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From: Yohan L. v. F. <nobody@e.feedspot.com> - 2015-10-05 05:31:05
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<a style="color:black!important;text-decoration:none" href="http://www.feedspot.com/r_be23734764ab_*_ce...@li...#monthlycode" target="_blank"><div style="white-space:nowrap;font-size:26px;font-weight:700">Feedspot</div></a>
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<td style="font-family:Helvetica,Arial,sans-serif;color:#333333"><b>Yohan Lee</b> would like to connect on Feedspot. How would you like to respond?</td>
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<a href="http://www.feedspot.com/r_be23734764ab_*_ce...@li...#monthlycode" style="text-decoration:none" target="_blank">
<img alt="Yohan Lee" src="http://s3.amazonaws.com/feedspot/1a777443318832d5be76e997f60febba.jpg" width="150" height="150" border="0" style="border:none;text-decoration:none;outline:hidden;display:block" class="CToWUd">
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<td valign="top"><a href="http://www.feedspot.com/r_be23734764ab_*_ce...@li...#monthlycode" style="font-size:20px;font-weight:bold;color:#000000;text-decoration:none" target="_blank">Yohan Lee</a></td>
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<a href="http://www.feedspot.com/r_be23734764ab_*_ce...@li...#monthlycode" style="text-decoration:none;font-size:13px;font-family:Helvetica,Arial,sans-serif;font-weight:bold;color:white;white-space:nowrap;display:block" target="_blank"><span style="font-size:13px;font-family:Helvetica,Arial,sans-serif;font-weight:bold;color:white;white-space:nowrap;display:block">Confirm you know Yohan</span></a>
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<a href="http://www.feedspot.com/r_be23734764ab_*_ce...@li...#monthlycode" style="text-decoration:none;font-size:13px;font-family:Helvetica,Arial,sans-serif;font-weight:bold;color:white;white-space:nowrap;display:block" target="_blank"><span style="font-size:13px;font-family:Helvetica,Arial,sans-serif;font-weight:bold;color:#333333;text-decoration:none;white-space:nowrap;display:block">Go to Feedspot</span></a>
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<td>This email was sent to cel...@li.... You are receiving pending invitation emails. <br/>
You received this email because your friend Yohan Lee (yoh...@gm...) invited you to join
Feedspot. <br/>
Click <a style="color:gray;text-decoration:underline;cursor:pointer" href="http://www.feedspot.com/fs/unsubscribe?i=FEv4vW5MGCJYGiZY0flLDxRO1OyXXCcpEyQgWhb4S/8eVPvlXFcYKg==">here to Unsubscribe</a> if you wish not to receive pending invitation from Yohan Lee via Feedspot.<br/>
Feedspot.com, 303 Cape Court, Mill Valley, CA 94941 </td>
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From: l. at M. <04....@me...> - 2008-12-29 20:36:54
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lou is a member of MySpace and is inviting you to join. Join MySpace and you will instantly be connected to lou, and to each of lou's friends. Click Here to Join: http://www.myspace.com/reloc.cfm?c=2&id=fa443fad-9fec-41c8-94a5-25358a4d2ad7 What is MySpace? ====================== MySpace is an online community that lets you meet your friends' friends. * Create a Custom Profile * Upload & Share Photos * Send Mail and IM's * Write Blogs & Comments * Discover new Music, Filmmakers, and Comedians * Watch and share Funny Videos * It's FREE! Who Uses MySpace? ======================= MySpace is for everyone: * Friends who want to talk Online * Bands that want to share their music * Filmmakers that want to reach their fans * Families who want to keep in touch * Professionals interested in networking * Classmates and study partners * Anyone looking for long lost friends! What Do I Do? ====================== 1. Click the Link In This E-mail 2. Create Your Profile 3. Start Communicating with Your Friend and Your Friend's Friends 4. Invite Your Friends to Join! Click Here to Learn More: http://www.myspace.com/reloc.cfm?c=2&id=fa443fad-9fec-41c8-94a5-25358a4d2ad7 ------------------------- This email was sent by someone who knows you on MySpace.com. If you want to block any emails from MySpace members in the future, you can click here: http://www.myspace.com/index.cfm?fuseaction=block&iid=fa443fad-9fec-41c8-94a5-25358a4d2ad7 Or send a single blank email with the subject line "BLOCK" to: pr...@my... You can also block future email or direct any other inquiries by regular postal mail to: MySpace, Inc. 8391 Beverly Blvd. #349 Los Angeles, CA 90048 USA ©2003-2008 MySpace.com. All Rights Reserved. |
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From: Allen D. <all...@gm...> - 2008-05-15 08:27:14
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Hey, Thanks for taking point on this. You'll want to make sure you TRUNCATE on both plier and plier_byq, there is a trigger that sends data from one table to the other to keep them synced. I don't really have a good undertanding of pgdump, generally. Maybe you should do a VACUUM FULL on the database first though after making such a large change by dropping those tables. -Allen On Wed, May 14, 2008 at 7:07 PM, Bret Harry <ja...@ga...> wrote: > The celsius postgres database is ~2T. I have been wrestling with this behemoth over the last month or so, trying to get a complete database dump as a prerequisite for doing backups. My goal is to make a clean standalone installation that is documented and can be replicated at other sites. Here is a brief narrative of what has happened so far: > > Following the postgres user manual, I initially did a pg_dumpall which wrote ~500 GB data in ~20 hours before throwing the following error: > > bash-3.00$ pg_dumpall -U postgres --oids | split --suffix-length=3 --bytes=1073741824 - `date "+axis.pg_dumpall.%Y.%m.%d.%H.%M."` > > pg_dump: ERROR: invalid page header in block 2325630 of relation "plier" > pg_dump: SQL command to dump the contents of table "plier" failed: PQendcopy() failed. > pg_dump: Error message from server: ERROR: invalid page header in block 2325630 of relation "plier" > pg_dump: The command was: COPY part_elementresult.plier (elementresult_id, element_id, quantification_id, signal) TO stdout; > pg_dumpall: pg_dump failed on database "chado-celsius", exiting > > After researching the error a bit, speaking with Allen, and trying a unsuccessful VACUUM (same error as above). I tried to truncate part_elementresult.plier, which caused the following error: > > chado-celsius=> truncate part_elementresult.plier; > WARNING: could not remove relation 1663/16387/1945642: Read-only file system > TRUNCATE TABLE > chado-celsius=> select * from part_elementresult.plier; > ERROR: could not open relation 1663/16387/4822791: Read-only file system > > May 9 15:11:41 axis kernel: EXT3-fs error (device md0): ext3_free_blocks_sb: bit already cleared for block 973843591 > May 9 15:11:41 axis kernel: Aborting journal on device md0. > May 9 15:11:41 axis kernel: ext3_abort called. > May 9 15:11:41 axis kernel: EXT3-fs error (device md0): ext3_journal_start_sb: Detected aborted journal > May 9 15:11:41 axis kernel: Remounting filesystem read-only > May 9 15:11:41 axis kernel: EXT3-fs error (device md0) in ext3_free_blocks_sb: Journal has aborted > May 9 15:11:41 axis kernel: EXT3-fs error (device md0) in ext3_reserve_inode_write: Journal has aborted > May 9 15:11:41 axis kernel: __journal_remove_journal_head: freeing b_committed_data > > Scary stuff. I did a shutdown -r on axis, and mercifully, postgres appeared to come back online. The part_elementresult.plier table was empty. I restarted the dump as before, however this time around the dump is extremely slow, I estimate it will take ~40 days to complete... > > I wanted to see if anyone has any ideas on how I might be able to speed up the dump. > > Regards, > > -bret > > > On Wed, May 14, 2008 at 07:55:54PM -0600, Bret Harry wrote: > > I am moving this over to celsius-devel. > > -bret > > > > On Fri, May 09, 2008 at 06:27:17PM -0700, Allen Day wrote: > > > you should send this to the celsius-users list as well. > > > > > > On Fri, May 9, 2008 at 4:27 PM, Bret Harry <ja...@ga...> wrote: > > > > Hello Folks, > > > > > > > > While trying to backup celsius' postgres database, there was a filesystem error on axis.genome.ucla.edu which caused the main data volume to become read-only. Unfortunately, this machine will have to be taken offline in order to run a filesystem check. I will update the list when it finishes. > > > > > > > > -bret > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > > > > Don't miss this year's exciting 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 > > > > _______________________________________________ > > > > Nelsonlab-main mailing list > > > > Nel...@li... > > > > https://lists.sourceforge.net/lists/listinfo/nelsonlab-main > > > > > > > > > > > > > > > > -- > > > allenday.skype > > > +1 (415) 335-4654 (office) > > > +1 (310) 804-5304 (mobile) > > > +1 (515) 474-9337 (fax) > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > Celsius-devel mailing list > > Cel...@li... > > https://lists.sourceforge.net/lists/listinfo/celsius-devel > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Celsius-devel mailing list > Cel...@li... > https://lists.sourceforge.net/lists/listinfo/celsius-devel > -- allenday.skype +1 (415) 335-4654 (office) +1 (310) 804-5304 (mobile) +1 (515) 474-9337 (fax) |
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From: Bret H. <ja...@ga...> - 2008-05-15 02:10:59
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The celsius postgres database is ~2T. I have been wrestling with this behemoth over the last month or so, trying to get a complete database dump as a prerequisite for doing backups. My goal is to make a clean standalone installation that is documented and can be replicated at other sites. Here is a brief narrative of what has happened so far: Following the postgres user manual, I initially did a pg_dumpall which wrote ~500 GB data in ~20 hours before throwing the following error: bash-3.00$ pg_dumpall -U postgres --oids | split --suffix-length=3 --bytes=1073741824 - `date "+axis.pg_dumpall.%Y.%m.%d.%H.%M."` pg_dump: ERROR: invalid page header in block 2325630 of relation "plier" pg_dump: SQL command to dump the contents of table "plier" failed: PQendcopy() failed. pg_dump: Error message from server: ERROR: invalid page header in block 2325630 of relation "plier" pg_dump: The command was: COPY part_elementresult.plier (elementresult_id, element_id, quantification_id, signal) TO stdout; pg_dumpall: pg_dump failed on database "chado-celsius", exiting After researching the error a bit, speaking with Allen, and trying a unsuccessful VACUUM (same error as above). I tried to truncate part_elementresult.plier, which caused the following error: chado-celsius=> truncate part_elementresult.plier; WARNING: could not remove relation 1663/16387/1945642: Read-only file system TRUNCATE TABLE chado-celsius=> select * from part_elementresult.plier; ERROR: could not open relation 1663/16387/4822791: Read-only file system May 9 15:11:41 axis kernel: EXT3-fs error (device md0): ext3_free_blocks_sb: bit already cleared for block 973843591 May 9 15:11:41 axis kernel: Aborting journal on device md0. May 9 15:11:41 axis kernel: ext3_abort called. May 9 15:11:41 axis kernel: EXT3-fs error (device md0): ext3_journal_start_sb: Detected aborted journal May 9 15:11:41 axis kernel: Remounting filesystem read-only May 9 15:11:41 axis kernel: EXT3-fs error (device md0) in ext3_free_blocks_sb: Journal has aborted May 9 15:11:41 axis kernel: EXT3-fs error (device md0) in ext3_reserve_inode_write: Journal has aborted May 9 15:11:41 axis kernel: __journal_remove_journal_head: freeing b_committed_data Scary stuff. I did a shutdown -r on axis, and mercifully, postgres appeared to come back online. The part_elementresult.plier table was empty. I restarted the dump as before, however this time around the dump is extremely slow, I estimate it will take ~40 days to complete... I wanted to see if anyone has any ideas on how I might be able to speed up the dump. Regards, -bret On Wed, May 14, 2008 at 07:55:54PM -0600, Bret Harry wrote: > I am moving this over to celsius-devel. > -bret > > On Fri, May 09, 2008 at 06:27:17PM -0700, Allen Day wrote: > > you should send this to the celsius-users list as well. > > > > On Fri, May 9, 2008 at 4:27 PM, Bret Harry <ja...@ga...> wrote: > > > Hello Folks, > > > > > > While trying to backup celsius' postgres database, there was a filesystem error on axis.genome.ucla.edu which caused the main data volume to become read-only. Unfortunately, this machine will have to be taken offline in order to run a filesystem check. I will update the list when it finishes. > > > > > > -bret > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > > > Don't miss this year's exciting 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 > > > _______________________________________________ > > > Nelsonlab-main mailing list > > > Nel...@li... > > > https://lists.sourceforge.net/lists/listinfo/nelsonlab-main > > > > > > > > > > > -- > > allenday.skype > > +1 (415) 335-4654 (office) > > +1 (310) 804-5304 (mobile) > > +1 (515) 474-9337 (fax) > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Celsius-devel mailing list > Cel...@li... > https://lists.sourceforge.net/lists/listinfo/celsius-devel |
