42
To: BASE ML
Subject: Re: [base] Offline files
There is a possibility to get access to the subversion repository
A new minor release is available for download at
http://base.thep.lu.se/wiki/DownloadPage
A list of fixed item is available here
http://base.thep.lu.se/query?status=closedmilestone=BASE+2.1.1order=id
Jari
--
Jari Häkkinen, PhD
Complex Systems Divisionmailto:[EMAIL
Hi,
There is a getting started document available at
http://base.thep.lu.se/chrome/site/doc/user/index.html
Jari
Gabe Dagani wrote:
Greetings,
Has anyone created a simple walkthru for setting up a simple experiment,
uploading GPR, GPS, TIFF files into a project and doing some
A list of all core plug-ins with sample configuration files (also for
plate importer) is available at
http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html
Jari
Nicklas Nordborg wrote:
Audrey Bihouee wrote:
Hi everybody,
A little question in BASE 2 : I'm very
Hi,
there is sample code available at
http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients that
runs against the demo server. The code is written in Perl and R. The
Perl can be used as a script or used to get BASE/R connectivity from an
R environment.
Jari
Nicklas Nordborg
Hi all,
Our best BASE so far is available for download at
http://base.thep.lu.se/wiki/DownloadPage
Happy BASEing,
The Lund BASE team
--
Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics phone: +46
Hi,
You have probably not imported all probeset into the reporter table.
Please make sure that ALL reporters are imported, that is check that the
number of imported and updated reporters match the number of probesets
in the affychip you use.
Cheers,
Jari
[EMAIL PROTECTED] wrote:
Dear
Hi,
The plier and rmaexpress plug-ins calculates the probeset expression
values using information from the cel/cdf files. The plugins are
presented on the BASE plugin site
http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix How the
expression values are calculated is presented elsewhere
Hi all,
We are happy to announce BASE 2.4. The packages are added to the
download area, http://base.thep.lu.se/wiki/DownloadPage
Please send feedback through the mailing lists.
Happy BASEing
The Lund BASE team
-
This
Why not use the clustering in the MeV plugin shipped with BASE?
Jari
Johan Enell wrote:
Hj Bob,
The clustering from Base1 will not work in Base2. Or more precisely,
you will be able to run the plugin but you wont be able to se the
result. The visualization page in Base1 was a
Hi,
jesse paquette wrote:
Hello,
I'm still trying to get through the 2.1 getting started document
(http://base.thep.lu.se/chrome/site/doc/user/getting_started.html).
Moving on to section 2d, Analysing an experiment step I. I'm getting
an error when I try to run the RMAExpress plug-in
There is no need to delete the database between upgrade in a stable
release of BASE. Please read
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html
for upgrading instructions.
Jari
Dave Hau wrote:
2.4.3 release followed closely
Just for your information:
Dominic Oyeniran wrote:
This is a known issue and has been documented here:
http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt.
Please scroll to the usage section right after the installation section.
We prefer to use links
However, given the performance improvement you should go for 2.4.4
Jari
Nicklas Nordborg wrote:
vegard nygaard wrote:
When I briefly inspected what was created in BASE it looked OK despite the
error messages in the log. The overview tab for the experiment crashed
though, but it has done
Select 'Download BASE' at http://base1.thep.lu.se/ and download version
1.2.17b. Follow the instructions in the package to upgrade from 1.2.16
to 1.2.17b
The 1.2.20/21 is a reference to the underlying database schema version
and not the BASE application version. It is a little bit confusing.
A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage
This release contains one fix removing a debug sleep statement. Server
performance is improved when upgrading to this release.
The Lund BASE team
Nicklas Nordborg wrote:
vegard nygaard wrote:
F633 Median not working but giving a funny error message: Error: For input
string: F633 MEdian on line..., (The E's in the input has been
uppercased!)
That is because string like '1.23e-2' are not recognised as numbers
unless the 'e' is first
I moved it to the BASE core ticketing system as
http://base.thep.lu.se/ticket/811
Jari
Nicklas Nordborg wrote:
vegard nygaard wrote:
Thanks for quick answers.
