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From: Matthew L. <ma...@jh...> - 2001-10-23 17:59:52
|
Todd,
Sorry, I pasted the wrong URL's on the last email. The following =
is what I have done:
Control Bundle URL: =
http://128.220.136.28/cgi-bin/genex/curation-tool/cb-login.pl
Experiment Set Submit URL: =
http://128.220.136.28/cgi-bin/genex/curation-tool/expset-submit.pl
Experiment Set Download URL: =
http://128.220.136.28/cgi-bin/genex/curation-tool/expset-login.pl
After I changed those URL's, I got the page can't be displaied message =
in browser. 128.220.136.28 is the IP address of the GeneX server. I also =
tried the host name, genex.wbmei.jhu.edu, instead of the IP address, but =
I got the same message in the browser. I have another question. Where is =
"cgi-bin" directory suppose to be? Please give me some pointers. Thank =
you.
Matt
1:57pm
10/23/2001
|
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From: Todd F. P. <tf...@nc...> - 2001-10-23 17:50:59
|
Dear Matthew: The first URL has '////' after the http:. The server will not like that. Also, you must change genebox.ncgr.org to be yourserver.yourloacation.???. Probably will be something like yourserver.jhu.edu. Let us know if you have any more problems or questions. Todd Peterson NCGR On Tue, 23 Oct 2001, Matthew Lin wrote: > I have problem connecting Curation Tool on a client computer to GeneX server. I started the postmaster on the server, and on a client computer, I changed the URL in Curation Tools as the followings: > > Control Bundle URL: http:////genebox.ncgr.org/cgi-bin/genex/curation-tool/cb-login.pl > Experiment Set Submit URL: http://genebox.ncgr.org/cgi-bin/genex/curation-tool/expset-submit.pl > Experiment Set Download URL: http://genebox.ncgr.org/cgi-bin/genex/curation-tool/expset-login.pl > > However, after I clicked the "DOWNLOAD EXP SET" button in Curation Tool, the brower gave me a message saying the page can't be displayed. Did I set the URL's wrong or I need to change something on the GeneX server? Please give me some pointers. > > > Matt > 1:31pm > 10/23/2001 > |
|
From: Todd F. P. <tf...@nc...> - 2001-10-23 17:35:24
|
Dear Tony: The noted links have been fixed. Enjoy! Todd Peterson NCGR On Tue, 23 Oct 2001, Todd F. Peterson wrote: > Dear Tony: > > The gen...@li... group is the correct place to send bug > reports. We are actively fixing broken links. Thank you very much for your > help. > > Todd Peterson > NCGR > > On Tue, 23 Oct 2001, Tony Kusalik wrote: > > > I hope that I am sending this message to the correct place. > > Unfortunately, nowhere at http://genex.ncgr.org/ does it > > say where to send bug reports (about the web page) to. > > > > In the left-hand frame, under "Documentation & Help", > > the links "NCGR GeneX Pages" and "Schema Description" > > are dead (give 404 errors). > > > > > > > > > > _______________________________________________ > > Genex-dev mailing list > > Gen...@li... > > https://lists.sourceforge.net/lists/listinfo/genex-dev > > > > |
|
From: Matthew L. <ma...@jh...> - 2001-10-23 17:34:38
|
I have problem connecting Curation Tool on a client computer to =
GeneX server. I started the postmaster on the server, and on a client =
computer, I changed the URL in Curation Tools as the followings:
Control Bundle URL: =
http:////genebox.ncgr.org/cgi-bin/genex/curation-tool/cb-login.pl
Experiment Set Submit URL: =
http://genebox.ncgr.org/cgi-bin/genex/curation-tool/expset-submit.pl
Experiment Set Download URL: =
http://genebox.ncgr.org/cgi-bin/genex/curation-tool/expset-login.pl
However, after I clicked the "DOWNLOAD EXP SET" button in Curation Tool, =
the brower gave me a message saying the page can't be displayed. Did I =
set the URL's wrong or I need to change something on the GeneX server? =
Please give me some pointers.
Matt
1:31pm
10/23/2001
|
|
From: Todd F. P. <tf...@nc...> - 2001-10-23 16:38:48
|
Dear Tony: The gen...@li... group is the correct place to send bug reports. We are actively fixing broken links. Thank you very much for your help. Todd Peterson NCGR On Tue, 23 Oct 2001, Tony Kusalik wrote: > I hope that I am sending this message to the correct place. > Unfortunately, nowhere at http://genex.ncgr.org/ does it > say where to send bug reports (about the web page) to. > > In the left-hand frame, under "Documentation & Help", > the links "NCGR GeneX Pages" and "Schema Description" > are dead (give 404 errors). > > > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev > |
|
From: Tony K. <ku...@cs...> - 2001-10-23 15:52:02
|
I hope that I am sending this message to the correct place. Unfortunately, nowhere at http://genex.ncgr.org/ does it say where to send bug reports (about the web page) to. In the left-hand frame, under "Documentation & Help", the links "NCGR GeneX Pages" and "Schema Description" are dead (give 404 errors). |
|
From: Todd F. P. <tf...@nc...> - 2001-10-14 17:54:46
|
Ron, Glad to hear that you are in business. Will fix the link ASAP. Todd On Sun, 14 Oct 2001, Ron Ophir wrote: > Todd, > That is it. That what makes the difference. Since I know installation by heart I didn't look at the manual to update database version rather I looked for a link the only you have is http://www.ncgr.org/genex/doc/genex-dump-001202.pg6.gz. I saw that Sakuji got the error I got so I guess he download the same version. Would you please update this link. > Thanks for everything, > Ron > > > > >>> "Todd F. Peterson" <tf...@nc...> 10/11/01 10:09PM >>> > This could make a difference. I used the noted genex-initdb-latest.gz and > the genexadmin table was created and populated. > > Todd > > On Thu, 11 Oct 2001, Ron Ophir wrote: > > > Hey Todd, > > I'm at home but without doing this I can tell that it works. the problem is that genexadmin doesnot exist because install all do not update genex database right. > > If that what you are getting at let start from this. > > However the scheme I used was genex-dump-001202.pg6.gz > > at the url: http://www.ncgr.org/genex/doc/ > > Does this make the difference? > > Ron > > > > >>> "Todd F. Peterson" <tf...@nc...