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From: Bret H. <ja...@ga...> - 2008-05-15 01:59:28
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I am moving this over to celsius-devel. -bret On Fri, May 09, 2008 at 06:27:17PM -0700, Allen Day wrote: > you should send this to the celsius-users list as well. > > On Fri, May 9, 2008 at 4:27 PM, Bret Harry <ja...@ga...> wrote: > > Hello Folks, > > > > While trying to backup celsius' postgres database, there was a filesystem error on axis.genome.ucla.edu which caused the main data volume to become read-only. Unfortunately, this machine will have to be taken offline in order to run a filesystem check. I will update the list when it finishes. > > > > -bret > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > > Don't miss this year's exciting 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 > > _______________________________________________ > > Nelsonlab-main mailing list > > Nel...@li... > > https://lists.sourceforge.net/lists/listinfo/nelsonlab-main > > > > > > -- > allenday.skype > +1 (415) 335-4654 (office) > +1 (310) 804-5304 (mobile) > +1 (515) 474-9337 (fax) |
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From: Bret H. <ja...@ga...> - 2008-05-15 01:27:56
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Allen, I am moving this thread over to the celsius-devel list. -bret > looks like no new data loaded for the last 2.5 months: > http://genome.ucla.edu/cacti/graph.php?action=view&local_graph_id=45&rra_id=all > > -allen > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Nelsonlab-devel mailing list > Nel...@li... > https://lists.sourceforge.net/lists/listinfo/nelsonlab-devel |
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From: Bret H. <ja...@ga...> - 2008-05-15 01:24:51
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Hello Folks, My name is Bret Harry, I have been tasked with supporting the UCLA Celsius site. Please let me know what needs to be fixed (a lot at the moment). Regards, -bret |
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From: Barton, G. R <g.b...@im...> - 2008-04-01 10:39:49
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Hi Stan, We have not heard back from the celsius team. We are deploying our microarray app to various users at the moment, we have a presentation next Monday and then we have a work shop to give the following week and we would like to have demonstrate that users can import and analyse data from celsius. We are also writing up our project for the main biological funding body in the UK, the BBSRC and would like to mention our links with celsius as it great example of data sharing. However we are having a problem with the download step. Once a user chooses which CEL file they would like to import into our app from celsius, we call this address for example. http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1008265 At the moment this redirects to here http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1008265 And that is as far as we get, nothing else happens. Look forward to hearing from you All the best geraint -----Original Message----- From: Barton, Geraint R Sent: 28 March 2008 17:02 To: 'sn...@uc...' Cc: Chiba, Norie K Subject: FW: [Celsius-users] FW: Hi Stan, Sorry to bother you with this again, its just we have not hear back from allen or the guys maintaining the celsius mailing list. Please find the mail forwarded the mail my colleague norie describing the problem. All the best geraint -----Original Message----- From: cel...@li... [mailto:cel...@li...] On Behalf Of Chiba, Norie K Sent: 03 March 2008 15:28 To: all...@uc... Cc: cel...@li...; cel...@li...; Barton, Geraint R Subject: Re: [Celsius-users] FW: Dear Allen, When I request a cel file using JSP, I have the following error 03 Mar 2008 15:07:29 () DEBUG (Download_005fCel_jsp.java:85) - conn.toString() sun.net.www.protocol.http.HttpURLConnection:http://celsius.genomics.ctrl .ucla.edu/service/cel/cel?id=SN:1067991 03 Mar 2008 15:10:55 () ERROR (Download_005fCel_jsp.java:104) - Server returned HTTP response code: 502 for URL: http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1067991 Also when I access to your site http://celsius.genomics.ctrl.ucla.edu/ I have the same Proxy Error. Do I need to change a way to access these cel files or The site is not available now? Thanks Norie -----Original Message----- From: all...@gm... [mailto:all...@gm...] On Behalf Of Allen Day Sent: Friday, February 08, 2008 5:33 PM To: Barton, Geraint R Cc: louis fridkis; Chiba, Norie K; cel...@li...; cel...@li... Subject: Re: FW: Hi Geraint, I have no idea what's going on here, but I'll look at this later today. Celsius shouldn't be redirecting to my home directory like that. We can drop Louis Fridkis off the CC from now on, he has left our group. Also, there is a mailing list set up though for Celsius users, you may want to subscribe there, it is very low volume. -Allen On Feb 8, 2008 7:26 AM, Barton, Geraint R <g.b...@im...> wrote: > > > Hi > > we are just about to go live with our microarray portal and there seems to > be a problem connecting to celsius at the moment, which is a shame because > we have spent some time on our interace to celsius and we were able to > filter the various ontologies and array types to download the required cel > files. > > We are getting a 403 forbidden error. Have you blocked us at imperial > college from using Celsius? > > this is the error caught in the jsp > 08 Feb 2008 14:55:46 () DEBUG (Download_005fCel_jsp.java:85) - > conn.toString() > sun.net.www.protocol.http.HttpURLConnection:http://celsius.genomics.ctrl .ucla.edu/service/cel/cel?id=SN:1004324 > > > 08 Feb 2008 14:55:46 () ERROR (Download_005fCel_jsp.java:104) - Server > returned HTTP response code: 403 for URL: > http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1004324 > > > > > > and when we enter the url directly into a browser it looks like it is being > redirected from: > > http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1004324 > > to > > http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1000008 > > > > can you please also reply to norie chiba cc'd in this emal > > > > thanks > > > > geraint -- allenday.skype +1 (415) 335-4654 (o) +1 (310) 804-5304 (m) ------------------------------------------------------------------------ - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketp lace _______________________________________________ Celsius-users mailing list Cel...@li... https://lists.sourceforge.net/lists/listinfo/celsius-users |
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From: Chiba, N. K <nor...@cs...> - 2008-03-14 14:32:10
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Dear Allen, We still cannot download a cel file. Please let me know whether I have to change a method to get it or Your site has some problems Thanks norie -----Original Message----- From: Chiba, Norie K Sent: Tuesday, March 11, 2008 10:10 AM To: 'all...@uc...' Cc: 'cel...@li...'; 'cel...@li...'; Barton, Geraint R Subject: download cel files Dear Allen, When I request a cel file from a browser http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1000008 I have http code 404 not found and Redirected to http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1000008 Do I need to change a way to download these cel files or The site is not available now? While you are updating your repository, Can I download a data file or not? Thanks Norie |
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From: Chiba, N. K <nor...@cs...> - 2008-03-11 10:12:07
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Dear Allen, When I request a cel file from a browser http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1000008 I have http code 404 not found and Redirected to http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1000008 Do I need to change a way to download these cel files or The site is not available now? While you are updating your repository, Can I download a data file or not? Thanks Norie |
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From: Chiba, N. K <nor...@cs...> - 2008-03-03 15:30:56
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Dear Allen, When I request a cel file using JSP, I have the following error 03 Mar 2008 15:07:29 () DEBUG (Download_005fCel_jsp.java:85) - conn.toString() sun.net.www.protocol.http.HttpURLConnection:http://celsius.genomics.ctrl .ucla.edu/service/cel/cel?id=SN:1067991 03 Mar 2008 15:10:55 () ERROR (Download_005fCel_jsp.java:104) - Server returned HTTP response code: 502 for URL: http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1067991 Also when I access to your site http://celsius.genomics.ctrl.ucla.edu/ I have the same Proxy Error. Do I need to change a way to access these cel files or The site is not available now? Thanks Norie -----Original Message----- From: all...@gm... [mailto:all...@gm...] On Behalf Of Allen Day Sent: Friday, February 08, 2008 5:33 PM To: Barton, Geraint R Cc: louis fridkis; Chiba, Norie K; cel...@li...; cel...@li... Subject: Re: FW: Hi Geraint, I have no idea what's going on here, but I'll look at this later today. Celsius shouldn't be redirecting to my home directory like that. We can drop Louis Fridkis off the CC from now on, he has left our group. Also, there is a mailing list set up though for Celsius users, you may want to subscribe there, it is very low volume. -Allen On Feb 8, 2008 7:26 AM, Barton, Geraint R <g.b...@im...> wrote: > > > Hi > > we are just about to go live with our microarray portal and there seems to > be a problem connecting to celsius at the moment, which is a shame because > we have spent some time on our interace to celsius and we were able to > filter the various ontologies and array types to download the required cel > files. > > We are getting a 403 forbidden error. Have you blocked us at imperial > college from using Celsius? > > this is the error caught in the jsp > 08 Feb 2008 14:55:46 () DEBUG (Download_005fCel_jsp.java:85) - > conn.toString() > sun.net.www.protocol.http.HttpURLConnection:http://celsius.genomics.ctrl .ucla.edu/service/cel/cel?id=SN:1004324 > > > 08 Feb 2008 14:55:46 () ERROR (Download_005fCel_jsp.java:104) - Server > returned HTTP response code: 403 for URL: > http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1004324 > > > > > > and when we enter the url directly into a browser it looks like it is being > redirected from: > > http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1004324 > > to > > http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1000008 > > > > can you please also reply to norie chiba cc'd in this emal > > > > thanks > > > > geraint -- allenday.skype +1 (415) 335-4654 (o) +1 (310) 804-5304 (m) |
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From: Allen D. <all...@uc...> - 2008-02-08 17:33:31
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Hi Geraint, I have no idea what's going on here, but I'll look at this later today. Celsius shouldn't be redirecting to my home directory like that. We can drop Louis Fridkis off the CC from now on, he has left our group. Also, there is a mailing list set up though for Celsius users, you may want to subscribe there, it is very low volume. -Allen On Feb 8, 2008 7:26 AM, Barton, Geraint R <g.b...@im...> wrote: > > > Hi > > we are just about to go live with our microarray portal and there seems to > be a problem connecting to celsius at the moment, which is a shame because > we have spent some time on our interace to celsius and we were able to > filter the various ontologies and array types to download the required cel > files. > > We are getting a 403 forbidden error. Have you blocked us at imperial > college from using Celsius? > > this is the error caught in the jsp > 08 Feb 2008 14:55:46 () DEBUG (Download_005fCel_jsp.java:85) - > conn.toString() > sun.net.www.protocol.http.HttpURLConnection:http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1004324 > > > 08 Feb 2008 14:55:46 () ERROR (Download_005fCel_jsp.java:104) - Server > returned HTTP response code: 403 for URL: > http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1004324 > > > > > > and when we enter the url directly into a browser it looks like it is being > redirected from: > > http://celsius.genomics.ctrl.ucla.edu/service/cel/cel?id=SN:1004324 > > to > > http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/cel?id=SN:1000008 > > > > can you please also reply to norie chiba cc'd in this emal > > > > thanks > > > > geraint -- allenday.skype +1 (415) 335-4654 (o) +1 (310) 804-5304 (m) |
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From: Allen D. <all...@gm...> - 2007-12-19 00:25:47
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neuron is the submit host. maybe other reasons i'm not thinking of as well. On Dec 18, 2007 4:23 PM, louis fridkis <lou...@gm...> wrote: > Allen, > > In the web page: > > http://genomics.ctrl.ucla.edu/wiki/index.php/Celsius_maintenance_procedures#.22make_all.22 > > is says: > Quantify > > make quantify runs etl/script/queue to run quantification jobs on the > compute farm. This must be run on neuron. Do you know specifically why is > can't be run on another hosts? E.g. computer-0-07? > > Thank you, > > -- > Lou Fridkis > UCLA Geffen School of Medicine > Department of Human Genetics > Nelson Lab > 695 Charles E Young Drive S. > Los Angeles, CA 90095 USA > 310-825-7920 > ------------------------------------------------------------------------- > SF.Net email is sponsored by: > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services > for just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > Celsius-devel mailing list > Cel...@li... > https://lists.sourceforge.net/lists/listinfo/celsius-devel > > -- allenday.skype +1 (415) 335-4654 (o) +1 (310) 804-5304 (m) |