I would like column mappings to support wildcards or regular expressions.
Not a big thing, but I took the liberty to add it as a
Are you logged in as with administrator privileges? Only users with
administrator privileges are allowed to use the Reporter map importer
and thus configure it. There is no need to create this plug-in it comes
with pre-installed with BASE.
Jari
Diana Bernal wrote:
Dear BASE staff, I am
We cannot recreate this problem. We have used the CDF importer on BASE
2.5.0beta and 2.4.5 with no problems. One difference may be that we use
jobagents (i.e., running jobs in a different thread than the core BASE
application) but we did not experience any failures prior to switching
to
Hi all,
We are happy to announce the release of BASE 2.5. The packages are added
to the download area, http://base.thep.lu.se/wiki/DownloadPage
Please send feedback through the mailing lists.
Happy BASEing
The Lund BASE team
A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage
Fixed issues are listed at
http://base.thep.lu.se/query?status=closedmilestone=BASE+2.5.1
The Lund BASE team
-
This SF.net email
Nice work. I've successfully tested the apt-summarize plug-in. I do not
have any genotype data so I have to leave that for someone else to test.
I miss a short description of the two plug-ins. How to use them and what
to expect from them. Specifically the genotyoe plug-in requires some
Hi,
We are working on a backup scheme here in Lund. We'll send a note when
we have something that at least works. Then we can all improve our
backup strategy ;-)
Why use svn? Do you need to track changes to files? For the userfiles
directory a simple rsync should be fine, it is incremental
There is support for Illumina using the Illumina plug-in package,
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina. Illumina is
bead-based and maybe a similar package can be created for Luminex? So,
BASE supports bead based data but luminex is currently not directly
supported.
Jari
Good Morning All,
I have a lot of Affymetrix array data that I would like to analyze together.
The zip that contains these files is very big and I can't upload it to
BASE to use Batch Data Importer to import it into my experiment.
There is a known issue with files larger than 2GB,
The problem is now being fixed, http://base.thep.lu.se/ticket/1077.
Unfortunately this problem affects all versions of BASE2 and everyone
are recommended to upgrade to the future 2.7.2 (or later).
The problem is localized and 2.7.2 will be released later today or at
latest tomorrow. More
Hi all,
We have released BASE 2.7.2. The release includes important bug fixes
in the LOWESS plug-in shipped as a part of the BASE package. Some
other improvement are also included in the release.
It is highly recommended at all BASE installations where LOWESS is
used as a part of their analysis
Hi,
In ftp/config.xml the nio-listener tag there is a port property set to
2121. I think this sets the port number. See
http://baseplugins.thep.lu.se/browser/extensions/net.sf.basedb.ftp/trunk/ftp-config.xml#L29
Jari
Pawel Sztromwasser wrote:
Hi all,
I have just upgraded to the latest
Hi Bob,
Sorry for not commenting your thoughs on storing sequencing data in
BASE. We have discussed it here and will be looking into it later. This
will become an issue for us also since we have sequencing equipment
generating huge quantities of data. So far we are only getting friendly
with
Micha Bayer wrote:
Hi,
I have been trying to look at the example file for the batch import but
it seems corrupted. I am trying to open it in OpenOffice 2.3.0 and the
file does load but then Calc instantly hangs.
The file is created with OpenOffice 2.4 and works. I downloaded it and
could
Are the raw data files visible to the plug-in? If you upload the files
with ftp they are not automatically assigned to a project. You need to
set the parameter defining how the plug-in should find existing items
referenced in the file. If this is not the problem, can you try to only
map the
I have not encountered any problems with attaching files earlier. I
decided to play around with partially filled import files. I succeeded
in creating a file that fails to attach files even though the importer
reports success. BASE 2.8.4 and my 2.9pre test version both fails but
the resolution
There is an ftp-server extension for BASE,
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp Maybe this can
help? It should be possible to get Perl to download files using ftp. And
the names are the native names, i.e. no translation is needed to the
internal name.