> 10/11/01 17:08 PM >>> > > OK...how about > > psql -U genex > > if that works, try \d in psql which will report the tables in the genex > > database. > > if that doens't work, either the genex user doesn't exist or the genex > > database doesn't exist (substitute the name that you used to set up the > > data). > > > > to start over with the database, type the following: > > dropdatabase genex > > dropuser genex > > createuser genex > > createuser readonly > > createdatabase genex > > > > download genex-initdb-latest.gz from http://genex.ncgr.org/download/DB > > unzip it: > > gunzip genex-initdb-latest.gz > > > > start psql again: > > psql -U genex > > > > build db: > > \i genex-initdb-latest > > > > list tables: > > \d > > > > Let me know if that helps. > > > > Todd > > > > On Thu, 11 Oct 2001, Ron Ophir wrote: > > > > > Great I love such surveys. > > > > > > What do you wanted to do by > > > psql -D /usr/local/pgsql/data > > > > > > this is what I got: > > > psql: invalid option -- D > > > Try -? for help. > > > > > > I remained you I use RedHat 7.1 and postgresql-7.0.3-8. > > > my psql option are: > > > Usage: > > > psql [options] [dbname [username]] > > > > > > Options: > > > -a Echo all input from script > > > -A Unaligned table output mode (-P format=unaligned) > > > -c <query> Run only single query (or slash command) and exit > > > -d <dbname> Specify database name to connect to (default: root) > > > -e Echo queries sent to backend > > > -E Display queries that inernal commands generate > > > -f <filename> Execute queries from file, then exit > > > -F <string> Set field separator (default: "|") (-P fieldsep=) > > > -h <host> Specify database server host (default: domain socket) > > > -H HTML table output mode (-P format=html) > > > -l List available databases, then exit > > > -n Disable readline > > > -o <filename> Send query output to filename (or |pipe) > > > -p <port> Specify database server port (default: hardwired) > > > -P var[=arg] Set printing option 'var' to 'arg' (see \pset command) > > > -q Run quietly (no messages, only query output) > > > -R <string> Set record separator (default: newline) (-P recordsep=) > > > -s Single step mode (confirm each query) > > > -S Single line mode (newline terminates query) > > > -t Print rows only (-P tuples_only) > > > -T text Set HTML table tag options (width, border) (-P tableattr=) > > > -U <username> Specify database username (default: root) > > > -v name=val Set psql variable 'name' to 'value' > > > -V Show version information and exit > > > -W Prompt for password (should happen automatically) > > > -x Turn on expanded table output (-P expanded) > > > -X Do not read startup file (~/.psqlrc) > > > > > > and database directory is at > > > > > > /var/lib/pgsql/data > > > > > > Ron > > > > > > >>> "Todd F. Peterson" <tf...@nc...> 10/10/01 06:58PM >>> > > > Ron > > > > > > Hmmmm...I would think that you could avoid reformatting and reinstalling > > > Redhat (except as a last resort). I've been messing with Postgres quite a > > > bit lately (trying to get the GeneX Server working on Windows 2000). > > > Setting up Postgres can be very tricky. But, in the end I was finally > > > successful. Here are some things to try: > > > > > > 1. first, locate the directory where the postgres data resides. By > > > default, this would be /usr/local/pgsql/data. > > > 2. try running psql by typing psql -D /usr/local/pgsql/daa > > > 3. let me know what happens > > > > > > We could do a variety of things to repair your installation (at least > > > that's what I think). > > > > > > Todd > > > > > > On Wed, 10 Oct 2001, Ron Ophir wrote: > > > > > > > Hi Todd, > > > > We've been in Jewish holiday period. Well, We're in a situation where Jas has done the procedure of database installation successfully, which put in a situation that the only thing I can do is format the disk and install RedHat again. An indication that I have an old DB is that I don't have the GenexAdmin table, but the question is why it does not install the new database version. It might be a fundamental problem with my PostgresQL as result of broken link or something else since I "rpm -e" it and reinstall. What is strange is that except expset-download everything is OK. So until I reinstall RedHat I think there is nothing to do unless you would like to instruct how to debug this problem. > > > > > > > > Thanks Todd, > > > > Ron > > > > > > > > >>> "Todd F. Peterson" <tf...@nc...> 10/04/01 11:12PM >>> > > > > Ron > > > > > > > > Did Jason help you out with this? > > > > > > > > Todd > > > > > > > > On Tue, 25 Sep 2001, Ron Ophir wrote: > > > > > > > > > Hi Jas and Todd, > > > > > I reinstalled the database the messages when install GeneX.pm runs fast, However I' ve catch part of it > > > > > > > > > > Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 114. > > > > > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > > > > > Compilation failed in require at t/XMLUtils.t line 16. > > > > > BEGIN failed--compilation aborted at t/XMLUtils.t line 16. > > > > > t/XMLUtils..........dubious > > > > > Test returned status 2 (wstat 512, 0x200) > > > > > DIED. FAILED tests 1-31 > > > > > Failed 31/31 tests, 0.00% okay > > > > > Failed Test Status Wstat Total Fail Failed List of Failed > > > > > -------------------------------------------------------------------------------- > > > > > t/Chromosome.t 2 512 5 5 100.00% 1-5 > > > > > t/Citation.t 2 512 5 5 100.00% 1-5 > > > > > t/Contact.t 2 512 5 5 100.00% 1-5 > > > > > t/DBUtils.t 2 512 21 21 100.00% 1-21 > > > > > t/Genex.t 2 512 14 14 100.00% 1-14 > > > > > t/GroupLink.t 2 512 4 4 100.00% 1-4 > > > > > t/GroupSec.t 2 512 5 5 100.00% 1-5 > > > > > t/HTMLUtils.t 2 512 4 4 100.00% 1-4 > > > > > t/Protocol.t 2 512 2 2 100.00% 1-2 > > > > > t/Sample.t 2 512 5 5 100.00% 1-5 > > > > > t/Scanner.t 2 512 2 2 100.00% 1-2 > > > > > t/Software.t 2 512 5 5 100.00% 1-5 > > > > > t/Species.t 2 512 9 9 100.00% 1-9 > > > > > t/Spotter.t 2 512 2 2 100.00% 1-2 > > > > > t/UserSec.t 2 512 5 5 100.00% 1-5 > > > > > t/XMLUtils.t 2 512 31 31 100.00% 1-31 > > > > > Failed 16/36 test scripts, 55.56% okay. 124/196 subtests failed, 36.73% okay. > > > > > make: *** [test_dynamic] Error 2 > > > > > > > > > > maybe that is why I can't download expset? > > > > > Ron > > > > > > > > > > > > > > > > > > > > > > |
|
From: <ja...@op...> - 2001-10-12 04:19:05
|