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From: louis f. <lou...@gm...> - 2007-12-19 00:23:06
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Allen, In the web page: http://genomics.ctrl.ucla.edu/wiki/index.php/Celsius_maintenance_procedures#.22make_all.22 is says: Quantify make quantify runs etl/script/queue to run quantification jobs on the compute farm <http://genomics.ctrl.ucla.edu/wiki/index.php/Compute_farm>. *This must be run on neuron.* Do you know specifically why is can't be run on another hosts? E.g. computer-0-07? Thank you, -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
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From: Yohan L. <yoh...@gm...> - 2007-12-15 17:05:12
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Great! That's wonderful, and thank you for y our quick help on this. Yohan On Dec 14, 2007 2:45 PM, louis fridkis <lou...@gm...> wrote: > Yohan, > > All of the brlmm analyses are done. > > Thanks, > > > On Dec 3, 2007 8:59 AM, louis fridkis <lou...@gm...> wrote: > > > Yohan, > > > > The modified celsius pipeline (doing brlmm and pqi in addition to the > > expression algorithms) has been running since 10:39 A.M. Fri 30-Nov. It > > has processed brlmm on 667 cel files. There are a total of 14378 such cel > > files, but I don't know how many have already been processed in the past. (I > > don't believe any have been processed in the last year.) We could consider > > allocating more resources to the celsius pipeline, if this rate is too slow. > > Please let me know what you think. > > > > Thanks, > > > > > > On Nov 30, 2007 11:15 AM, Yohan Lee <yoh...@gm...> wrote: > > > > > What does pqi do? > > > Is there a webpage or paper i can look at? > > > > > > Yohan > > > > > > > > > On 11/30/07, louis fridkis <lou...@gm... > wrote: > > > > > > > > Yohan, > > > > > > > > Alan says ok, so I am now running the celsius pipeline configured to > > > > apply the brlmm and pqi algorithms. > > > > > > > > Have a good weekend, > > > > > > > > On Nov 30, 2007 10:09 AM, louis fridkis < lou...@gm...> > > > > wrote: > > > > > > > > > Yohan is asking if I can turn on brlmm in celsius. Any problem > > > > > with this? I could do it now and let it run over the weekend > > > > > > > > > > > > > > > > > > > > -- > > > > Lou Fridkis > > > > UCLA Geffen School of Medicine > > > > Department of Human Genetics > > > > Nelson Lab > > > > 695 Charles E Young Drive S. > > > > Los Angeles, CA 90095 USA > > > > 310-825-7920 > > > > > > > > > > > > > > > -- > > Lou Fridkis > > UCLA Geffen School of Medicine > > Department of Human Genetics > > Nelson Lab > > 695 Charles E Young Drive S. > > Los Angeles, CA 90095 USA > > 310-825-7920 > > > > > > -- > Lou Fridkis > UCLA Geffen School of Medicine > Department of Human Genetics > Nelson Lab > 695 Charles E Young Drive S. > Los Angeles, CA 90095 USA > 310-825-7920 > |
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From: louis f. <lou...@gm...> - 2007-12-14 19:45:54
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Yohan, All of the brlmm analyses are done. Thanks, On Dec 3, 2007 8:59 AM, louis fridkis <lou...@gm...> wrote: > Yohan, > > The modified celsius pipeline (doing brlmm and pqi in addition to the > expression algorithms) has been running since 10:39 A.M. Fri 30-Nov. It > has processed brlmm on 667 cel files. There are a total of 14378 such cel > files, but I don't know how many have already been processed in the past. (I > don't believe any have been processed in the last year.) We could consider > allocating more resources to the celsius pipeline, if this rate is too slow. > Please let me know what you think. > > Thanks, > > > On Nov 30, 2007 11:15 AM, Yohan Lee <yoh...@gm...> wrote: > > > What does pqi do? > > Is there a webpage or paper i can look at? > > > > Yohan > > > > > > On 11/30/07, louis fridkis <lou...@gm... > wrote: > > > > > > Yohan, > > > > > > Alan says ok, so I am now running the celsius pipeline configured to > > > apply the brlmm and pqi algorithms. > > > > > > Have a good weekend, > > > > > > On Nov 30, 2007 10:09 AM, louis fridkis < lou...@gm...> wrote: > > > > > > > Yohan is asking if I can turn on brlmm in celsius. Any problem with > > > > this? I could do it now and let it run over the weekend > > > > > > > > > > > > > > > -- > > > Lou Fridkis > > > UCLA Geffen School of Medicine > > > Department of Human Genetics > > > Nelson Lab > > > 695 Charles E Young Drive S. > > > Los Angeles, CA 90095 USA > > > 310-825-7920 > > > > > > > > > -- > Lou Fridkis > UCLA Geffen School of Medicine > Department of Human Genetics > Nelson Lab > 695 Charles E Young Drive S. > Los Angeles, CA 90095 USA > 310-825-7920 > -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
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From: louis f. <lou...@gm...> - 2007-12-03 16:59:26
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Yohan, The modified celsius pipeline (doing brlmm and pqi in addition to the expression algorithms) has been running since 10:39 A.M. Fri 30-Nov. It has processed brlmm on 667 cel files. There are a total of 14378 such cel files, but I don't know how many have already been processed in the past. (I don't believe any have been processed in the last year.) We could consider allocating more resources to the celsius pipeline, if this rate is too slow. Please let me know what you think. Thanks, On Nov 30, 2007 11:15 AM, Yohan Lee <yoh...@gm...> wrote: > What does pqi do? > Is there a webpage or paper i can look at? > > Yohan > > > On 11/30/07, louis fridkis <lou...@gm... > wrote: > > > > Yohan, > > > > Alan says ok, so I am now running the celsius pipeline configured to > > apply the brlmm and pqi algorithms. > > > > Have a good weekend, > > > > On Nov 30, 2007 10:09 AM, louis fridkis < lou...@gm...> wrote: > > > > > Yohan is asking if I can turn on brlmm in celsius. Any problem with > > > this? I could do it now and let it run over the weekend > > > > > > > > > > -- > > Lou Fridkis > > UCLA Geffen School of Medicine > > Department of Human Genetics > > Nelson Lab > > 695 Charles E Young Drive S. > > Los Angeles, CA 90095 USA > > 310-825-7920 > > > -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
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From: Yohan L. <yoh...@gm...> - 2007-11-30 19:15:20
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What does pqi do? Is there a webpage or paper i can look at? Yohan On 11/30/07, louis fridkis <lou...@gm...> wrote: > > Yohan, > > Alan says ok, so I am now running the celsius pipeline configured to apply > the brlmm and pqi algorithms. > > Have a good weekend, > > On Nov 30, 2007 10:09 AM, louis fridkis < lou...@gm...> wrote: > > > Yohan is asking if I can turn on brlmm in celsius. Any problem with > > this? I could do it now and let it run over the weekend > > > > > -- > Lou Fridkis > UCLA Geffen School of Medicine > Department of Human Genetics > Nelson Lab > 695 Charles E Young Drive S. > Los Angeles, CA 90095 USA > 310-825-7920 |
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From: louis f. <lou...@gm...> - 2007-11-30 18:52:52
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Yohan, Alan says ok, so I am now running the celsius pipeline configured to apply the brlmm and pqi algorithms. Have a good weekend, On Nov 30, 2007 10:09 AM, louis fridkis <lou...@gm...> wrote: > Yohan is asking if I can turn on brlmm in celsius. Any problem with this? > I could do it now and let it run over the weekend -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
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From: louis f. <lou...@gm...> - 2007-11-30 18:09:11
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Yohan is asking if I can turn on brlmm in celsius. Any problem with this? I could do it now and let it run over the weekend |
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From: louis f. <lou...@gm...> - 2007-11-26 21:45:28
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The new celsius pipeline run has completed successfully. It was modified to run the web scraper (make load) and normalization (make quantify) once each, with the normalization making one full pass through the entire DB. It processed 58545 DB rows, each corresponding to 1 CEL file. So, it would seem that this is the true number of CEL files in our system, not 80 - 90k. In the course of processing those rows, the following numbers of normalizations were applied: gcrma 1068 rma 615 mas5 2111 Total 3794 The pipeline ran on neuron and submitted normalizations jobs to the cluster. Only a maximum of 4 cluster jobs ran concurrently. Dchip and Plier were intentionally excluded since they fail due to insufficient memory. They will have to be done with a similar, separate run on the new cluster. The total run time for this pipeline run was 3.5 days. So, it seems viable to set up a celsius-pipeline daemon to run this pipeline over-and-over continuously. -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
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From: louis f. <lou...@gm...> - 2007-11-06 22:44:03
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Allen, I never received an answer to the questions in the forwarded message below. I am forwarding it to the celsius-dev list per your request. ---------- Forwarded message ---------- From: louis fridkis <lou...@gm...> Date: Oct 29, 2007 11:55 AM Subject: Re: [Fwd: Re: celsius support] To: Marc Carlson <mr...@gm...>, nelsonlab-devel < nel...@li...> Marc, Allen Should I be encouraging R and discouraging XML. I.e. In your opinion, should we be going in the direction of only supporting R? P.S. Allen, for backgound/context see Marc's answer in the first message below and the original question, labelled 3), in the second message below. On 10/29/07, Marc Carlson <mr...@gm...> wrote: > > This is really another web server question but I will tell you what I > remember. I think the answer is that the xml was made first. But for the > annotations, I wanted the tab file for the R client (the xml was too huge to > parse easily). Anyhow, I think that the xml was just never updated with the > newer fields that were added to the tab format file. This should all be > moot if the client is using the R client anyhow since that should get the > fields they ask for anyways. At this point this guy is just being nosy. > > Marc > > > > On 10/29/07, louis fridkis < lou...@gm...> wrote: > > > > Marc, > > > > Thanks again for your answer. I followed up with a question to Allen and > > Brian and sent a partial answer to the client. Here is the next question: > > > > 3) The annot table retrieval seems to work fine eg: > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > > > > When I do the equivalient query returning in xml: > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A > > The tags are different to the column names from the table. And the > > tissuename/anatomyname are in the 'platform' tag and all the tags values > > seem to have shifted to the tag to its left. > > > > On 10/26/07, Marc Carlson < mr...@gm...> wrote: > > > > > > To answer the 1st question, I don't believe that we ever defined those > > > because we felt they were pretty obvious. SNID as you know is the internal > > > ID. The next set of names are each made of two parts. tissue, path, sex, > > > cell, pheno and dev refer to different ontologies to descibe tissue type, > > > pathology state, cell type, phenotype, and developmental stage. The second > > > part of each name is name, part or accession. Name is just the common name, > > > accession is the precise ID from the ontology, and the ontologies are > > > namespaced themselves, so you know where the information has come from. For > > > example MA is the mouse anatomy ontology, which is what is used for the > > > tissue type annotations... I don't remember what "part" stands for anymore, > > > but it looks like its just the type of annotation (like allenday hand) > > > though you had better check this last one over with Allen... > > > > > > Unfortunately, for your second question, this is more about the web > > > server, and that is Allens domain. The R package I wrote has man pages. > > > And I think there are web pages telling about the web service (there > > > certainly used to be). Allen or Brian would probably know where those are. > > > > > > There should be at least two kinds of documentation for the web > > > service. One is the specification which tells what kind of info is supposed > > > to be in each part of a URL. Allen was working on this with the DAS guys. > > > The other part is a how to use the web service section in the wiki which was > > > put together in part to get the paper published. > > > > > > > > > Marc > > > > > > > > > > > > > > > On 10/26/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > Marc, > > > > > > > > Here's the next question: > > > > > > > > 2) The annot table retrieval seems to work fine eg: > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > > > > > > Where can I find the definitions of the column headings? I know some > > > > are obvious, but best to make sure > > > > > > > > I have a similar question, which might help me to answere questions > > > > like this without having to bother you. My question is: > > > > > > > > lou 1) You have shown me how to see the man pages in R, but how can > > > > I find man pages, or other documentation, for commands of the type in > > > > question 2) above, which are embedded in a URL? > > > > > > > > Have a good weekend, > > > > > > > > On 10/25/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > > > Marc, > > > > > > > > > > Thanks again. With G-d's help I will send you another question > > > > > tomorrow. > > > > > > > > > > On 10/25/07, Marc Carlson < mr...