Jari
Offord, Victoria
The default project permission for items created with an active projects
is 'RUWD'. Can I change this default to a simple 'R'? It is of course
possible to restrict all project members credential to 'R' individually,
but I would prefer to set the project credentials for new items to 'R'.
Hi all,
The 2.11 release will target performance issues. The next release is
2.10 but we have not set a dead line for the 2.10 release yet. However,
a hopefully performance boosted BASE 2.11 should be out during the
spring, until then we have to live with some slow BASE clicks. I agree
with
Hi Louise,
Maybe you should look into the
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.normalizers package for
inspiration on how to create a plug-in for your needs.
Jari
Nicklas Nordborg wrote:
Louise Donnison wrote:
Hi
We have some raw bioassays in an experiment and I am trying
I am running BASE on a 64-bit mac but my mysql server is a 32-bit binary
(java is 64-bit). I have no problems to report related to the bitness
but then again I am not completely in the 64-bit domain.
Jari
michael watson (IAH-C) wrote:
Dear All
Quick question with a quick answer I expect
Hi,
As you describe it it seems like you have bead level data in your data
files. The Illumina package for BASE expects bead summary data, i.e.,
the average for each bead type (together with some other numbers as
described in
Hi Chad,
The requested class will appear in BASE. We missed it for the 2.10
release but the request is now added to the ticketing system,
http://base.thep.lu.se/ticket/1242
Cheers,
Jari
Chad Matsalla wrote:
Greetings!
I'm using base-2.9.2 on tomcat 6.0.18 in Geronimo 2.1.3.
We use
Hi,
The problem seems to be in the apt-probeset-summarize program as you
point out. Have you tried to run the same analysis outside of BASE? What
is the outcome of that?
Cheers,
Jari
philipp-1.kai...@novartis.com wrote:
Hi,
I am trying to get BASE 2.9.2 working with the APT 0.2 plugin
Klybeckstrasse 141
CH-4057 Basel
Switzerland
Phone: +41 61 6962720
Fax: +41 61 6963373
Email : philipp-1.kai...@novartis.com
Jari Häkkinen j...@thep.lu.se
04.03.2009 15:37
Please respond to
BASE ML basedb-users@lists.sourceforge.net
To
BASE ML basedb-users@lists.sourceforge.net
cc
I notice that I closed the ticket. Maybe we should reopen it and put it
out BASE 3 milestone?
Disclaimer: There is NO plans to start on a BASE 3 in the foreseeable
future.
Jari
Nicklas Nordborg wrote:
This was requested some time ago. There is a ticket at
http://base.thep.lu.se/ticket/978
A new version of the MeV extension for BASE was released yesterday and
already improved today! The new extension is based on the latest MeV
(4.3.02) and supports expression data analysis from BASE with simple clicks.
MeV web page http://www.tm4.org/mev.html
MeV BASE extension web page
Hi Lavinia,
I apologize the delayed response but I needed to check whether we
anticipate this need for our own purposes. The good news is that our lab
will be interested in getting methylation array support into BASE, the
bad news is that we have no real time line for BASE methylation
Hi Klemens,
When using the batch importers you must create the names for all items
yourself. We use a spreadsheet that follows the naming convention
adopted in BASE.
See the attached file that we use at our facility.
Cheers,
Jari
Klemens Vierlinger wrote:
Hi everyone,
I quite like the
YANNICK wrote:
Hi BASE2 users!
I am using BASE 2.11 and have some questions.
I want to calculate Ratios from 2 bioassays organized as following:
- 1st bioassay = control
- 2nd = treatment
Labellings are performed as following:
Cy5= pool of all samples extracts. Same in all arrays (serves
Hi,
It is a while since Paulo asked the below question. I have added a
ticket on this to the plug-in dev site,
http://baseplugins.thep.lu.se/ticket/209
This means that we are going to look into creating a submission tool. It
will probably target GEO submission since there are work done on
Yannick Lippi wrote:
__SECOND QUESTION: R/G quantile normalization
Jari said:
Obviously R-G quantile is not supported since the methods in
net.sf.basedb.normalizers only work on ratios.
