[base] GenePix Raw Importer config

These are the values that seem to work for the gpr files that we have. Data Header = "Block"\t"Column".* strip quotes = True mysql select p.name, s.value from PluginConfigurationValues as p, StringValues as s where s.id=p.value_id and p.pluginconfiguration_id=2;

[base] Nimblegen

be practical? Should I just store the raw datafiles as file attachments? It would be nice to have some compression built into the file attachments as this could save 75% on the disk space as each expt is 3 gigs or so. thanks, Keith Ching

Re: [base] Nimblegen

of rows of data, but i can't imagine that its very fast even if indexed properly.. -keith Nicklas Nordborg wrote: Keith Ching wrote: Hi, I am looking into using BASE2 to store ChIP-chip data from the NimbleGen platform. Each whole genome scan has 14 million probes, divided up into 38

[base] create slide wizard numbering

Under Array Slides / Create multiple the Start at field is limited to 3 digits. is it possible to increase this to 4 digits as we continuously number our slides and it's in the thousands already. ( ie. i'd like to make slides 1100-1150 ) thanks, Keith Ching

[base] file storage system question

, i noticed that the file storage for base2 physically places all files in the same directory regardless of where they appear in the file tree hierarchy. is there any practical limit on the number of files that can be stored here? i am planning to put thousands. thank you, Keith Ching

[base] comment on ticket 334 Project default items

, Keith Ching - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based

Re: [base] file storage system question

to the specified raw file. Keith Ching wrote: is there a way to link the original source file to the raw bioassay into which it was imported? say i have an experiment which contains 20 raw bioassays. what would be the best way to be able to list / retrieve the original data files that were used to create

Re: [base] file storage system question

of a plug-in to take all files in a directory, create a raw bioassay, and generate a link to the source file? thanks, Keith Ching Nicklas Nordborg wrote: Keith Ching wrote: it seems you can make a String annotation type and attach it to raw bioassay and fill it with a href=""

Re: [base] create slide wizard numbering

thanks for fixing this.. it works great.. you're a wrist saver.. -keith Nicklas Nordborg wrote: Under Array Slides / Create multiple the Start at field is limited to 3 digits. is it possible to increase this to 4 digits as we continuously number our slides and it's in the

Re: [base] Offline files

mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Keith Ching, Ph.D. Bioinformatics, Laboratory of Gene Regulation Ludwig Institute for Cancer Research 9500 Gilman Drive, #0653 CMM East, Room 3020 La Jolla, CA 92093-0653

[base] Location of original source files

that i want to download. It's just I can't find what file was originally used to create it. thanks, Keith -- Keith Ching, Ph.D. Bioinformatics, Laboratory of Gene Regulation Ludwig Institute for Cancer Research 9500 Gilman Drive, #0653 CMM East, Room 3020 La Jolla, CA 92093-0653 [EMAIL PROTECTED

Re: [base] Location of original source files

nothing to do with the file names. /Nicklas Am I off track? Cheers Charles On Dec 8, 2006, at 9:00 AM, Nicklas Nordborg wrote: Keith Ching wrote: Hi, I am trying to write a plugin that will download the original source files used to populate the RawBioAssay objects. When

[base] downloading files

and download the archive from inside their home dir? is there a nice File.Action.addZip ? thanks, -keith -- Keith Ching, Ph.D. Bioinformatics, Laboratory of Gene Regulation Ludwig Institute for Cancer Research 9500 Gilman Drive, #0653 CMM East, Room 3020 La Jolla, CA 92093-0653 [EMAIL PROTECTED] 858-822

Re: [base] downloading files

that downloads bioassays, 2.0, 2006, Keith Ching, null, null, http://bioinformatics-renlab.ucsd.edu; ); /* From the AbstractExporterPlugin class

Re: [base] downloading files

sorry.. i'm careless.. i called my jar file DownloadFilePlugins.jar instead of DownloadFilePlugin.jar and it couldn't find / load it but it threw a pretty impressive stack trace.. -keith Keith Ching wrote: Hi, I am getting a peculiar stack trace upon trying to define the plugin. do

Re: [base] downloading files

wrote: Keith Ching wrote: Hi, I am getting a peculiar stack trace upon trying to define the plugin. do you think it could be caused by using Base2.2 classes in a Base2.1.1 codebase? i tried to include the revised classes in the plugin JAR.. but i suppose this probably doesn't work.. i had

Re: [base] walk thru

. thanks - Gabe -- Keith Ching, Ph.D. Bioinformatics, Laboratory of Gene Regulation Ludwig Institute for Cancer Research 9500 Gilman Drive, #0653 CMM East, Room 3020 La Jolla, CA 92093-0653 [EMAIL PROTECTED] 858-822-5767

[base] can you run a plugin outside of the web interface?

Hi, i have written a plugin that takes a spreadsheet and creates samples - rawbioassay and links the data file to the rawbioassay. is there a way i can also run the plugin without going through the web interface.. ie. initiate running it from another program? thanks, -keith -- Keith Ching

Re: [base] Bug fix release 2.2.1 is available now

/query?status=newstatus=assignedstatus=reopenedstatus=closedmilestone=BASE+2.2order=id Enjoy, The Lund BASE Team -- Keith Ching, Ph.D. Bioinformatics, Laboratory of Gene Regulation Ludwig Institute for Cancer Research 9500 Gilman Drive, #0653 CMM East, Room 3020 La Jolla, CA 92093-0653

Re: [base] Bug fix release 2.2.1 is available now

weird.. at one point 2.2.1 was working.. i restored back to 2.1.2 and it worked.. so i upgraded to 2.2.1 and it blows again w/ the same error.. without doing anything.. maybe i'll try to reinstall 2.2.1 w/ fresh codebase, maybe i messed up the config somewhere.. -keith