"Todd F. Peterson" <tf...@nc...> writes: > Dear Sakuji: > > I am cc'ing this message to gen...@li... since more > experts monitor that list. We will look into this problem to determine > what could be causing this problem. Seems funny that it reports an error > on the same line (72) in TestDb.pm (which is in > GeneX-Server-1.0.4/Genex/t). Konicha Wa Sakujisan, To test the installation, the GeneX API installer attempts to connect to your local GeneX DB (in the TestDB.pm file). It retrieves some values from the DB that are installed in the default DB. This error indicates that either you did not install the default DB using the installer, or this is some problem with your DB. I attempted to connect to your machine (http://cosmos.toyama.dummy.ne.jp/genex) but it was not publicly available. You can test your DB by loggin into the query tool: http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex/gxquery/query_intro.pl If you are able to connect to this page, then you installation is OK, and something else went wrong. If you get some error attempting to connect then either you did not install the default DB, or the installation did not succeed. jas. > On Fri, 12 Oct 2001, Sakuji Toyama wrote: > > > I have attempted to install the program GeneX-Server-1.0.4 in > > my local machine. Installation proceeded without any trouble. But > > the test was failed with following comments; |
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From: Todd F. P. <tf...@nc...> - 2001-10-12 02:15:58
|
Dear Sakuji: I am cc'ing this message to gen...@li... since more experts monitor that list. We will look into this problem to determine what could be causing this problem. Seems funny that it reports an error on the same line (72) in TestDb.pm (which is in GeneX-Server-1.0.4/Genex/t). Todd Peterson NCGR On Fri, 12 Oct 2001, Sakuji Toyama wrote: > I have attempted to install the program GeneX-Server-1.0.4 in > my local machine. Installation proceeded without any trouble. But > the test was failed with following comments; > > t/AL_Spots..........ok > t/AM_FactorValues...ok > t/AM_Spots..........ok > t/AM_SuspectSpots...ok > t/ArrayLayout.......ok > t/ArrayMeasurement..ok > t/BlastHits.........ok > t/Chromosome........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Chromosome.t line 16. > BEGIN failed--compilation aborted at t/Chromosome.t line 16. > t/Chromosome........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-5 > Failed 5/5 tests, 0.00% okay > t/Citation..........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Citation.t line 16. > BEGIN failed--compilation aborted at t/Citation.t line 16. > t/Citation..........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-5 > Failed 5/5 tests, 0.00% okay > t/Contact...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Contact.t line 17. > BEGIN failed--compilation aborted at t/Contact.t line 17. > t/Contact...........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-5 > Failed 5/5 tests, 0.00% okay > t/ControlledVocab...ok > t/DBUtils...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/DBUtils.t line 28. > BEGIN failed--compilation aborted at t/DBUtils.t line 28. > t/DBUtils...........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-21 > Failed 21/21 tests, 0.00% okay > t/ExperimentFactors.ok > t/ExperimentSet.....ok > t/ExternalDatabase..ok > t/Genex.............Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Genex.t line 23. > BEGIN failed--compilation aborted at t/Genex.t line 23. > t/Genex.............dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-14 > Failed 14/14 tests, 0.00% okay > t/GenexAdmin........ok > t/GroupLink.........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/GroupLink.t line 17. > BEGIN failed--compilation aborted at t/GroupLink.t line 17. > t/GroupLink.........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-4 > Failed 4/4 tests, 0.00% okay > t/GroupSec..........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/GroupSec.t line 17. > BEGIN failed--compilation aborted at t/GroupSec.t line 17. > t/GroupSec..........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-5 > Failed 5/5 tests, 0.00% okay > t/HTMLUtils.........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/HTMLUtils.t line 17. > BEGIN failed--compilation aborted at t/HTMLUtils.t line 17. > t/HTMLUtils.........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-4 > Failed 4/4 tests, 0.00% okay > t/HotSpots..........ok > t/Protocol..........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Protocol.t line 17. > BEGIN failed--compilation aborted at t/Protocol.t line 17. > t/Protocol..........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-2 > Failed 2/2 tests, 0.00% okay > t/Sample............Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Sample.t line 17. > BEGIN failed--compilation aborted at t/Sample.t line 17. > t/Sample............dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-5 > Failed 5/5 tests, 0.00% okay > t/SampleProtocols...ok > t/Scanner...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Scanner.t line 17. > BEGIN failed--compilation aborted at t/Scanner.t line 17. > t/Scanner...........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-2 > Failed 2/2 tests, 0.00% okay > t/Software..........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Software.t line 17. > BEGIN failed--compilation aborted at t/Software.t line 17. > t/Software..........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-5 > Failed 5/5 tests, 0.00% okay > t/Species...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Species.t line 19. > BEGIN failed--compilation aborted at t/Species.t line 19. > t/Species...........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-9 > Failed 9/9 tests, 0.00% okay > t/SpotLink..........ok > t/Spotter...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/Spotter.t line 17. > BEGIN failed--compilation aborted at t/Spotter.t line 17. > t/Spotter...........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-2 > Failed 2/2 tests, 0.00% okay > t/TL_FactorValues...ok > t/TreatmentLevel....ok > t/Treatment_AMs.....ok > t/USF_ExternalDBLink.ok > t/UserSec...........Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/UserSec.t line 17. > BEGIN failed--compilation aborted at t/UserSec.t line 17. > t/UserSec...........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-5 > Failed 5/5 tests, 0.00% okay > t/UserSequenceFeature.ok > t/XMLUtils..........Using /home/stoyama/GeneX-Server-1.0.4/Genex/blib > Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 72. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/XMLUtils.t line 16. > BEGIN failed--compilation aborted at t/XMLUtils.t line 16. > t/XMLUtils..........