- i am not expert on java developping.. but what does mean: methods in
net.sf.basedb.normalizers only
Hi,
Olivier Lefevre wrote:
I am not having much luck installing that plugin. It wants you to
run updatedb.sh. When I do that it says Building database, which
is alarming in and of itself since that suggests it is rebuilding
the db from scratch, which begs the question of whether it is
Before starting to clone BASE you could try to reset list settings with
File - Reset list settings ... select memory and database in the pop-up.
BASE stores uploaded or generated files as files in the filesystem. The
database keep tracks of file locations. There is no information in files
The steps I send covers my needs in that I do not use a secondary
storage area, user files area is covered in my previous posting, and
installed plug-ins are backed up by normal computer backups. But you are
right, for a full clone you should also copy your complete BASE
installation and the
Hi,
The document you are looking for is obsolete, try the getting started
section link at http://base.thep.lu.se instead. If you really want the
outdated document you'll find it at
http://base.thep.lu.se/browser/trunk/doc/historical/user/getting_started.html
You'll need to download the file
Nicklas Nordborg wrote:
Daniel Octavio Palenzuela Gardon wrote:
By other side, when we try to launch Mev in the Tools column when
viewing bioassay sets of an experiment, there is a file with extension
…TDMS.TXT that it`s suppose to be save in raw data, but when we do
browse, there isn’t
I can confirm Pawels problem. I run Firefox 3.5.3 on Mac OS X 10.6.1
(Snowleopard).
My 63k file is now only 32k.
Jari
Nicklas Nordborg wrote:
Pawel Sztromwasser wrote:
I just tested it again (FF3.5.3). Here is how to reproduce:
- upload a text file which is larger then 8kb
- memorize
Jari Häkkinen wrote:
I can confirm Pawels problem. I run Firefox 3.5.3 on Mac OS X 10.6.1
(Snowleopard).
My 63k file is now only 32k.
And redoing edit saves a 16k file, redoing the edit saves a 8k file, and
another edit will not halve the size but a 7.99k file is saved.
Jari
Nicklas Nordborg wrote:
I downloaded and installed Tomcat 6.0.16 and got the same problem. It works
with Tomcat 6.0.20.
And our production server runs 6.0.16. So, it is time to upgrade.
Jari
--
Come build with us!
Offord, Victoria wrote:
I gather that the 2009 is the year and the 02 refers to the date the
file was uploaded. How are the other numbers/values created as I
wanted to add folders/directories from a program I am running which
creates reults files for the data stored in BASE and wanted to keep
tropy wrote:
Nicklas Nordborg wrote:
tr...@valdelsa.net wrote:
1. Log2 ratio transform
MeV behaved (still behaves) inconsistently with data it read from TDMS
with respect to logging data or not. In some cases MeV auto-logged data
and in some other cases it did not. When we began to
Jari Häkkinen wrote:
MeV behaved (still behaves) inconsistently with data it read from TDMS
The above line was meant to say
MeV behaved (still behaves?) inconsistently with data it read from TDMS
...
The question mark because I have not actually checked it. It may be that
the issues
Hi,
There is already a property Gene Symbol but maybe this won't cut it for you?
Jari
On 1/12/10 4:25 PM, flap...@free.fr wrote:
Hello,
I'm using the base-2.14.1 and I'm trying to import a genepix GAL file.
I've add in the file named extended-properties.xml, this :
Hi,
Was this mail was intended for the mailing list?