@gm...> wrote: > > > > > > > > > > > > > > > > > > Yeah I think that web site is probably just out of date. I > > > > > > don't maintain the website, only the package. The true location for the > > > > > > documentation for an R package is supposed to be within the package itself. > > > > > > One of these days I aim to get a proper vignette written for the celsius > > > > > > package, but in the meantime, all the directions you need should need should > > > > > > be included in the standard man pages. This is better because when you run > > > > > > 'R CMD check celsius' on the package all of the examples in the INTERNAL man > > > > > > pages should get TESTED. The web page is (unfortunately) completely free to > > > > > > become horribly out of date and there is little that I can do about that... > > > > > > > > > > > > In fact I don't even recognize that web site anymore... So this > > > > > > particular question has very little to do with me. I just wrote the R > > > > > > package. If there is something to do with the R package, then I can help > > > > > > you. If its the web server then it's either Allen or possibly someone > > > > > > else... > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/25/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > Thanks again, your answer to my question was helpful as I can > > > > > > > now find the man pages. Let's do 1 question at a time. Here's today's > > > > > > > question: > > > > > > > > > > > > > > 1) in the example in the documentation on: > > > > > > > http://celsius.genomics.ctrl.ucla.edu/doc/Celsius/Controller/Service/Cel.htm. > > > > > > > The url uses - http://jugular.ctrl.ucla.edu:4000 - doesn't > > > > > > > work. Should it be changed to: > > > > > > > http://celsius.genomics.ctrl.ucla.edu in the documentation?? > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > On 10/25/07, Marc Carlson <mr...@gm...> wrote: > > > > > > > > > > > > > > > > Yes. But you have to send me more information. Such as > > > > > > > > what are the questions exactly? The email before this one was nearly > > > > > > > > impossible to follow. And I just can't answer if I don't understand the > > > > > > > > questions. > > > > > > > > > > > > > > > > If you want to get the help pages for celsius, you should > > > > > > > > only have to launch R, load the celsius packges with library(celsius) and > > > > > > > > then type ?celsius (for the main celsius help page - as an example). Once > > > > > > > > the page loads you should be able to scroll up and down to read it (it > > > > > > > > should launch inside of less). There are also help pages for most of the > > > > > > > > other functions. You could also always look at the source for these help > > > > > > > > pages by looking at the man folder that the package installs but its easier > > > > > > > > to read inside of R since that is where it will be formatted for you. The > > > > > > > > main celsius page should list all the basic functions. > > > > > > > > > > > > > > > > Hope this helps, > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/23/07, louis fridkis <lou...@gm...> wrote: > > > > > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > Is it possible that you could help me answer one of these > > > > > > > > > questions every few days? > > > > > > > > > > > > > > > > > > On 10/17/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > Thanks, I really appreciate your help. How do I access > > > > > > > > > > the man pages? Is blank the same as 0? These are my questions. Here are some > > > > > > > > > > more questions from the client (I have numbered them so there is a unique > > > > > > > > > > number for each question regardless of which batch [first or second]): > > > > > > > > > > > > > > > > > > > > 6. a method to check which platforms are available > > > > > > > > > > for their annotations > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/platform/platforms > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > return all available platforms > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <platforms> > > > > > > > > > > > > > > > > > > > > <platform name="" count="467" annotated="-1"/> > > > > > > > > > > > > > > > > > > > > <platform name="1286_s01" count="41" annotated="-1"/> > > > > > > > > > > > > > > > > > > > > <platform name="AG" count="141" annotated="1"/> > > > > > > > > > > > > > > > > > > > > .... > > > > > > > > > > > > > > > > > > > > </platforms> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ?? not sure the value -1, 1 for attribute annotated > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 7. their host name to check my program is reachable > > > > > > > > > > > > > > > > > > > > giving the host name (celsius.genomics.ctrl.ucla.edu), > > > > > > > > > > > > > > > > > > > > a code shown below returns whether their web page is > > > > > > > > > > reachable or not and > > > > > > > > > > > > > > > > > > > > it also return ip address ( 164.67.183.98) > > > > > > > > > > > > > > > > > > > > when I enter this ip address in the browser (http://164.67.183.98), > > > > > > > > > > it redirects and shows > > > > > > > > > > http://genomics.ctrl.ucla.edu/pmwiki/ (2) > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Can I use (2) web page to get to know whether > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/ is running or not > > > > > > > > > > ? > > > > > > > > > > > > > > > > > > > > Or are there other ways to check by a program? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > public static void main(String[] args) { > > > > > > > > > > > > > > > > > > > > try { > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > InetAddress address = InetAddress.getByName("celsius.genomics.ctrl.ucla.edu > > > > > > > > > > "); > > > > > > > > > > > > > > > > > > > > System.out.println("Name: " + address.getHostName > > > > > > > > > > ()); > > > > > > > > > > > > > > > > > > > > System.out.println("Addr: " + > > > > > > > > > > address.getHostAddress()); > > > > > > > > > > > > > > > > > > > > System.out.println ("Reach: " + > > > > > > > > > > address.isReachable(60000)); > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > catch (UnknownHostException e) { > > > > > > > > > > > > > > > > > > > > System.err.println("Unable to lookup web.mit.edu > > > > > > > > > > "); > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > catch (IOException e) { > > > > > > > > > > > > > > > > > > > > System.err.println("Unable to reach web.mit.edu"); > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 8. please shift the attribute values to right : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <cel id="SN:1000008" platform="hippocampus" > > > > > > > > > > anatomyname="allenday_hand" anatomypart="MA:0000191" anatomyacc="" > > > > > > > > > > pathology="" pathologypart="" pathologyacc="female" > > > > > > > > > > sexname="allenday_comp_sex" sexpart="null:female" sexacc="" cell="" > > > > > > > > > > cellpart="" cellacc="" phenotypename="" phenotypepart="" phenotypeacc="" > > > > > > > > > > devname="" devpart="" devacc=""/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > And not repeated a value more than once : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <cel id="SN:1000252" platform="extraocular skeletal > > > > > > > > > > muscle|extraocular skeletal muscle|extraocular skeletal muscle|extraocular > > > > > > > > > > skeletal muscle" > > > > > > > > > > anatomyname="allenday_hand|allenday_hand|rjandali_hand|rjandali_hand" > > > > > > > > > > anatomypart="MA:0001271|MA:0001271|MA:0001271|MA:0001271" > > > > > > > > > > anatomyacc="normal|normal|normal|normal" > > > > > > > > > > pathology="allenday_hand|rjandali_hand|allenday_hand|rjandali_hand" > > > > > > > > > > pathologypart="MPATH:458|MPATH:458|MPATH:458|MPATH:458" > > > > > > > > > > pathologyacc="male|male|male|male" > > > > > > > > > > sexname="allenday_comp_sex|allenday_comp_sex|allenday_comp_sex|allenday_comp_sex" > > > > > > > > > > sexpart="null:male|null:male|null:male|null:male" sexacc="" > > > > > > > > > > cell="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > > > > > > > > > cellpart="CL:0000001|CL:0000001|CL:0000001|CL:0000001" cellacc="normal > > > > > > > > > > phenotype|normal phenotype|normal phenotype|normal phenotype" > > > > > > > > > > phenotypename="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > > > > > > > > > phenotypepart="MP:0002873|MP:0002873|MP:0002873|MP:0002873" > > > > > > > > > > phenotypeacc="adult|adult|adult|adult" > > > > > > > > > > devname="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > > > > > > > > > devpart="null:adult|null:adult|null:adult|null:adult" devacc=""/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 9. /service/cel/annots method > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > l optional stringency level. > > > > > > > > > > annotations below level are suppressed (i.e. considered > > > > > > > > > > as NULL). > > > > > > > > > > > > > > > > > > > > defaults to 0. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > level type > > > > > > > > > > > > > > > > > > > > ===== ===== > > > > > > > > > > > > > > > > > > > > 100 assigned by web robot, > > > > > > > > > > experimental > > > > > > > > > > > > > > > > > > > > 200 assigned by curator > > > > > > > > > > robot, experimental > > > > > > > > > > > > > > > > > > > > 300 assigned by web robot > > > > > > > > > > > > > > > > > > > > 400 assigned by curator > > > > > > > > > > robot > > > > > > > > > > > > > > > > > > > > 500 assigned by web user > > > > > > > > > > > > > > > > > > > > 600 assigned by curator > > > > > > > > > > > > > > > > > > > > Are these levels 1, 2,,6 instead of 100, 200, > > > > > > > > > > 600 ? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > For example When we enter the url : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=mask;m=MA:0000168 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > it returns > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > #SNID mask=MA:0000168 level=0 > > > > > > > > > > > > > > > > > > > > SN:1000008 1 > > > > > > > > > > > > > > > > > > > > SN:1000009 1 > > > > > > > > > > > > > > > > > > > > SN:1000010 1 > > > > > > > > > > > > > > > > > > > > SN:1000011 1 > > > > > > > > > > > > > > > > > > > > SN:1000012 1 > > > > > > > > > > > > > > > > > > > > SN:1000013 1 > > > > > > > > > > > > > > > > > > > > SN:1000014 1 > > > > > > > > > > > > > > > > > > > > SN:1000015 1 > > > > > > > > > > > > > > > > > > > > SN:1000016 1 > > > > > > > > > > > > > > > > > > > > SN:1000017 1 > > > > > > > > > > > > > > > > > > > > SN:1000018 1 > > > > > > > > > > > > > > > > > > > > SN:1000019 1 > > > > > > > > > > > > > > > > > > > > SN:1000020 1 > > > > > > > > > > > > > > > > > > > > SN:1000021 1 > > > > > > > > > > > > > > > > > > > > SN:1000081 > > > > > > > > > > > > > > > > > > > > SN:1000098 0 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > This level (level=0) has the same meaning of the > > > > > > > > > > optional parameter l which has > > > > > > > > > > > > > > > > > > > > level type > > > > > > > > > > > > > > > > > > > > ===== ===== > > > > > > > > > > > > > > > > > > > > 100 assigned by web robot, experimental > > > > > > > > > > > > > > > > > > > > 200 assigned by curator robot, experimental > > > > > > > > > > > > > > > > > > > > 300 assigned by web robot > > > > > > > > > > > > > > > > > > > > 400 assigned by curator robot > > > > > > > > > > > > > > > > > > > > 500 assigned by web user > > > > > > > > > > > > > > > > > > > > 600 assigned by curator > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Or not. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > If they have the same meaning, > > > > > > > > > > > > > > > > > > > > 100 should be replaced with 1 and so on > > > > > > > > > > > > > > > > > > > > On 10/12/07, Marc Carlson <mr...@gm...> wrote: > > > > > > > > > > > > > > > > > > > > > > Louis, > > > > > > > > > > > > > > > > > > > > > > I have not had time to look at questions 1-3 yet, > > > > > > > > > > > though I suspect that the documentation is just referring to an older > > > > > > > > > > > instance of the web server (now decomissioned). As for 4 and 5, the > > > > > > > > > > > ontology searches are always recursive through the ontology (ie. you should > > > > > > > > > > > ALWAYS get all the child nodes for a term - if you want to only find a more > > > > > > > > > > > specific term, then you should use THAT term instead otherwise it will get > > > > > > > > > > > lumped along with the less specific term). Also, 1 is true, 0 is false and > > > > > > > > > > > ! indicates that there is a conflict about the annotations for that sample. > > > > > > > > > > > I think that the man pages detailed this, but its been a while since I have > > > > > > > > > > > been "in there". > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/10/07, Marc Carlson < mca...