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-31 > Failed 31/31 tests, 0.00% okay > Failed Test Status Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------------- > > Please teach me the way to solve this problem. > > > genex-errors.txt: > > !! System Error: Illegal seek @ line: 2502 (make -s test) > > > Option.Reminders: > > Following are the Directory and URLs you set or allowed to be set: > CGIDIR = /home/httpd/cgi-bin > CGITMPDIR = /tmp/genex > CGITMPURL = http://cosmos.toyama.dummy.ne.jp/genex/tmp > CGI_ROOT_URL = http://cosmos.toyama.dummy.ne.jp/cgi-bin > CONTACT_EMAIL = st...@ae... > CURA_TOOL = genex/curation-tool > CYBERT_DIR = genex/cybert > CyberT_Demo_DIR = genex/CyberT-Demo > DB_NAME = genex > DOWNLOAD_DIR = genex/download > DTD2HTML = /usr/local/bin/dtd2html > DTD_DIR = genex/DTD > DTD_HTML_DIR = /usr/local/bio/genex/lib/dtd/genexml-html > DTD_HTML_URL = http://cosmos.toyama.dummy.ne.jp/genex/DTD/genexml-html > ENV_HOME = /tmp/genex > GENEXML_DIR = /usr/local/bio/genex/lib/dtd > GENEXML_URL = http://cosmos.toyama.dummy.ne.jp/genex/DTD > GENEX_CACHE_DIR = /usr/local/bio/genex/cache > GENEX_CB_CACHE_DIR = /usr/local/bio/genex/cache/db2xml/cb > GENEX_CGIDIR = /home/httpd/cgi-bin/genex > GENEX_CGI_URL = http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex > GENEX_CONNECT = $Bio::Genex::LOCAL = 1; > GENEX_CURATOR = st...@ae... > GENEX_CUR_TOOL_DIR = /home/httpd/cgi-bin/genex/curation-tool > GENEX_DBMS = Pg > GENEX_DB_USERSEC = gevAPKZ/mAr2o > GENEX_DIR = genex > GENEX_EXAMPLE_DIR = /home/httpd/cgi-bin/genex/samples > GENEX_EXP_CACHE_DIR = /usr/local/bio/genex/cache/db2xml/exp > GENEX_EXTRALIBS = use lib q[/usr/local/bio/genex/perl5]; > > GENEX_GRAPHICS_URL = http://cosmos.toyama.dummy.ne.jp/genex/graphics > GENEX_HOST = localhost > GENEX_HTM_URL = http://cosmos.toyama.dummy.ne.jp/genex > GENEX_INSTALLSITE = /usr/local/bio/genex/perl5 > GENEX_LOCAL = 1 > GENEX_MAN1 = /usr/local/bio/genex/man/man1 > GENEX_MAN3 = /usr/local/bio/genex/man/man3 > GENEX_PORT = 5432 > GENEX_QUERY_DIR = /home/httpd/cgi-bin/genex/gxquery > GENEX_RO_PASSWORD = > GENEX_RO_USER = readonly > GENEX_SECRET = Fri Oct 12 10:15:40 2001 > GENEX_SERVER_INSTALLED_BY = st...@ae... > GENEX_SUBMISSION_HOME = /usr/local/bio/genex/submission > GENEX_SU_PASSWORD = sumi786 > GENEX_SU_USER = genex > GENEX_URL_CUR_TOOL = http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex/curation- > tool > GENEX_URL_EXAMPLE = http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex/samples > GENEX_URL_QUERY = http://cosmos.toyama.dummy.ne.jp/cgi-bin/genex/gxquery > GNUCUT = /usr/bin/cut > GNUINSTALL = /usr/bin/install > GNUMKDIR = /bin/mkdir > GNUSORT = /bin/sort > GNUTAIL = /usr/bin/tail > GNUTAR = /bin/tar > GRAPHICS_DIR = genex/graphics > GS = /usr/bin/gs > GXQUERY_DIR = genex/gxquery > HTMLDIR = /home/httpd/htdocs > HTMLTMPDIR = /home/httpd/htdocs/genex/tmp > HTML_ROOT_URL = http://cosmos.toyama.dummy.ne.jp > HTTP_ERR_LOG = /var/log/httpd/logs > INCLUDE_DIR = genex/include > JAR = /usr/local/bin/jar > LOCAL_BIN = /usr/local/bio/genex/bin > LOCAL_LIB = /usr/local/bio/genex/lib > LOCAL_ROOT = /usr/local/bio/genex > LOCAL_SHARE = /usr/local/bio/genex/share > LOCAL_VAR = /usr/local/bio/genex/var > LOGIN_DIR = genex/login > MAX_SYSTMP_SIZE = 15 > MAX_TMPFILE_AGE = 24 > MERGEM_DIR = genex/mergem > MPAGE = /usr/bin/mpage > PATH = /usr/kerberos/sbin:/opt/adabas/bin:/opt/adabas/pgm:/usr/kerberos/bin:/ > bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/usr/local/lib:/u > sr/local/include:/usr/local/share:/usr/X11R6/bin:/usr/local/genome/bin:/usr/l > ocal/bio/bin:/usr/local/bio/blast:/usr/local/bio/fasta34:/usr/local/bio/wu-bl > ast2:/usr/local/bio/bin/blimpse:/usr/local/bio/wise2/bin:/usr/local/bio/charm > /net-linux/bin:/usr/local/bio/charm/net-linux/lib:/usr/local/bio/charm/net-li > nux/include:/usr/local/bio/autodock/bin:/usr/local/bio/autodock/utils:/usr/pg > i/linux86/bin:/opt/schily/bin:/usr/local/Corbatools/ORBacus/bin:/usr/local/bi > o/LigBuilder/bin:/usr/local/bio/3D_Dock/progs:/usr/local/bio/3D_Dock/scripts: > /usr/java/jdk1.3.1_01/bin:/usr/local/bio/staden/linux-bin:/usr/local/bio/mode > ller4/bin > PREFIX = /usr/local/bio/genex/perl5 > R = /usr/local/bin/R > RCLUSTER_PERL_LIB = /usr/local/bio/genex/perl5/RCluster > RCLUST_DIR = genex/rcluster > RCluster_Demo_DIR = genex/RCluster-Demo > R_VERSION = R 1.3.1 (2001-08-31). > SENDMAIL = /usr/sbin/sendmail > START_PERL = #!/usr/bin/perl > SYSTMP = /tmp/genex > TOP_LEVEL_DIR = genex/top_level > VERSION_STRING = $Id: install-all.pl,v 1.84.2.6 2001/06/05 00:08:36 hjm Exp $ > > VNCSERVER = /usr/bin/vncserver > WWWHOST = cosmos.toyama.dummy.ne.jp > XCLUSTER = > XCLUSTER_DIR = genex/xcluster > XGOBI = /usr/local/xgobi/src/xgobi > XGOBID = /usr/local/src/xgobi > XGVIS = /usr/local/xgobi/src/xgvis > XML_WRITER = /usr/local/bio/genex/bin/db2xml.pl > > > Following are the Application Paths you set or allowed to be set: > R = /usr/local/bin/R > cut = /usr/bin/cut > dtd2html = /usr/local/bin/dtd2html > gs = /usr/bin/gs > install = /usr/bin/install > jar = /usr/local/bin/jar > mkdir = /bin/mkdir > mpage = /usr/bin/mpage > sendmail = /usr/sbin/sendmail > sort = /bin/sort > tail = /usr/bin/tail > tar = /bin/tar > vncserver = /usr/bin/vncserver > xcluster = > xgobi = /usr/local/xgobi/src/xgobi > xgvis = /usr/local/xgobi/src/xgvis > > > Following are the ENVIRONMENT VARIABLES you set or allowed to be set: > ENV_HOME = /tmp/genex > PATH = /usr/kerberos/sbin:/opt/adabas/bin:/opt/adabas/pgm:/usr/kerberos/bin:/ > bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/usr/local/lib:/u > sr/local/include:/usr/local/share:/usr/X11R6/bin:/usr/local/genome/bin:/usr/l > ocal/bio/bin:/usr/local/bio/blast:/usr/local/bio/fasta34:/usr/local/bio/wu-bl > ast2:/usr/local/bio/bin/blimpse:/usr/local/bio/wise2/bin:/usr/local/bio/charm > /net-linux/bin:/usr/local/bio/charm/net-linux/lib:/usr/local/bio/charm/net-li > nux/include:/usr/local/bio/autodock/bin:/usr/local/bio/autodock/utils:/usr/pg > i/linux86/bin:/opt/schily/bin:/usr/local/Corbatools/ORBacus/bin:/usr/local/bi > o/LigBuilder/bin:/usr/local/bio/3D_Dock/progs:/usr/local/bio/3D_Dock/scripts: > /usr/java/jdk1.3.1_01/bin:/usr/local/bio/staden/linux-bin:/usr/local/bio/mode > ller4/bin > XGOBID = /usr/local/src/xgobi > > Sakuji Toyama M.D. > Institute for Virus Research > Kyoto University > E-Mail: st...@vi... > |