Jari
On 2/21/10 12:34 AM, alaa gaber wrote:
HI,
I am asking
1-if the base2 uses a tab2mage format
2-i have a problem in converting tab2mage into mage-tab format
3-displaying both in base2
4-can base2 understand perl language
my
On 2/21/10 12:34 AM, alaa gaber wrote:
4-can base2 understand perl language
Not directly, BASE is written in Java. You can write plug-ins using Perl
or other languages. See plug-in developer documents for more details and
browse plug-ins in http://baseplugins.thep.lu.se where several plug-ins
Hi,
This question was asked the other day on the BASE user mailing list
(http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01954.html)
and Nicklas responded to it.
The problem is that user qouta is too low. Your BASE administrator must
increase the quota or you must delete
On 5/28/10 5:43 AM, Irina Maltseva wrote:
I followed the installation instruction on
http://base.thep.lu.se/chrome/site/doc/html/admindoc/installation_upgrade/installation_upgrade.html
and
change the user to ‘root’ in base.config file.
I've created base2 and dynamic.base2 on mysql server
Hi,
We are currently working on how to incorporate sequence data in BASE. We
now have in-house sequencing capacity and need to manage all data
generated. We have not formalized our ideas yet but we'll post whatever
we will are planning to do in another mail/ticket in very near future.
We
Hi,
On 2010-10-18 20.35, Adam Halstead wrote:
Thanks for your response Jari.
I understand support for next generation sequencing data is currently being
developed by the BASE developers - is there a beta version we can look at?
Do you need help developing this functionality? What kind of
Have you followed the instructions in the README
http://baseplugins.thep.lu.se/browser/plugins/base2/se.lu.thep.affymetrix/tags/0.7/README
Do you have an CDF file attached to the design?
Jari
On 2010-12-06 07.56, Irina 264 wrote:
I am trying to run the RMAExpress plug-in to import
Are you sure that all prerequisites are met? The plug-in configuration
and the Base1PluginExecutor should be shared appropriately. Also,
Virtual array works only on 2-channel data.
Jari
On 2011-03-10 17.25, Thomas Person wrote:
Thanks!
That change allows installation but once I atmpt to
Can the problem be that the jobagent does not get enough memory?
CATALINA OPTS will only influence the BASE core server and if there are
separate jobagent processed then these may need an increased memory
setting? I may be completely off here but just a thought.
Jari
On 2011-05-23 08.27,
On 2011-11-22 09.43, Nicklas Nordborg wrote:
On 2011-11-21 21:32, Nantel Andre wrote:
We don't have any regular users yet since we are still figuring out
how it works. I am doing everything from my administrator account.
Have you created a file format configuration for the files you are
Hi,
The procedure to upgrade from 1.2 to latest BASE is uncharted territory
for us. We switched from 1.2 when BASE 2.6 was current. One path forward
may be as outlined below. Each BASE 2 and newer distribution contains
upgrade instructions. Please read them.
Please report if you succeed and
We have realized that migration from BASE 1.2 to BASE 2/3 is only
supported from a BASE 1.2 server running MySQL.
We do think that adding support for other database engines is possible
but we have not tested it and will not actively work on extending
migration support beyond what can be found
On 2013-09-12 16:47, Laurent TROXLER wrote:
Yes, I can axes to Tomcat Home page and login as root. There I can see
that base2 is uploaded.
There isn't any obvious error on the web interface.
To answer to Jari, I am working presently directly on the server to
avoid any internet problem.
Ok.
On 2013-09-11 10:57, Laurent Troxler wrote:
going through the log files here is what I can get:
system.log: repeating those two lines
Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
CGErrorBreakpoint() to catch errors as they are logged.
Sep 11 10:32:02 seridi
Hi,
There is no cloud-deployable BASE available and there is no plans for
one either.
The demo server has moved and the redirect seems to be broken. I have
sent a mail to the network administrator of the previous facilities
asking them to restore the redirect.
The demo server is located at
On 2015-03-12 09:24, Jari Häkkinen wrote:
One source for the problem is that the underlying RMAExpressConsole
program doesn't handle ST arrays, or maybe treats ST arrays differently.
I meant to say that problem may be with RMAExpressConsole but I don't know.
Jari
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