@fh...> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ---------- Forwarded message ---------- > > > > > > > > > > > > From: "louis fridkis" < lou...@gm...> > > > > > > > > > > > > To: "Marc Carlson" < mca...@fh...> > > > > > > > > > > > > Date: Wed, 10 Oct 2007 16:25:07 -0700 > > > > > > > > > > > > Subject: Re: celsius support > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > > > > > The client wants to allow users to download affy > > > > > > > > > > > > data (rather than having to create individual download scripts for each > > > > > > > > > > > > rep). > > > > > > > > > > > > > > > > > > > > > > > > What they would like to do is: > > > > > > > > > > > > 1) search all experiments and display some of the > > > > > > > > > > > > experimental level annotation eg title, species > > > > > > > > > > > > > > > > > > > > > > > > 2) filter eg by array type, species, disease term > > > > > > > > > > > > > > > > > > > > > > > > 3) select an experiment > > > > > > > > > > > > > > > > > > > > > > > > 4) download cel files and associated annotation from > > > > > > > > > > > > chosen experiment > > > > > > > > > > > > > > > > > > > > > > > > Here are his specific questions: > > > > > > > > > > > > > > > > > > > > > > > > 1) in the example in the documentation on: http://celsius.genomics.ctrl.ucla.edu/doc/Celsius/Controller/Service/Cel.htm > > > > > > > > > > > > . The url uses - http://jugular.ctrl.ucla.edu:4000 - > > > > > > > > > > > > doesn't work. Should it be changed to: http://celsius.genomics.ctrl.ucla.edu > > > > > > > > > > > > in the documentation?? > > > > > > > > > > > > > > > > > > > > > > > > 2) The annot table retrieval seems to work fine eg: > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > > > > > > > > > > > > > > > > > > > > > > Where can I find the definitions of the column > > > > > > > > > > > > headings? I know some are obvious, but best to make sure > > > > > > > > > > > > > > > > > > > > > > > > 3) when I do the equivalient query returning in xml: > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A > > > > > > > > > > > > > > > > > > > > > > > > The tags are different to the column names from the > > > > > > > > > > > > table. And the tissuename/anatomyname are in the 'platform' tag and all the > > > > > > > > > > > > tags values seem to have shifted to the tag to its left. > > > > > > > > > > > > > > > > > > > > > > > > 4)not quite sure how to interpret the results if we > > > > > > > > > > > > want to say retrieve all the hgu-133a cel files that have associated with > > > > > > > > > > > > brain tissue (MA:0000168).eg > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=mask;m=MA:0000168 > > > > > > > > > > > > Returns something like: > > > > > > > > > > > > #SNID mask=MA:0000168 level=0 > > > > > > > > > > > > SN:1000008 1 > > > > > > > > > > > > SN:1000009 1 > > > > > > > > > > > > SN:1000081 > > > > > > > > > > > > SN:1000098 0 > > > > > > > > > > > > SN:1000170 0 > > > > > > > > > > > > SN:1000221 0 > > > > > > > > > > > > Etc > > > > > > > > > > > > Presumably: 1=true i.e. this sample is associated > > > > > > > > > > > > with brain tissue > > > > > > > > > > > > > > > > > > > > > > > > What is the difference between "0" and " " (blank) > > > > > > > > > > > > and what does "!" mean? > > > > > > > > > > > > > > > > > > > > > > > > 5) In the above example if 4 I searched for the > > > > > > > > > > > > 'brain' ontology group, MA:0000168. Presumably this returns all child nodes > > > > > > > > > > > > of this ontology which is why SN:1000008 and SN:1000009 returned 1 even > > > > > > > > > > > > though they do not mention brain or MA:0000168? > > > > > > > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > > > > > > > On 10/10/07, Marc Carlson < mca...@fh...> > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > louis fridkis wrote: > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > > > > > > > > > Are you available to help with a Celsius user's > > > > > > > > > > > > > questions? > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > Lou Fridkis > > > > > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > > > > > Department of Human Genetics > > > > > > > > > > > > > > Nelson Lab > > > > > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > I can take a stab at it. I don't have gobs of > > > > > > > > > > > > > free time, but I want to > > > > > > > > > > > > > support this package because I intend to polish it > > > > > > > > > > > > > up more and submit it > > > > > > > > > > > > > to bioconductor eventually. > > > > > > > > > > > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > Lou Fridkis > > > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > > > Department of Human Genetics > > > > > > > > > > > > Nelson Lab > > > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > Lou Fridkis > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > Department of Human Genetics > > > > > > > > > > Nelson Lab > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Lou Fridkis > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > Department of Human Genetics > > > > > > > > > Nelson Lab > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Lou Fridkis > > > > > > > UCLA Geffen School of Medicine > > > > > > > Department of Human Genetics > > > > > > > Nelson Lab > > > > > > > 695 Charles E Young Drive S. > > > > > > > Los Angeles, CA 90095 USA > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Lou Fridkis > > > > > UCLA Geffen School of Medicine > > > > > Department of Human Genetics > > > > > Nelson Lab > > > > > 695 Charles E Young Drive S. > > > > > Los Angeles, CA 90095 USA > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > -- > > > > Lou Fridkis > > > > UCLA Geffen School of Medicine > > > > Department of Human Genetics > > > > Nelson Lab > > > > 695 Charles E Young Drive S. > > > > Los Angeles, CA 90095 USA > > > > 310-825-7920 > > > > > > > > > > > > > > > > -- > > Lou Fridkis > > UCLA Geffen School of Medicine > > Department of Human Genetics > > Nelson Lab > > 695 Charles E Young Drive S. > > Los Angeles, CA 90095 USA > > 310-825-7920 > > > > -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
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From: louis f. <lou...@gm...> - 2007-11-06 22:34:43
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Brian, Allen, I looked in the perdoc for this function but was not able to find the answer to the client question below. Then I asked Marc, but he doesn't know either. I need help on this from one of you. Thank you, 6. It seems that the following is a method to check which platforms are available for their annotations: http://celsius.genomics.ctrl.ucla.edu/service/platform/platforms It returns all available platforms <platforms> <platform name="" count="467" annotated="-1"/> <platform name="1286_s01" count="41" annotated="-1"/> <platform name="AG" count="141" annotated="1"/> .... </platforms> What do the values -1 and 1 for attribute annotated mean? -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
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From: louis f. <lou...@gm...> - 2007-11-02 18:05:07
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Allen, I am forwarding this message to celsius-dev per your request. Thank you, ---------- Forwarded message ---------- From: louis fridkis <lou...@gm...> Date: Oct 29, 2007 12:55 PM Subject: Re: [Fwd: Re: celsius support] To: Marc Carlson <mr...@gm...>, nelsonlab-devel < nel...@li...> Marc, Allen Should I be encouraging R and discouraging XML. I.e. In your opinion, should we be going in the direction of only supporting R? P.S. Allen, for backgound/context see Marc's answer in the first message below and the original question, labelled 3), in the second message below. On 10/29/07, Marc Carlson <mr...@gm...> wrote: > > This is really another web server question but I will tell you what I > remember. I think the answer is that the xml was made first. But for the > annotations, I wanted the tab file for the R client (the xml was too huge to > parse easily). Anyhow, I think that the xml was just never updated with the > newer fields that were added to the tab format file. This should all be > moot if the client is using the R client anyhow since that should get the > fields they ask for anyways. At this point this guy is just being nosy. > > Marc > > > > On 10/29/07, louis fridkis < lou...@gm...> wrote: > > > > Marc, > > > > Thanks again for your answer. I followed up with a question to Allen and > > Brian and sent a partial answer to the client. Here is the next question: > > > > 3) The annot table retrieval seems to work fine eg: > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > > > > When I do the equivalient query returning in xml: > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A > > The tags are different to the column names from the table. And the > > tissuename/anatomyname are in the 'platform' tag and all the tags values > > seem to have shifted to the tag to its left. > > > > On 10/26/07, Marc Carlson < mr...@gm...> wrote: > > > > > > To answer the 1st question, I don't believe that we ever defined those > > > because we felt they were pretty obvious. SNID as you know is the internal > > > ID. The next set of names are each made of two parts. tissue, path, sex, > > > cell, pheno and dev refer to different ontologies to descibe tissue type, > > > pathology state, cell type, phenotype, and developmental stage. The second > > > part of each name is name, part or accession. Name is just the common name, > > > accession is the precise ID from the ontology, and the ontologies are > > > namespaced themselves, so you know where the information has come from. For > > > example MA is the mouse anatomy ontology, which is what is used for the > > > tissue type annotations... I don't remember what "part" stands for anymore, > > > but it looks like its just the type of annotation (like allenday hand) > > > though you had better check this last one over with Allen... > > > > > > Unfortunately, for your second question, this is more about the web > > > server, and that is Allens domain. The R package I wrote has man pages. > > > And I think there are web pages telling about the web service (there > > > certainly used to be). Allen or Brian would probably know where those are. > > > > > > There should be at least two kinds of documentation for the web > > > service. One is the specification which tells what kind of info is supposed > > > to be in each part of a URL. Allen was working on this with the DAS guys. > > > The other part is a how to use the web service section in the wiki which was > > > put together in part to get the paper published. > > > > > > > > > Marc > > > > > > > > > > > > > > > On 10/26/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > Marc, > > > > > > > > Here's the next question: > > > > > > > > 2) The annot table retrieval seems to work fine eg: > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > > > > > > Where can I find the definitions of the column headings? I know some > > > > are obvious, but best to make sure > > > > > > > > I have a similar question, which might help me to answere questions > > > > like this without having to bother you. My question is: > > > > > > > > lou 1) You have shown me how to see the man pages in R, but how can > > > > I find man pages, or other documentation, for commands of the type in > > > > question 2) above, which are embedded in a URL? > > > > > > > > Have a good weekend, > > > > > > > > On 10/25/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > > > Marc, > > > > > > > > > > Thanks again. With G-d's help I will send you another question > > > > > tomorrow. > > > > > > > > > > On 10/25/07, Marc Carlson < mr...@gm...> wrote: > > > > > > > > > > > > > > > > > > Yeah I think that web site is probably just out of date. I > > > > > > don't maintain the website, only the package. The true location for the > > > > > > documentation for an R package is supposed to be within the package itself. > > > > > > One of these days I aim to get a proper vignette written for the celsius > > > > > > package, but in the meantime, all the directions you need should need should > > > > > > be included in the standard man pages. This is better because when you run > > > > > > 'R CMD check celsius' on the package all of the examples in the INTERNAL man > > > > > > pages should get TESTED. The web page is (unfortunately) completely free to > > > > > > become horribly out of date and there is little that I can do about that... > > > > > > > > > > > > In fact I don't even recognize that web site anymore... So this > > > > > > particular question has very little to do with me. I just wrote the R > > > > > > package. If there is something to do with the R package, then I can help > > > > > > you. If its the web server then it's either Allen or possibly someone > > > > > > else... > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/25/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > Thanks again, your answer to my question was helpful as I can > > > > > > > now find the man pages. Let's do 1 question at a time. Here's today's > > > > > > > question: > > > > > > > > > > > > > > 1) in the example in the documentation on: > > > > > > > http://celsius.genomics.ctrl.ucla.edu/doc/Celsius/Controller/Service/Cel.htm. > > > > > > > The url uses - http://jugular.ctrl.ucla.edu:4000 - doesn't > > > > > > > work. Should it be changed to: > > > > > > > http://celsius.genomics.ctrl.ucla.edu in the documentation?? > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > On 10/25/07, Marc Carlson <mr...