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From: Dave C. G. H. D. <gmo...@go...> - 2009-08-24 23:50:19
|
Hello Ken, and the CMap community, On Sept 15, GMOD's CVS repository is moving to Subversion. Rob Buels of Cornell is doing the heavy lifting. See below for details. Ken, I see that there are already both a CVS and SVN version of CMap. Should Rob do anything to either version, or has CMap already effectively been migrated to SVN? Thanks, Dave C. ---------- Forwarded message ---------- From: Dave Clements, GMOD Help Desk <gmo...@go...> Date: Mon, Aug 24, 2009 at 4:15 PM Subject: CVS to SVN Conversion, 2009/09/15 To: GMOD Announce <gmo...@li...>, GMOD Developers <gmo...@li...> Cc: Robert Buels <rm...@co...> Hello all, Rob Buels of Cornell / SGN has offered to upgrade GMOD's source code repositories to use Subversion (SVN) instead of CVS. After a two month discussion on the GMOD Developers list (see http://comments.gmane.org/gmane.science.biology.gmod.devel/364), this update has been scheduled for September 15, 2009. If you are NOT a GMOD developer then this will, at most, change how you get pre-release copies of GMOD components. In the future you will do SVN checkouts instead of CVS checkouts. The doc on the web site will be updated to describe how to do this. If you ARE a GMOD developer and your project is in GMOD's CVS repository then please read the rest of this email carefully. A complete list of projects in GMOD CVS is at http://gmod.cvs.sourceforge.net/gmod/. Over the next two weeks we will contact project developers to confirm what projects are still active. All projects will be moved to SVN, but any projects that are no longer active will then be deleted. A backup copy will exist in SVN, but users, by default, will no longer see the deleted projects. This should clean things up considerably. All projects will remain in CVS as a read only archive. We have tentatively identified these projects as NO LONGER ACTIVE: bop citrina gds gmod gmod-home goet graphbrowse imdb jalview javaSean labdoc org.bdgp pubfetch pubtrack sample_dbs There may be additional inactive projects as well. Again, we will contact project developers before deleting any projects from SVN. Rob has created a preview version of the repository at http://bugs.sgn.cornell.edu/trac/gmod_test_svn/browser/. Feel free to poke around. This version does not have any projects removed from it. Rob will move the projects on September 15. Before then everyone with uncommitted code changes should commit them to CVS. After September 15, all CVS checkouts you have should be removed and new checkouts made with SVN. We'll provide doc on how to do this. We will send out exact details on the move a few days before it happens. Please let Rob and I know if you have any questions. Again, we'll send out a reminder and additional info a few days before the conversion. Thanks, Dave Clements and Rob Buels -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback |
From: Dave C. G. H. D. <gmo...@go...> - 2009-07-14 06:38:52
|
Hello all, Just a reminder that the August 2009 GMOD Meeting is being held 6-7 August, in Oxford, UK. With a little over 3 weeks to go, the meeting is now 40% full. All remaining space is available on a first come first served basis, and I encourage you to register now, before all open slots are taken. (The January meeting was completely full.) You can register at http://gmod.org/wiki/August_2009_GMOD_Meeting. Please let me know if you have any questions. Cheers, Dave C. On Wed, Jul 1, 2009 at 1:43 PM, Dave Clements, GMOD Help Desk<gmo...@go...> wrote: > Hello all, > > The next GMOD meeting will be held 6-7 August, at the University of > Oxford, in Oxford, United Kingdom. Registration is now open. Space is > available on a first come, first served basis and there is room for 55 > attendees. The meeting cost is £50. See > http://gmod.org/wiki/August_2009_GMOD_Meeting to register > > As with previous GMOD meetings, this meeting will have a mixture of > project, component, and user talks. The agenda is driven by attendee > suggestions, and you are encouraged to add your suggestions now (see > http://gmod.org/wiki/August_2009_GMOD_Meeting#Agenda_Suggestions). > > For examples of what happens at a GMOD meeting, see the writeups of > the January 2009, July 2008, or any other previous meeting (see > http://gmod.org/wiki/Meetings). GMOD meetings are an excellent way to > meet other GMOD developers and users and to learn (and affect) what's > coming in the project. > > Please join us in Oxford this August, > > Dave Clements > GMOD Help Desk > > Note: Unless you have applied to and been admitted to the Summer > School, don't you dare register for it. The registration web site will > let you do this, but bureaucratic hellishness will ensue. > > -- > * Learn more about GMOD at: ISMB/ECCB: http://www.iscb.org/ismbeccb2009/ > (BioMart, Chado, Galaxy, InterMine) > * Please keep responses on the list! > * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback > -- * Register now for the August GMOD Meeting: http://gmod.org/wiki/August_2009_GMOD_Meeting * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback |
From: Dave C. G. H. D. <gmo...@go...> - 2009-07-01 17:43:35
|