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From: Todd F. P. <tf...@nc...> - 2001-10-10 15:22:49
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Dear Daoud: Thank you for your interest in GeneX. I am cc'ing this message to the Sourceforge mailing list since more experts subscribe to it. Todd Peterson Software Developer NCGR On Wed, 10 Oct 2001, D.L.S. Sie wrote: > Hello, > > In our lab we are currently not working with Microarray setups, which is I > think the main aim of GeneX, we are working with Quantitative PCR setups. Are > there any users using GeneX also for these kinds of experiments? Any > advice on using the scheme with QPCR data? > > Regards, > > Daoud > > ======================================================== > Daoud Sie Vrije Universiteit > ComputerGroep Biologie De Boelelaan 1087 > Room M120 1081HV Amsterdam > Tel: (+31)-(0)20-4447040 > Fax: (+31)-(0)20-4447123 > Mob: (+31)-(0)6-27092378 > ======================================================== > > > |
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From: Todd F. P. <tf...@nc...> - 2001-10-10 00:29:47
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Karen 'SELECT' is used to relate a record to another. For example, when linking a Contact to a Sample or an Array Layout to a Hybridization. MOD/VIEW is used to edit an existing record. In the case of an Array Measurement, the record is implicitly linked to a Hybridization because you had to go through a Hybridization screen to get to the Array Measurement screen. So, bottom line is, if you created an Array Measurement in the wrong Hybridization you would have to delete the Array Measurement from it's current Hybridization and open the correct Hybridization and add the Array Measurement again. Here's the hierarchy: An Experiment Set (ES) has Hybridizations (1 or more). A Hybridization has an Array Layout (exactly 1). A Hybridization also has Array Measurements (1 or more). An Array Measurement has a Sample (exactly 1). etc. etc. The Array Layout for a Hybridization and all of the Array Measurements for the same Hybridization must be compatible. That is, the User Sequence Features (USFs) for the Array Layout must match up with the USFs of the measurement. That would be the purpose of the dummy names column I mentioned a while back. Or, in terms of the col file doc, the column identified in your raw data in the sequence feature file as usf_name maps to the column identified in your raw data in the array layout file as als_usf_name which further maps to the raw data in the spot measurement data file as spot_value_usf_name. The first 2 files (usf and array layout raw data) are the same file in our example and the same column is used for usf_name and als_usf_name. Hopefully, this is a quick synopsis of the coldef doc. Look there for more details. Also, referring to the schema helps to visualize the hierarchy. Todd On Tue, 9 Oct 2001, Karen Vranizan wrote: > Hi. I replicated the spot in the demo that did not seem to work correctly. > It's in the Table Name: Array Measurements screen. After I added a new > Array Measurement and highlighted the row containing that info, I expected > to see a Select Row button, but there is none. Only ADD ROW, MOD/VIEW ROW, > DEL ROW, USE ROW AS TEMPLATE, PARENT, CLOSE, HELP. This confuses me. kv > > > Karen Vranizan > Principal Statistician > Functional Genomics Lab > 261A Life Sciences Addition > Mail Code #3200 > UC Berkeley, CA 94720-3200 > > Phone: 510-642-7520 > Fax: 510-642-5741 > email: vra...@uc... > > |
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From: Todd F. P. <tf...@nc...> - 2001-10-09 18:25:32
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Dear Karen The tutorial is slightly incorrect about this message at the moment. The tutorial states: "An Array Measurement Spots Error panel will appear three times, informing you that there is a problem with the mur:gene, the y:gene, and the hfl:gene. This is expected in this example. Click [OK] each time.." The tool now reports all 3 missing usf's in one message and it it misleading by saying 'FATAL'. The measurement still shows up in the array measurement table viewer and more measurements may be added. Each added measurement will display this screen. Note that if you view one of the measurements, it will show 4287 sequence features. If you look at the array layout, it shows 4290 sequence features. The discrepancy of 3 features is due to these features not being a row of data in array_meas.txt. What this does show is that you have completed the most difficult part of the tool which is importing and validating the data files. Congratulations! Todd ----------Forwarded message ---------- Date: Tue, 9 Oct 2001 10:49:17 -0700 From: Karen Vranizan <vra...@uc...> To: Todd F. Peterson <tf...@nc...> Subject: error Hi. What is the following error telling me? I got it following the tutorial. Note mispelling of 'dulplicates' in your error message. kv FATAL ERROR: The below-listed sequence feature names were not found in the imported Array Layout file or are dulplicates as indicated. Every sequence feature listed in the Array Measurement import file (C:\Program Files\ct150_usrwin\data\testdata\arraymeas.txt) must exist in the Array Layout import file, and each sequence feature name must resolve to a unique valid triad = usfname:usftype:usfspecies. It would not be useful to continue. Please exit the program after noting the missing names and reading any other remaining message panels... file row=(320); incorrect usf name=(mur:gene_name:Escherichia coli); problem=(not in als) file row=(1456); incorrect usf name=(y:gene_name:Escherichia coli); problem=(not in als) file row=(3496); incorrect usf name=(hfl:gene_name:Escherichia coli); problem=(not in als) Karen Vranizan Principal Statistician Functional Genomics Lab 261A Life Sciences Addition Mail Code #3200 UC Berkeley, CA 94720-3200 Phone: 510-642-7520 Fax: 510-642-5741 email: vra...@uc... |
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From: Harry M. <man...@ho...> - 2001-10-09 15:42:49