@gm...> wrote: > > > > > > > > > > > > > > > > Yes. But you have to send me more information. Such as > > > > > > > > what are the questions exactly? The email before this one was nearly > > > > > > > > impossible to follow. And I just can't answer if I don't understand the > > > > > > > > questions. > > > > > > > > > > > > > > > > If you want to get the help pages for celsius, you should > > > > > > > > only have to launch R, load the celsius packges with library(celsius) and > > > > > > > > then type ?celsius (for the main celsius help page - as an example). Once > > > > > > > > the page loads you should be able to scroll up and down to read it (it > > > > > > > > should launch inside of less). There are also help pages for most of the > > > > > > > > other functions. You could also always look at the source for these help > > > > > > > > pages by looking at the man folder that the package installs but its easier > > > > > > > > to read inside of R since that is where it will be formatted for you. The > > > > > > > > main celsius page should list all the basic functions. > > > > > > > > > > > > > > > > Hope this helps, > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/23/07, louis fridkis <lou...@gm...> wrote: > > > > > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > Is it possible that you could help me answer one of these > > > > > > > > > questions every few days? > > > > > > > > > > > > > > > > > > On 10/17/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > Thanks, I really appreciate your help. How do I access > > > > > > > > > > the man pages? Is blank the same as 0? These are my questions. Here are some > > > > > > > > > > more questions from the client (I have numbered them so there is a unique > > > > > > > > > > number for each question regardless of which batch [first or second]): > > > > > > > > > > > > > > > > > > > > 6. a method to check which platforms are available > > > > > > > > > > for their annotations > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/platform/platforms > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > return all available platforms > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <platforms> > > > > > > > > > > > > > > > > > > > > <platform name="" count="467" annotated="-1"/> > > > > > > > > > > > > > > > > > > > > <platform name="1286_s01" count="41" annotated="-1"/> > > > > > > > > > > > > > > > > > > > > <platform name="AG" count="141" annotated="1"/> > > > > > > > > > > > > > > > > > > > > .... > > > > > > > > > > > > > > > > > > > > </platforms> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ?? not sure the value -1, 1 for attribute annotated > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 7. their host name to check my program is reachable > > > > > > > > > > > > > > > > > > > > giving the host name (celsius.genomics.ctrl.ucla.edu), > > > > > > > > > > > > > > > > > > > > a code shown below returns whether their web page is > > > > > > > > > > reachable or not and > > > > > > > > > > > > > > > > > > > > it also return ip address ( 164.67.183.98) > > > > > > > > > > > > > > > > > > > > when I enter this ip address in the browser (http://164.67.183.98), > > > > > > > > > > it redirects and shows > > > > > > > > > > http://genomics.ctrl.ucla.edu/pmwiki/ (2) > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Can I use (2) web page to get to know whether > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/ is running or not > > > > > > > > > > ? > > > > > > > > > > > > > > > > > > > > Or are there other ways to check by a program? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > public static void main(String[] args) { > > > > > > > > > > > > > > > > > > > > try { > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > InetAddress address = InetAddress.getByName("celsius.genomics.ctrl.ucla.edu > > > > > > > > > > "); > > > > > > > > > > > > > > > > > > > > System.out.println("Name: " + address.getHostName > > > > > > > > > > ()); > > > > > > > > > > > > > > > > > > > > System.out.println("Addr: " + > > > > > > > > > > address.getHostAddress()); > > > > > > > > > > > > > > > > > > > > System.out.println ("Reach: " + > > > > > > > > > > address.isReachable(60000)); > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > catch (UnknownHostException e) { > > > > > > > > > > > > > > > > > > > > System.err.println("Unable to lookup web.mit.edu > > > > > > > > > > "); > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > catch (IOException e) { > > > > > > > > > > > > > > > > > > > > System.err.println("Unable to reach web.mit.edu"); > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 8. please shift the attribute values to right : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <cel id="SN:1000008" platform="hippocampus" > > > > > > > > > > anatomyname="allenday_hand" anatomypart="MA:0000191" anatomyacc="" > > > > > > > > > > pathology="" pathologypart="" pathologyacc="female" > > > > > > > > > > sexname="allenday_comp_sex" sexpart="null:female" sexacc="" cell="" > > > > > > > > > > cellpart="" cellacc="" phenotypename="" phenotypepart="" phenotypeacc="" > > > > > > > > > > devname="" devpart="" devacc=""/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > And not repeated a value more than once : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <cel id="SN:1000252" platform="extraocular skeletal > > > > > > > > > > muscle|extraocular skeletal muscle|extraocular skeletal muscle|extraocular > > > > > > > > > > skeletal muscle" > > > > > > > > > > anatomyname="allenday_hand|allenday_hand|rjandali_hand|rjandali_hand" > > > > > > > > > > anatomypart="MA:0001271|MA:0001271|MA:0001271|MA:0001271" > > > > > > > > > > anatomyacc="normal|normal|normal|normal" > > > > > > > > > > pathology="allenday_hand|rjandali_hand|allenday_hand|rjandali_hand" > > > > > > > > > > pathologypart="MPATH:458|MPATH:458|MPATH:458|MPATH:458" > > > > > > > > > > pathologyacc="male|male|male|male" > > > > > > > > > > sexname="allenday_comp_sex|allenday_comp_sex|allenday_comp_sex|allenday_comp_sex" > > > > > > > > > > sexpart="null:male|null:male|null:male|null:male" sexacc="" > > > > > > > > > > cell="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > > > > > > > > > cellpart="CL:0000001|CL:0000001|CL:0000001|CL:0000001" cellacc="normal > > > > > > > > > > phenotype|normal phenotype|normal phenotype|normal phenotype" > > > > > > > > > > phenotypename="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > > > > > > > > > phenotypepart="MP:0002873|MP:0002873|MP:0002873|MP:0002873" > > > > > > > > > > phenotypeacc="adult|adult|adult|adult" > > > > > > > > > > devname="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > > > > > > > > > devpart="null:adult|null:adult|null:adult|null:adult" devacc=""/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 9. /service/cel/annots method > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > l optional stringency level. > > > > > > > > > > annotations below level are suppressed (i.e. considered > > > > > > > > > > as NULL). > > > > > > > > > > > > > > > > > > > > defaults to 0. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > level type > > > > > > > > > > > > > > > > > > > > ===== ===== > > > > > > > > > > > > > > > > > > > > 100 assigned by web robot, > > > > > > > > > > experimental > > > > > > > > > > > > > > > > > > > > 200 assigned by curator > > > > > > > > > > robot, experimental > > > > > > > > > > > > > > > > > > > > 300 assigned by web robot > > > > > > > > > > > > > > > > > > > > 400 assigned by curator > > > > > > > > > > robot > > > > > > > > > > > > > > > > > > > > 500 assigned by web user > > > > > > > > > > > > > > > > > > > > 600 assigned by curator > > > > > > > > > > > > > > > > > > > > Are these levels 1, 2,,6 instead of 100, 200, > > > > > > > > > > 600 ? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > For example When we enter the url : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=mask;m=MA:0000168 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > it returns > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > #SNID mask=MA:0000168 level=0 > > > > > > > > > > > > > > > > > > > > SN:1000008 1 > > > > > > > > > > > > > > > > > > > > SN:1000009 1 > > > > > > > > > > > > > > > > > > > > SN:1000010 1 > > > > > > > > > > > > > > > > > > > > SN:1000011 1 > > > > > > > > > > > > > > > > > > > > SN:1000012 1 > > > > > > > > > > > > > > > > > > > > SN:1000013 1 > > > > > > > > > > > > > > > > > > > > SN:1000014 1 > > > > > > > > > > > > > > > > > > > > SN:1000015 1 > > > > > > > > > > > > > > > > > > > > SN:1000016 1 > > > > > > > > > > > > > > > > > > > > SN:1000017 1 > > > > > > > > > > > > > > > > > > > > SN:1000018 1 > > > > > > > > > > > > > > > > > > > > SN:1000019 1 > > > > > > > > > > > > > > > > > > > > SN:1000020 1 > > > > > > > > > > > > > > > > > > > > SN:1000021 1 > > > > > > > > > > > > > > > > > > > > SN:1000081 > > > > > > > > > > > > > > > > > > > > SN:1000098 0 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > This level (level=0) has the same meaning of the > > > > > > > > > > optional parameter l which has > > > > > > > > > > > > > > > > > > > > level type > > > > > > > > > > > > > > > > > > > > ===== ===== > > > > > > > > > > > > > > > > > > > > 100 assigned by web robot, experimental > > > > > > > > > > > > > > > > > > > > 200 assigned by curator robot, experimental > > > > > > > > > > > > > > > > > > > > 300 assigned by web robot > > > > > > > > > > > > > > > > > > > > 400 assigned by curator robot > > > > > > > > > > > > > > > > > > > > 500 assigned by web user > > > > > > > > > > > > > > > > > > > > 600 assigned by curator > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Or not. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > If they have the same meaning, > > > > > > > > > > > > > > > > > > > > 100 should be replaced with 1 and so on > > > > > > > > > > > > > > > > > > > > On 10/12/07, Marc Carlson <mr...@gm...> wrote: > > > > > > > > > > > > > > > > > > > > > > Louis, > > > > > > > > > > > > > > > > > > > > > > I have not had time to look at questions 1-3 yet, > > > > > > > > > > > though I suspect that the documentation is just referring to an older > > > > > > > > > > > instance of the web server (now decomissioned). As for 4 and 5, the > > > > > > > > > > > ontology searches are always recursive through the ontology (ie. you should > > > > > > > > > > > ALWAYS get all the child nodes for a term - if you want to only find a more > > > > > > > > > > > specific term, then you should use THAT term instead otherwise it will get > > > > > > > > > > > lumped along with the less specific term). Also, 1 is true, 0 is false and > > > > > > > > > > > ! indicates that there is a conflict about the annotations for that sample. > > > > > > > > > > > I think that the man pages detailed this, but its been a while since I have > > > > > > > > > > > been "in there". > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/10/07, Marc Carlson < mca...@fh...> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ---------- Forwarded message ---------- > > > > > > > > > > > > From: "louis fridkis" < lou...@gm...> > > > > > > > > > > > > To: "Marc Carlson" < mca...@fh...> > > > > > > > > > > > > Date: Wed, 10 Oct 2007 16:25:07 -0700 > > > > > > > > > > > > Subject: Re: celsius support > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > > > > > The client wants to allow users to download affy > > > > > > > > > > > > data (rather than having to create individual download scripts for each > > > > > > > > > > > > rep). > > > > > > > > > > > > > > > > > > > > > > > > What they would like to do is: > > > > > > > > > > > > 1) search all experiments and display some of the > > > > > > > > > > > > experimental level annotation eg title, species > > > > > > > > > > > > > > > > > > > > > > > > 2) filter eg by array type, species, disease term > > > > > > > > > > > > > > > > > > > > > > > > 3) select an experiment > > > > > > > > > > > > > > > > > > > > > > > > 4) download cel files and associated annotation from > > > > > > > > > > > > chosen experiment > > > > > > > > > > > > > > > > > > > > > > > > Here are his specific questions: > > > > > > > > > > > > > > > > > > > > > > > > 1) in the example in the documentation on: http://celsius.genomics.ctrl.ucla.edu/doc/Celsius/Controller/Service/Cel.htm > > > > > > > > > > > > . The url uses - http://jugular.ctrl.ucla.edu:4000 - > > > > > > > > > > > > doesn't work. Should it be changed to: http://celsius.genomics.ctrl.ucla.edu > > > > > > > > > > > > in the documentation?? > > > > > > > > > > > > > > > > > > > > > > > > 2) The annot table retrieval seems to work fine eg: > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > > > > > > > > > > > > > > > > > > > > > > Where can I find the definitions of the column > > > > > > > > > > > > headings? I know some are obvious, but best to make sure > > > > > > > > > > > > > > > > > > > > > > > > 3) when I do the equivalient query returning in xml: > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A > > > > > > > > > > > > > > > > > > > > > > > > The tags are different to the column names from the > > > > > > > > > > > > table. And the tissuename/anatomyname are in the 'platform' tag and all the > > > > > > > > > > > > tags values seem to have shifted to the tag to its left. > > > > > > > > > > > > > > > > > > > > > > > > 4)not quite sure how to interpret the results if we > > > > > > > > > > > > want to say retrieve all the hgu-133a cel files that have associated with > > > > > > > > > > > > brain tissue (MA:0000168).eg > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=mask;m=MA:0000168 > > > > > > > > > > > > Returns something like: > > > > > > > > > > > > #SNID mask=MA:0000168 level=0 > > > > > > > > > > > > SN:1000008 1 > > > > > > > > > > > > SN:1000009 1 > > > > > > > > > > > > SN:1000081 > > > > > > > > > > > > SN:1000098 0 > > > > > > > > > > > > SN:1000170 0 > > > > > > > > > > > > SN:1000221 0 > > > > > > > > > > > > Etc > > > > > > > > > > > > Presumably: 1=true i.e. this sample is associated > > > > > > > > > > > > with brain tissue > > > > > > > > > > > > > > > > > > > > > > > > What is the difference between "0" and " " (blank) > > > > > > > > > > > > and what does "!" mean? > > > > > > > > > > > > > > > > > > > > > > > > 5) In the above example if 4 I searched for the > > > > > > > > > > > > 'brain' ontology group, MA:0000168. Presumably this returns all child nodes > > > > > > > > > > > > of this ontology which is why SN:1000008 and SN:1000009 returned 1 even > > > > > > > > > > > > though they do not mention brain or MA:0000168? > > > > > > > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > > > > > > > On 10/10/07, Marc Carlson < mca...