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"Todd F. Peterson" wrote: > > Dear Dr. Chen: > > I have forwarded this to our internal developer mailing list and the > sourceforge list. More experts on these problems you are experiencing > subscribe to these lists. Meanwhile, I will study the problem. > > Sincerely, > Todd Peterson > Software Developer > NCGR > > On Mon, 8 Oct 2001, hao chen wrote: > > > Hello, > > > > I am in the process of installing GeneX server and have a few questions. > > > > My platform is Redhat 7.1. I have done the perl, postgres, etc and > > running the install-all.pl using --DEBUG switch. > > > > Here are the problems: > > > > 1. I have xcluster installed in /opt/xcluster. I tell put in the path > > but was still told it could not find it: > > ### > > ### I still cannot find it, but I will take your word that you will > > ### install it where you said you would. I will spit out a block of code at > > ### the end which will remind you where you said you would put it. > > ### This is asking for the path to the application, not the path to the directory - if you put xcluster (named xcluster) in the directory '/opt/xcluster', it would fail as you described. If the application itself was /opt/xcluster, it should work. Admittedly, this could be re-written to recursively glob all files in the directory (I've modified the script to do so now), but since it's pretty straightforward, I neglected to do so at the time. I've got a bunch of changes to submit to the CVS, so I'll try to get them checked in today. > > > > 2. I also got this message: > > > > Could not find an installed [jar]. If you have one installed, but not > > visible on your PATH, please tell me where it is. Otherwise cancel (^C) > > this > > installation, get > > http://java.sun.com/j2se/1.3/docs/api/java/util/jar/package-summary.html > > compile & install it, then try this installation again. > > > > I have no experience with Java but I looked at the webpage and didn't > > find a place I could download a file and compile it. I do have java on > > my system and jre is in my path. I tried to put /usr/java/jdk1.3.1/bin > > in the path and got the same problem. 'jar' is the java equivalent of 'compress' and should be available in a standard java install. It's often installed in /usr/bin or certainly as part of the Java jdk. It may *NOT* be installed as a default part of the jre, tho. Again, the installer would fail if you gave it the directory and not the path to the app (/usr/java/jdk1.3.1/bin/jar) - same problem as above. > > > > > > 3. It compained about xgobi and xgvis not in the path. I give it the > > path where the binaries (xgobi and xgvis) are but it still says it > > cannot find it. This sounds like the same problem as above. > > > > > > Any help is very much appreciated!! > > > > Hao Chen > > > > :: : > > :: Hao Chen, Ph.D. > > :: Postdoc > > :: Department of Pharmacology > > :: University of Tennessee Health Science Center > > :: 115 Crowe Research Building > > :: 874 Union Ave. > > :: Memphis, TN, 38163 > > :: Phone: 901 448 6017 > > :: Fax: 901 448 7300 > > :: Email: hc...@ut... > > :: : > > > > > > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... [plain text appreciated] |
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From: Todd F. P. <tf...@nc...> - 2001-10-09 03:58:40
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Dear Dr. Chen: I have forwarded this to our internal developer mailing list and the sourceforge list. More experts on these problems you are experiencing subscribe to these lists. Meanwhile, I will study the problem. Sincerely, Todd Peterson Software Developer NCGR On Mon, 8 Oct 2001, hao chen wrote: > Hello, > > I am in the process of installing GeneX server and have a few questions. > > My platform is Redhat 7.1. I have done the perl, postgres, etc and > running the install-all.pl using --DEBUG switch. > > Here are the problems: > > 1. I have xcluster installed in /opt/xcluster. I tell put in the path > but was still told it could not find it: > ### > ### I still cannot find it, but I will take your word that you will > ### install it where you said you would. I will spit out a block of code at > ### the end which will remind you where you said you would put it. > ### > > 2. I also got this message: > > Could not find an installed [jar]. If you have one installed, but not > visible on your PATH, please tell me where it is. Otherwise cancel (^C) > this > installation, get > http://java.sun.com/j2se/1.3/docs/api/java/util/jar/package-summary.html > compile & install it, then try this installation again. > > I have no experience with Java but I looked at the webpage and didn't > find a place I could download a file and compile it. I do have java on > my system and jre is in my path. I tried to put /usr/java/jdk1.3.1/bin > in the path and got the same problem. > > > 3. It compained about xgobi and xgvis not in the path. I give it the > path where the binaries (xgobi and xgvis) are but it still says it > cannot find it. > > > Any help is very much appreciated!! > > Hao Chen > > :: : > :: Hao Chen, Ph.D. > :: Postdoc > :: Department of Pharmacology > :: University of Tennessee Health Science Center > :: 115 Crowe Research Building > :: 874 Union Ave. > :: Memphis, TN, 38163 > :: Phone: 901 448 6017 > :: Fax: 901 448 7300 > :: Email: hc...@ut... > :: : > > > |
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From: Todd F. P. <tf...@nc...> - 2001-10-04 21:13:13
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Ron Did Jason help you out with this? Todd On Tue, 25 Sep 2001, Ron Ophir wrote: > Hi Jas and Todd, > I reinstalled the database the messages when install GeneX.pm runs fast, However I' ve catch part of it > > Can't use an undefined value as an ARRAY reference at t/TestDB.pm line 114. > BEGIN failed--compilation aborted at t/TestDB.pm line 162. > Compilation failed in require at t/XMLUtils.t line 16. > BEGIN failed--compilation aborted at t/XMLUtils.t line 16. > t/XMLUtils..........dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-31 > Failed 31/31 tests, 0.00% okay > Failed Test Status Wstat Total Fail Failed List of Failed > -------------------------------------------------------------------------------- > t/Chromosome.t 2 512 5 5 100.00% 1-5 > t/Citation.t 2 512 5 5 100.00% 1-5 > t/Contact.t 2 512 5 5 100.00% 1-5 > t/DBUtils.t 2 512 21 21 100.00% 1-21 > t/Genex.t 2 512 14 14 100.00% 1-14 > t/GroupLink.t 2 512 4 4 100.00% 1-4 > t/GroupSec.t 2 512 5 5 100.00% 1-5 > t/HTMLUtils.t 2 512 4 4 100.00% 1-4 > t/Protocol.t 2 512 2 2 100.00% 1-2 > t/Sample.t 2 512 5 5 100.00% 1-5 > t/Scanner.t 2 512 2 2 100.00% 1-2 > t/Software.t 2 512 5 5 100.00% 1-5 > t/Species.t 2 512 9 9 100.00% 1-9 > t/Spotter.t 2 512 2 2 100.00% 1-2 > t/UserSec.t 2 512 5 5 100.00% 1-5 > t/XMLUtils.t 2 512 31 31 100.00% 1-31 > Failed 16/36 test scripts, 55.56% okay. 124/196 subtests failed, 36.73% okay. > make: *** [test_dynamic] Error 2 > > maybe that is why I can't download expset? > Ron > |
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From: Harry M. <man...@ho...> - 2001-10-04 15:17:44
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Hi when I typed 'cy3/cy5' I meant that the data was supposed to be a floating point ratio that resulted when you divided the cy3 value by the cy5 value (or vice versa) so if cy3=4885 and cy5=89773, the number would be the result fo teh operation '4885/89773' or 0.054415024562 <- this is the number that CyberT digests. Look at the sample data set for CyberT which is linked in at the top of each form. yes, the replication would be 3 in the example you gave. CyberT is a t test, with a bonferroni correction for repetitions and a Bayesian-like smoothing function for better estimation of variation. Std deviation is explained here: http://davidmlane.com/hyperstat/A16252.html hjm Yue Wang wrote: > > Dear Harry: > > Thank you very much for your help. But I still have > some questions about the data format. You said i can > input my data as: > > gene1 cy3/cy5 cy3/cy5 cy3/cy5 > gene1 cy3/cy5 cy3/cy5 cy3/cy5 > gene1 cy3/cy5 cy3/cy5 cy3/cy5 > gene2 cy3/cy5 cy3/cy5 cy3/cy5 > gene2 cy3/cy5 cy3/cy5 cy3/cy5 > gene2 cy3/cy5 cy3/cy5 cy3/cy5 > > Then give the replicate 3. Can I input my data as: > > gene1 cy3/cy5 cy3/cy5 cy3/cy5 > gene2 cy3/cy5 cy3/cy5 cy3/cy5 > gene3 cy3/cy5 cy3/cy5 cy3/cy5 > gene1 cy3/cy5 cy3/cy5 cy3/cy5 > gene2 cy3/cy5 cy3/cy5 cy3/cy5 > gene3 cy3/cy5 cy3/cy5 cy3/cy5 > > The replication is 3. > > The other question is the method that you are used to > analyze the data. Is it a t_test? If it is T_test, how > can you calculate the std(you only have 2 or 3 > replications). > > Thanks. > > Yue > > > -- > > Cheers, Harry > > > > Harry J Mangalam -- (949) 856 2847 (v&f) -- > > man...@ho... > > [plain text appreciated] > > __________________________________________________ > Do You Yahoo!? > NEW from Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. > http://geocities.yahoo.com/ps/info1 -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... [plain text appreciated] |
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From: Todd F. P. <tf...@nc...> - 2001-10-03 01:02:28
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Dear Karen: I took a look at your data and need to have some kind of file which maps the slides' indexs and/or grid_* and/or spot_* row values to some kind of feature such as a gene name, orf name. Also, if Cy3 and Cy5 and different samples are mixed in the same column of data, the data will need to be preprocessed to separate them into separate columns. The preprocessing shouldn't be too difficult. Todd > >=20 > > -----Original Message----- > > From: Karen Vranizan > > [mailto:vra...@uc...] > > Sent: Monday, September 24, 2001 11:26 AM > > To: ge...@nc... > > Subject: a few questions > >=20 > >=20 > > Hi.=A0 I am interested in exploring whether GeneX is a > > good choice for our lab to store data from spotted > > microarray experiments.=A0=20 > > =A0 > > First, is there a way to use your server version of > > GeneX with a sample of our data in order for us to > > demo the software?=A0 I am reading that there is a > > public version of GeneX running, but I want to be sure > > that it is comparable to what it would be like to use > > GeneX locally, our ultimate goal.=A0=A0=A0 > > =A0 > > Second, we do some complicated experimental designs.=A0 > > For example suppose we have three tissues.=A0 Rather > > than hybridize the three tissues with Cy5 on three > > arrays using a=A0common reference sample with Cy3 on > > each, we would do the following.=A0 We would hybridize > > tissue A in Cy5 and tissue B in Cy3 on one chip.=A0 We > > would hybridize tissue B in Cy5 and tissue C in Cy3 on > > a second chip.=A0 And we would hybridize tissue C in Cy5 > > and tissue A in Cy3 on the third chip.=A0 We also do dye > > swapping.=A0 That is, we reverse the Cy5 and Cy3 for a > > total of six arrays in this example.=A0 So I'm guessing > > from your schema that GeneX would expect these six > > arrays samples to be treated as six different > > treatment groups.=A0 Can you give me more specific > > information about how the experiment I've just > > mentioned would be stored?=A0 I want to be sure that the > > data can be easily brought back out of GeneX with a > > clear idea of which channel and which tissue and which > > array was used for each sample in the experiment given > > that it's not a simple common reference design.=A0=20 > >=20 > >=20 >=20 >=20 >=20 |
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From: Harry M. <man...@ho...> - 2001-10-02 23:10:06
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Ratio data is ... ratio data. data that consists of ratios between the cy3 and cy5 values. If you have the data you describe below, you'll have to create ratios out of it which is trivial in a
spreadsheet or via a perloid.
you need a format that looks like:
gene1 cy3/cy5 cy3/cy5 cy3/cy5
gene1 cy3/cy5 cy3/cy5 cy3/cy5
gene1 cy3/cy5 cy3/cy5 cy3/cy5
gene2 cy3/cy5 cy3/cy5 cy3/cy5
gene2 cy3/cy5 cy3/cy5 cy3/cy5
gene2 cy3/cy5 cy3/cy5 cy3/cy5
where 'cy3/cy5' is a floating point ratio which is the result of dividing the cy3 value by the cy5 value. In the above case, there would be 3 replicates.
hjm
Yue Wang wrote:
>
> Dear Harry:
>
> I have installed the Genex in my workstation. I try to
> learn how to use them. For cyberT part I can't
> understand what mean ratio data, label columns and
> Minimum non-zero Replicates Required. I read the
> documentation I still don't know how to fill them.
> Suppose I have a mircoarray data set as following:
>
> gene1 cy3 cy5 cy3 cy5 cy3 cy5
> gene1 cy3 cy5 cy3 cy5 cy3 cy5
> gene1 cy3 cy5 cy3 cy5 cy3 cy5
> gene2 cy3 cy5 cy3 cy5 cy3 cy5
> gene2 cy3 cy5 cy3 cy5 cy3 cy5
> gene2 cy3 cy5 cy3 cy5 cy3 cy5
>
> So how to fill the "ratio data"? Do i need calculate
> ratio cy3/ cy5 first, save them and give them label,
> then fill the blank? For the replicate is it 3? Is the
> format right for the above example?
>
> Thanks.
>
> Yue
--
Cheers, Harry
Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho...