@fh...> > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > louis fridkis wrote: > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > > > > > > > > > Are you available to help with a Celsius user's > > > > > > > > > > > > > questions? > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > Lou Fridkis > > > > > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > > > > > Department of Human Genetics > > > > > > > > > > > > > > Nelson Lab > > > > > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > I can take a stab at it. I don't have gobs of > > > > > > > > > > > > > free time, but I want to > > > > > > > > > > > > > support this package because I intend to polish it > > > > > > > > > > > > > up more and submit it > > > > > > > > > > > > > to bioconductor eventually. > > > > > > > > > > > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > Lou Fridkis > > > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > > > Department of Human Genetics > > > > > > > > > > > > Nelson Lab > > > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > Lou Fridkis > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > Department of Human Genetics > > > > > > > > > > Nelson Lab > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Lou Fridkis > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > Department of Human Genetics > > > > > > > > > Nelson Lab > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Lou Fridkis > > > > > > > UCLA Geffen School of Medicine > > > > > > > Department of Human Genetics > > > > > > > Nelson Lab > > > > > > > 695 Charles E Young Drive S. > > > > > > > Los Angeles, CA 90095 USA > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Lou Fridkis > > > > > UCLA Geffen School of Medicine > > > > > Department of Human Genetics > > > > > Nelson Lab > > > > > 695 Charles E Young Drive S. > > > > > Los Angeles, CA 90095 USA > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > -- > > > > Lou Fridkis > > > > UCLA Geffen School of Medicine > > > > Department of Human Genetics > > > > Nelson Lab > > > > 695 Charles E Young Drive S. > > > > Los Angeles, CA 90095 USA > > > > 310-825-7920 > > > > > > > > > > > > > > > > -- > > Lou Fridkis > > UCLA Geffen School of Medicine > > Department of Human Genetics > > Nelson Lab > > 695 Charles E Young Drive S. > > Los Angeles, CA 90095 USA > > 310-825-7920 > > > > -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
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From: louis f. <lou...@gm...> - 2007-10-31 17:29:47
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Allen, The forwarded message seems to have bounced. Please let me know through which emails you received this message. Thank you, ---------- Forwarded message ---------- From: louis fridkis <lou...@gm...> Date: Oct 30, 2007 3:05 PM Subject: Re: [Fwd: Re: celsius support] To: all...@uc... Cc: Brian O'Connor <boc...@uc...> Allen, Thank you for answering question #1. Question #2 remains. That is: How can I find man pages, or other documentation, for commands of the > type in question 1) above, which are embedded in a URL? I'm not sure what you mean by, "more structured". A wiki sounds like more work for me, and I am very overloaded currently. Also, the wiki has the disadvantage that it doesn't notify you or a new question or responce. So, its easily forgotten. I think using bug tracker would be cumbersome. Would it help if I just used a wiki to capture the questions and answers? On 10/30/07, Allen Day <all...@uc... > wrote: > > "part" column indicates where the annotation came from. who did it, > how they came up with it. sort of like a GO evidence code if you know > what that is. > > can we do this in a more structured way, like with a wiki or > bugtracker or something? > > On 10/29/07, louis fridkis < lou...@gm...> wrote: > > Allen, > > > > Marc has indicated that you are the person to ask 2 questions. Please > refer > > to his message (first message below) for the full context of these > > questions, which I summarize here: > > > > 1) In the output from the URL command: > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > what is the definintion of the column heading, "part"? > > > > 2) How can I find man pages, or other documentation, for commands of the > > type in question 1) above, which are embedded in a URL? > > > > Brian, > > > > Marc says you might also be able to help me with 2) above. > > > > > > On 10/26/07, Marc Carlson <mr...@gm...> wrote: > > > To answer the 1st question, I don't believe that we ever defined those > > because we felt they were pretty obvious. SNID as you know is the > internal > > ID. The next set of names are each made of two parts. tissue, path, > sex, > > cell, pheno and dev refer to different ontologies to descibe tissue > type, > > pathology state, cell type, phenotype, and developmental stage. The > second > > part of each name is name, part or accession. Name is just the common > name, > > accession is the precise ID from the ontology, and the ontologies are > > namespaced themselves, so you know where the information has come > from. For > > example MA is the mouse anatomy ontology, which is what is used for the > > tissue type annotations... I don't remember what "part" stands for > anymore, > > but it looks like its just the type of annotation (like allenday hand) > > though you had better check this last one over with Allen... > > > > > > Unfortunately, for your second question, this is more about the web > > server, and that is Allens domain. The R package I wrote has man pages. > > And I think there are web pages telling about the web service (there > > certainly used to be). Allen or Brian would probably know where those > are. > > > > > > There should be at least two kinds of documentation for the web > service. > > One is the specification which tells what kind of info is supposed to be > in > > each part of a URL. Allen was working on this with the DAS guys. The > other > > part is a how to use the web service section in the wiki which was put > > together in part to get the paper published. > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > On 10/26/07, louis fridkis < lou...@gm... > wrote: > > > > Marc, > > > > > > > > Here's the next question: > > > > > > > > 2) The annot table retrieval seems to work fine eg: > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > > Where can I find the definitions of the column headings? I know some > are > > obvious, but best to make sure > > > > > > > > I have a similar question, which might help me to answere questions > like > > this without having to bother you. My question is: > > > > > > > > lou 1) You have shown me how to see the man pages in R, but how can > I > > find man pages, or other documentation, for commands of the type in > question > > 2) above, which are embedded in a URL? > > > > > > > > Have a good weekend, > > > > > > > > > > > > > > > > On 10/25/07, louis fridkis < lou...@gm...> wrote: > > > > > Marc, > > > > > > > > > > Thanks again. With G-d's help I will send you another question > > tomorrow. > > > > > > > > > > > > > > > > > > > > On 10/25/07, Marc Carlson < mr...@gm...> wrote: > > > > > > > > > > > > Yeah I think that web site is probably just out of date. I > don't > > maintain the website, only the package. The true location for the > > documentation for an R package is supposed to be within the package > itself. > > One of these days I aim to get a proper vignette written for the celsius > > package, but in the meantime, all the directions you need should need > should > > be included in the standard man pages. This is better because when you > run > > 'R CMD check celsius' on the package all of the examples in the INTERNAL > man > > pages should get TESTED. The web page is (unfortunately) completely > free to > > become horribly out of date and there is little that I can do about > that... > > > > > > > > > > > > In fact I don't even recognize that web site anymore... So this > > particular question has very little to do with me. I just wrote the R > > package. If there is something to do with the R package, then I can > help > > you. If its the web server then it's either Allen or possibly someone > > else... > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/25/07, louis fridkis < lou...@gm...> wrote: > > > > > > > Marc, > > > > > > > > > > > > > > Thanks again, your answer to my question was helpful as I can > now > > find the man pages. Let's do 1 question at a time. Here's today's > question: > > > > > > > > > > > > > > 1) in the example in the documentation on: > > http://celsius.genomics.ctrl.ucla.edu/doc/Celsius/Controller/Service/Cel.htm > . > > The url uses - http://jugular.ctrl.ucla.edu:4000 - doesn't > > work. Should it be changed to: > > http://celsius.genomics.ctrl.ucla.edu in the > > documentation?? > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/25/07, Marc Carlson < mr...@gm...> wrote: > > > > > > > > Yes. But you have to send me more information. Such as > what > > are the questions exactly? The email before this one was nearly > impossible > > to follow. And I just can't answer if I don't understand the questions. > > > > > > > > > > > > > > > > If you want to get the help pages for celsius, you should > only > > have to launch R, load the celsius packges with library(celsius) and > then > > type ?celsius (for the main celsius help page - as an example). Once > the > > page loads you should be able to scroll up and down to read it (it > should > > launch inside of less). There are also help pages for most of the other > > functions. You could also always look at the source for these help > pages by > > looking at the man folder that the package installs but its easier to > read > > inside of R since that is where it will be formatted for you. The main > > celsius page should list all the basic functions. > > > > > > > > > > > > > > > > Hope this helps, > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/23/07, louis fridkis <lou...@gm...> wrote: > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > Is it possible that you could help me answer one of these > > questions every few days? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/17/07, louis fridkis < lou...@gm...> wrote: > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > Thanks, I really appreciate your help. How do I access > the > > man pages? Is blank the same as 0? These are my questions. Here are some > > more questions from the client (I have numbered them so there is a > unique > > number for each question regardless of which batch [first or second]): > > > > > > > > > > > > > > > > > > > > 6. a method to check which platforms are available > for > > their annotations > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/platform/platforms > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > return all available platforms > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <platforms> > > > > > > > > > > > > > > > > > > > > <platform name="" count="467" annotated="-1"/> > > > > > > > > > > > > > > > > > > > > <platform name="1286_s01" count="41" annotated="-1"/> > > > > > > > > > > > > > > > > > > > > <platform name="AG" count="141" annotated="1"/> > > > > > > > > > > > > > > > > > > > > .... > > > > > > > > > > > > > > > > > > > > </platforms> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ?? not sure the value -1, 1 for attribute annotated > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 7. their host name to check my program is reachable > > > > > > > > > > > > > > > > > > > > giving the host name (celsius.genomics.ctrl.ucla.edu), > > > > > > > > > > > > > > > > > > > > a code shown below returns whether their web page is > > reachable or not and > > > > > > > > > > > > > > > > > > > > it also return ip address ( 164.67.183.98) > > > > > > > > > > > > > > > > > > > > when I enter this ip address in the browser ( > > http://164.67.183.98), it redirects and shows > > http://genomics.ctrl.ucla.edu/pmwiki/ (2) > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Can I use (2) web page to get to know whether > > http://celsius.genomics.ctrl.ucla.edu/ is running or not ? > > > > > > > > > > > > > > > > > > > > Or are there other ways to check by a program? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > public static void main(String[] args) { > > > > > > > > > > > > > > > > > > > > try { > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > InetAddress address = InetAddress.getByName(" > > celsius.genomics.ctrl.ucla.edu"); > > > > > > > > > > > > > > > > > > > > System.out.println("Name: " + address.getHostName > ()); > > > > > > > > > > > > > > > > > > > > System.out.println("Addr: " + > > address.getHostAddress()); > > > > > > > > > > > > > > > > > > > > System.out.println ("Reach: " + > > address.isReachable(60000)); > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > catch (UnknownHostException e) { > > > > > > > > > > > > > > > > > > > > System.err.println("Unable to lookup web.mit.edu > "); > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > catch (IOException e) { > > > > > > > > > > > > > > > > > > > > System.err.println("Unable to reach web.mit.edu > "); > > > > > > > > > > > > > > > > > > > > } > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 8. please shift the attribute values to right : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <cel id="SN:1000008" platform="hippocampus" > > anatomyname="allenday_hand" anatomypart="MA:0000191" anatomyacc="" > > pathology="" pathologypart="" pathologyacc="female" > > sexname="allenday_comp_sex" sexpart="null:female" sexacc="" cell="" > > cellpart="" cellacc="" phenotypename="" phenotypepart="" phenotypeacc="" > > devname="" devpart="" devacc=""/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > And not repeated a value more than once : > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <cel id="SN:1000252" platform="extraocular skeletal > > muscle|extraocular skeletal muscle|extraocular skeletal > muscle|extraocular > > skeletal muscle" > > anatomyname="allenday_hand|allenday_hand|rjandali_hand|rjandali_hand" > > anatomypart="MA:0001271|MA:0001271|MA:0001271|MA:0001271" > > anatomyacc="normal|normal|normal|normal" > > pathology="allenday_hand|rjandali_hand|allenday_hand|rjandali_hand" > > pathologypart="MPATH:458|MPATH:458|MPATH:458|MPATH:458" > > pathologyacc="male|male|male|male" > > > sexname="allenday_comp_sex|allenday_comp_sex|allenday_comp_sex|allenday_comp_sex" > > > sexpart="null:male|null:male|null:male|null:male" sexacc="" > > cell="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > cellpart="CL:0000001|CL:0000001|CL:0000001|CL:0000001" > > cellacc="normal phenotype|normal phenotype|normal phenotype|normal > > phenotype" > > phenotypename="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > phenotypepart="MP:0002873|MP:0002873|MP:0002873|MP:0002873" > > phenotypeacc="adult|adult|adult|adult" > > devname="rjandali_hand|rjandali_hand|rjandali_hand|rjandali_hand" > > devpart="null:adult|null:adult|null:adult|null:adult" > > devacc=""/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 9. /service/cel/annots method > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > l optional stringency > level. annotations > > below level are suppressed (i.e. considered as NULL). > > > > > > > > > > > > > > > > > > > > defaults to 0. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > level type > > > > > > > > > > > > > > > > > > > > ===== ===== > > > > > > > > > > > > > > > > > > > > 100 assigned by web robot, > > experimental > > > > > > > > > > > > > > > > > > > > 200 assigned by curator > robot, > > experimental > > > > > > > > > > > > > > > > > > > > 300 assigned by web robot > > > > > > > > > > > > > > > > > > > > 400 assigned by curator > robot > > > > > > > > > > > > > > > > > > > > 500 assigned by web user > > > > > > > > > > > > > > > > > > > > 600 assigned by curator > > > > > > > > > > > > > > > > > > > > Are these levels 1, 2,,6 instead of 100, 200, > 600 ? > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > For example When we enter the url : > > > > > > > > > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=mask;m=MA:0000168 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > it returns > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > #SNID mask=MA:0000168 level=0 > > > > > > > > > > > > > > > > > > > > SN:1000008 1 > > > > > > > > > > > > > > > > > > > > SN:1000009 1 > > > > > > > > > > > > > > > > > > > > SN:1000010 1 > > > > > > > > > > > > > > > > > > > > SN:1000011 1 > > > > > > > > > > > > > > > > > > > > SN:1000012 1 > > > > > > > > > > > > > > > > > > > > SN:1000013 1 > > > > > > > > > > > > > > > > > > > > SN:1000014 1 > > > > > > > > > > > > > > > > > > > > SN:1000015 1 > > > > > > > > > > > > > > > > > > > > SN:1000016 1 > > > > > > > > > > > > > > > > > > > > SN:1000017 1 > > > > > > > > > > > > > > > > > > > > SN:1000018 1 > > > > > > > > > > > > > > > > > > > > SN:1000019 1 > > > > > > > > > > > > > > > > > > > > SN:1000020 1 > > > > > > > > > > > > > > > > > > > > SN:1000021 1 > > > > > > > > > > > > > > > > > > > > SN:1000081 > > > > > > > > > > > > > > > > > > > > SN:1000098 0 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > This level (level=0) has the same meaning of the > optional > > parameter l which has > > > > > > > > > > > > > > > > > > > > level type > > > > > > > > > > > > > > > > > > > > ===== ===== > > > > > > > > > > > > > > > > > > > > 100 assigned by web robot, experimental > > > > > > > > > > > > > > > > > > > > 200 assigned by curator robot, experimental > > > > > > > > > > > > > > > > > > > > 300 assigned by web robot > > > > > > > > > > > > > > > > > > > > 400 assigned by curator robot > > > > > > > > > > > > > > > > > > > > 500 assigned by web user > > > > > > > > > > > > > > > > > > > > 600 assigned by curator > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Or not. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > If they have the same meaning, > > > > > > > > > > > > > > > > > > > > 100 should be replaced with 1 and so on > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/12/07, Marc Carlson <mr...@gm... > wrote: > > > > > > > > > > > Louis, > > > > > > > > > > > > > > > > > > > > > > I have not had time to look at questions 1-3 yet, > though I > > suspect that the documentation is just referring to an older instance of > the > > web server (now decomissioned). As for 4 and 5, the ontology searches > are > > always recursive through the ontology (ie. you should ALWAYS get all the > > > child nodes for a term - if you want to only find a more specific term, > then > > you should use THAT term instead otherwise it will get lumped along with > the > > less specific term). Also, 1 is true, 0 is false and ! indicates that > there > > is a conflict about the annotations for that sample. I think that the > man > > pages detailed this, but its been a while since I have been "in there". > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/10/07, Marc Carlson < mca...@fh...> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ---------- Forwarded message ---------- > > > > > > > > > > > > From: "louis fridkis" < lou...@gm...> > > > > > > > > > > > > To: "Marc Carlson" < mca...@fh...> > > > > > > > > > > > > Date: Wed, 10 Oct 2007 16:25:07 -0700 > > > > > > > > > > > > Subject: Re: celsius support > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > > > > > The client wants to allow users to download affy > data > > (rather than having to create individual download scripts for each rep). > > > > > > > > > > > > > > > > > > > > > > > > > What they would like to do is: > > > > > > > > > > > > 1) search all experiments and display some of the > > experimental level annotation eg title, species > > > > > > > > > > > > > > > > > > > > > > > > 2) filter eg by array type, species, disease term > > > > > > > > > > > > > > > > > > > > > > > > 3) select an experiment > > > > > > > > > > > > > > > > > > > > > > > > 4) download cel files and associated annotation from > > > chosen experiment > > > > > > > > > > > > > > > > > > > > > > > > Here are his specific questions: > > > > > > > > > > > > > > > > > > > > > > > > 1) in the example in the documentation on: > > http://celsius.genomics.ctrl.ucla.edu/doc/Celsius/Controller/Service/Cel.htm > > > . The url uses - http://jugular.ctrl.ucla.edu:4000 - > > doesn't work. Should it be changed to: > > http://celsius.genomics.ctrl.ucla.edu in the > > documentation?? > > > > > > > > > > > > > > > > > > > > > > > > 2) The annot table retrieval seems to work fine eg: > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=tab > > > > > > > > > > > > > Where can I find the definitions of the column > headings? > > I know some are obvious, but best to make sure > > > > > > > > > > > > > > > > > > > > > > > > 3) when I do the equivalient query returning in xml: > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A > > > > > > > > > > > > The tags are different to the column names from the > > table. And the tissuename/anatomyname are in the 'platform' tag and all > the > > tags values seem to have shifted to the tag to its left. > > > > > > > > > > > > > > > > > > > > > > > > 4)not quite sure how to interpret the results if we > want > > to say retrieve all the hgu-133a cel files that have associated with > brain > > tissue (MA:0000168).eg > > > > > > > > > > > > > > > http://celsius.genomics.ctrl.ucla.edu/service/cel/annots?p=HG-U133A;f=mask;m=MA:0000168 > > > > > > > > > > > > Returns something like: > > > > > > > > > > > > #SNID mask=MA:0000168 level=0 > > > > > > > > > > > > SN:1000008 1 > > > > > > > > > > > > SN:1000009 1 > > > > > > > > > > > > SN:1000081 > > > > > > > > > > > > SN:1000098 0 > > > > > > > > > > > > SN:1000170 0 > > > > > > > > > > > > SN:1000221 0 > > > > > > > > > > > > Etc > > > > > > > > > > > > Presumably: 1=true i.e. this sample is associated > with > > brain tissue > > > > > > > > > > > > > > > > > > > > > > > > What is the difference between "0" and " " (blank) > and > > what does "!" mean? > > > > > > > > > > > > > > > > > > > > > > > > 5) In the above example if 4 I searched for the > 'brain' > > ontology group, MA:0000168. Presumably this returns all child nodes of > this > > ontology which is why SN:1000008 and SN:1000009 returned 1 even though > they > > do not mention brain or MA:0000168? > > > > > > > > > > > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 10/10/07, Marc Carlson < mca...@fh...> > wrote: > > > > > > > > > > > > > louis fridkis wrote: > > > > > > > > > > > > > > Marc, > > > > > > > > > > > > > > > > > > > > > > > > > > > > Are you available to help with a Celsius user's > > questions? > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > Lou Fridkis > > > > > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > > > > > Department of Human Genetics > > > > > > > > > > > > > > Nelson Lab > > > > > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > I can take a stab at it. I don't have gobs of > free > > time, but I want to > > > > > > > > > > > > > support this package because I intend to polish it > up > > more and submit it > > > > > > > > > > > > > to bioconductor eventually. > > > > > > > > > > > > > > > > > > > > > > > > > > Marc > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > Lou Fridkis > > > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > > > Department of Human Genetics > > > > > > > > > > > > Nelson Lab > > > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > > > > > > > Lou Fridkis > > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > > Department of Human Genetics > > > > > > > > > > Nelson Lab > > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > > > > > Lou Fridkis > > > > > > > > > UCLA Geffen School of Medicine > > > > > > > > > Department of Human Genetics > > > > > > > > > Nelson Lab > > > > > > > > > 695 Charles E Young Drive S. > > > > > > > > > Los Angeles, CA 90095 USA > > > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > Lou Fridkis > > > > > > > UCLA Geffen School of Medicine > > > > > > > Department of Human Genetics > > > > > > > Nelson Lab > > > > > > > 695 Charles E Young Drive S. > > > > > > > Los Angeles, CA 90095 USA > > > > > > > 310-825-7920 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > Lou Fridkis > > > > > UCLA Geffen School of Medicine > > > > > Department of Human Genetics > > > > > Nelson Lab > > > > > 695 Charles E Young Drive S. > > > > > Los Angeles, CA 90095 USA > > > > > 310-825-7920 > > > > > > > > > > > > > > > > -- > > > > > > > > Lou Fridkis > > > > UCLA Geffen School of Medicine > > > > Department of Human Genetics > > > > Nelson Lab > > > > 695 Charles E Young Drive S. > > > > Los Angeles, CA 90095 USA > > > > 310-825-7920 > > > > > > > > > > > > > > -- > > Lou Fridkis > > UCLA Geffen School of Medicine > > Department of Human Genetics > > Nelson Lab > > 695 Charles E Young Drive S. > > Los Angeles, CA 90095 USA > > 310-825-7920 > > > -- > allenday.skype > +1 (415) 335-4654 (o) > +1 (310) 804-5304 (m) > -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 -- Lou Fridkis UCLA Geffen School of Medicine Department of Human Genetics Nelson Lab 695 Charles E Young Drive S. Los Angeles, CA 90095 USA 310-825-7920 |