[plain text appreciated]
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From: Harry M. <man...@ho...> - 2001-09-27 17:51:10
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Hi Greg, I'm the moderator. Could you (and other note) please send these attachements to the person involved directly? If others want it they can write to you directly as well. Her address is: st...@we... hjm "Greg D. Colello" wrote: > > I sent a reply to Suzzane that included a new (350K-sized) document with figures > I have written that explains how to use the Curation Tool import subsystem in > general and also how to create Column Definition files manually (in view of the > fact the Column Definitions create screen has some problems other than the one > Suzzanne mentions below). However, the attachment surpassed the SourceForge 40K > limit, and my email is being held in limbo for moderator approval. > > I don't know who the moderator is or whether that person knows how to release my > email for distribution. If you are in a hurry for this information, send me a > personal email, and I will send you the document directly. > > Greg Colello > NCGR Developer > > >From: <st...@we...> > >To: <gen...@li...> > >Importance: Normal > >X-MSMail-Priority: Normal > >X-Priority: 3 > >MIME-Version: 1.0 > >Content-Transfer-Encoding: 8bit > >Subject: [GeneX-dev] creating column definition files > >X-Original-Date: Thu, 27 Sep 2001 16:34:47 +1000 (EST) > >Date: Thu, 27 Sep 2001 16:34:47 +1000 (EST) > > > >Hi. > > > >We've been familiarising ourselves with GeneX's Curation Tool & have been > >having a fair bit of trouble creating a column definition file. The main > >problem being that when we press "Save ...", an OPEN FILE menu pops up - so > >in effect we are not seeing an option to save our newly created file. > > > >Any feedback you have on this would be greatly appreciated :-) > > > >Suzanne > > > > > >_______________________________________________ > >Genex-dev mailing list > >Gen...@li... > >https://lists.sourceforge.net/lists/listinfo/genex-dev > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- man...@ho... [plain text appreciated] |
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From: Greg D. C. <gd...@nc...> - 2001-09-27 16:58:24
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I sent a reply to Suzzane that included a new (350K-sized) document with figures I have written that explains how to use the Curation Tool import subsystem in general and also how to create Column Definition files manually (in view of the fact the Column Definitions create screen has some problems other than the one Suzzanne mentions below). However, the attachment surpassed the SourceForge 40K limit, and my email is being held in limbo for moderator approval. I don't know who the moderator is or whether that person knows how to release my email for distribution. If you are in a hurry for this information, send me a personal email, and I will send you the document directly. Greg Colello NCGR Developer >From: <st...@we...> >To: <gen...@li...> >Importance: Normal >X-MSMail-Priority: Normal >X-Priority: 3 >MIME-Version: 1.0 >Content-Transfer-Encoding: 8bit >Subject: [GeneX-dev] creating column definition files >X-Original-Date: Thu, 27 Sep 2001 16:34:47 +1000 (EST) >Date: Thu, 27 Sep 2001 16:34:47 +1000 (EST) > >Hi. > >We've been familiarising ourselves with GeneX's Curation Tool & have been >having a fair bit of trouble creating a column definition file. The main >problem being that when we press "Save ...", an OPEN FILE menu pops up - so >in effect we are not seeing an option to save our newly created file. > >Any feedback you have on this would be greatly appreciated :-) > >Suzanne > > >_______________________________________________ >Genex-dev mailing list >Gen...@li... >https://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: Todd F. P. <tf...@nc...> - 2001-09-27 16:39:28
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Dear Suzanne: Yes, the "OPEN FILE" menu is confusing. This is just a standard window used for navigating to a directory and specifying a file. The file could already exist or be a new file which is indicated by typing a non-existent file in the File Name box. When you type a name into this box and select OPEN, the file will be created. Todd Peterson Software Developer NCGR On Thu, 27 Sep 2001 st...@we... wrote: > Hi. > > We've been familiarising ourselves with GeneX's Curation Tool & have been > having a fair bit of trouble creating a column definition file. The main > problem being that when we press "Save ...", an OPEN FILE menu pops up - so > in effect we are not seeing an option to save our newly created file. > > Any feedback you have on this would be greatly appreciated :-) > > Suzanne > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev > |
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From: <st...@we...> - 2001-09-27 06:34:59
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Hi. We've been familiarising ourselves with GeneX's Curation Tool & have been having a fair bit of trouble creating a column definition file. The main problem being that when we press "Save ...", an OPEN FILE menu pops up - so in effect we are not seeing an option to save our newly created file. Any feedback you have on this would be greatly appreciated :-) Suzanne |
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From: <ja...@op...> - 2001-09-26 20:38:21
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> On Wed, 26 Sep 2001, Daoud Sie wrote: > > > Hi, > > > > I still have one more question: > > > > - Do you forsee any problems when not using Apache as webserver. Our local > > webserver is running WN, and we like to keep it that way. Hey Daoud, The open-source developers of GeneX congregate at gen...@li..., you probably want to address future emails there. The only issue with using a different WWW server are installation instructions. Some of them won't apply. Other than that as long as your happy setting things up for your server, you should be good to go. In the future, we may be implementing certain pieces that assume Apache, such as Perl modules for authentication, or distributed queries. But right now there is nothing that requires apache. jas. |
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From: Todd F. P. <tf...@nc...> - 2001-09-26 17:02:32
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Dear Daoud: I'm not sure what the implications would be of switching webservers. Hopefully, one of the sourceforge list subscribers will respond to this question. Todd On Wed, 26 Sep 2001, Daoud Sie wrote: > Hi, > > I still have one more question: > > - Do you forsee any problems when not using Apache as webserver. Our local > webserver is running WN, and we like to keep it that way. > > Regards, > > Daoud > > ======================================================== > Daoud Sie Vrije Universiteit > ComputerGroep Biologie De Boelelaan 1087 > Room M120 1081HV Amsterdam > Tel: (+31)-(0)20-4447040 > Fax: (+31)-(0)20-4447123 > Mob: (+31)-(0)6-27092378 > ======================================================== > > > |
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From: Todd F. P. <tf...@nc...> - 2001-09-26 17:02:00
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Dear Daoud: Thank you for your interest in GeneX. I will answer your questions the best that I can. I have cc'd this message to the developer list on sourceforge which has a broader audience. Q1: Use of mysql: porting the server to use mysql should not pose too many problems. Q2: All documentation is within the server installation and on the main web page (genex.ncgr.org). Tutorials are available there as well. Many administrative material is available in the archives of the above mentioned newsgroup. Q3: Status of XML standard: see http://www.omg.org/techprocess/meetings/schedule/Gene_Expression_RFP.html As far as development news, you could subscribe to gen...@li... (http://lists.sourceforge.net/lists/listinfo/genex-dev). Sincerely, Todd Peterson Software Developer NCGR On Wed, 26 Sep 2001, Daoud Sie wrote: > Hello, > > My name is Daoud Sie, intern at the department of Molecular and > Cellular Neurobiology, VU Amsterdam. I'm currently reviewing GeneX to see > if we have any use for it here at our lab. So far I've installed genex > without major problems. Still I have some questions before I go on: > > - Do you forsee any problems when using MySQL instead of PostgresSQL? > - Is there any documentation available for adminitration and reference? > - What's the current status on an XML standard for Gene Expression data? > > Also, I'm very interested in the development of GeneX. Could you add > me to the listserv to keep me up to date with the latest developments? > > Regards, > > Daoud > > ======================================================== > Daoud Sie Vrije Universiteit > Dep. Mol & Cel Neurobiologie De Boelelaan 1087 > Room M120/A313 1081HV Amsterdam > Tel: (+31)-(0)20-4447116 > Fax: (+31)-(0)20-4447123 > Mob: (+31)-(0)6-27092378 > ======================================================== > > > |
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