Hello all, The next GMOD meeting will be held 6-7 August, at the University of Oxford, in Oxford, United Kingdom. Registration is now open. Space is available on a first come, first served basis and there is room for 55 attendees. The meeting cost is £50. See http://gmod.org/wiki/August_2009_GMOD_Meeting to register As with previous GMOD meetings, this meeting will have a mixture of project, component, and user talks. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now (see http://gmod.org/wiki/August_2009_GMOD_Meeting#Agenda_Suggestions). For examples of what happens at a GMOD meeting, see the writeups of the January 2009, July 2008, or any other previous meeting (see http://gmod.org/wiki/Meetings). GMOD meetings are an excellent way to meet other GMOD developers and users and to learn (and affect) what's coming in the project. Please join us in Oxford this August, Dave Clements GMOD Help Desk Note: Unless you have applied to and been admitted to the Summer School, don't you dare register for it. The registration web site will let you do this, but bureaucratic hellishness will ensue. -- * Learn more about GMOD at: ISMB/ECCB: http://www.iscb.org/ismbeccb2009/ (BioMart, Chado, Galaxy, InterMine) * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback |
From: Ken Youens-C. <kyc...@gm...> - 2009-06-15 15:07:10
|
On Jun 14, 2009, at 5:31 PM, Andrew Couperthwaite wrote: > Hi, > > I'm having trouble importing a .gff into cmap. Using the > cmap_admin.pl, I select import data, .gff, give it the file name (it > says it reads it correctly) I select the species and map set and it > goes to work reading in the data. It reads in all the data and the > purges the caches. > > When I check CMAP, it doesn't even display the species in the drop > down menu. > > Looking at the database using DBVis, cmap_species table seems to > contain the correct information, cmap_map_set seems to contain the > correct information, but cmap_feature does not contain any of the > features that it should have read in from the .gff file. > > The only differences I can see from when I imported data before and > this time, is that this time i'm using a .gff rather than a cmap tab- > delimited file and that this map is a 'physical' map rather than a > 'genetic' one. > > Any thoughts? > > Thanks, > -Andrew Andrew, Ben Faga wrote the GFF importer, and, unfortunately, he's no longer on the project. I'm not sure to what extent this code was vetted, and I'm not familiar with the code myself. I wonder if you have the data already in a tab-delimited format? If so, can you just import it that way? If not, what is the advantage for you to use GFF? -- Ken Youens-Clark kc...@cs... Gramene.org Project Manager Ware Lab/CSHL/USDA-ARS |
From: Andrew C. <aco...@gm...> - 2009-06-14 22:32:43
|
Hi, I'm having trouble importing a .gff into cmap. Using the cmap_admin.pl, I select import data, .gff, give it the file name (it says it reads it correctly) I select the species and map set and it goes to work reading in the data. It reads in all the data and the purges the caches. When I check CMAP, it doesn't even display the species in the drop down menu. Looking at the database using DBVis, cmap_species table seems to contain the correct information, cmap_map_set seems to contain the correct information, but cmap_feature does not contain any of the features that it should have read in from the .gff file. The only differences I can see from when I imported data before and this time, is that this time i'm using a .gff rather than a cmap tab- delimited file and that this map is a 'physical' map rather than a 'genetic' one. Any thoughts? Thanks, -Andrew |
From: Lee A. <ope...@gm...> - 2009-05-14 17:36:19
|
2009/5/14 S <so...@ya...>: > > Hello, > I am trying to upload data using a tab-delimited file and have the errors like below. > DBD::Pg::db do failed: called with 4 bind variables when 2 are needed at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line 5316, <GEN5> line 218. > Sometimes I get different line numbers than 218 but I always get line 5316. > Does anybody have any idea? > > Thanks > > Sook > > > > > > ------------------------------------------------------------------------------ > The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your > production scanning environment may not be a perfect world - but thanks to > Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 > Series Scanner you'll get full speed at 300 dpi even with all image > processing features enabled. http://p.sf.net/sfu/kodak-com > _______________________________________________ > gmod-cmap mailing list > gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-cmap > I suppose that you might have duplicated entries in your files, so you should check your raw tab-delimited data if some duplicated data exist. HTH Amy |
From: S <so...@ya...> - 2009-05-14 14:31:07
|
Hello, I am trying to upload data using a tab-delimited file and have the errors like below. DBD::Pg::db do failed: called with 4 bind variables when 2 are needed at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line 5316, <GEN5> line 218. Sometimes I get different line numbers than 218 but I always get line 5316. Does anybody have any idea? Thanks Sook |
From: Sook J. <so...@gm...> - 2009-05-13 17:34:57
|
Hello, I am trying to upload data using a tab-delimited file and have the errors like below. DBD::Pg::db do failed: called with 4 bind variables when 2 are needed at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line 5316, <GEN5> line 218. Sometimes I get different line numbers than 218 but I always get line 5316. Does anybody have any idea? Thanks Sook |
From: Ken Youens-C. <kyc...@gm...> - 2009-04-01 19:31:46
|
On Apr 1, 2009, at 1:59 PM, Andrew Couperthwaite wrote: > Hi, > > I'm having a problem displaying correspondences on my system. > I created an evidence type called 'Ortholog_Detection' in my config > file: > ------ > <evidence_type Ortholog_Detection> > evidence_type_acc OD Andrew, Try making "evidence_type_acc" = "Ortholog_Detection." I think that's the problem. ky |
From: Andrew C. <aco...@gm...> - 2009-04-01 18:59:55
|
Hi, I'm having a problem displaying correspondences on my system. I created an evidence type called 'Ortholog_Detection' in my config file: ------ <evidence_type Ortholog_Detection> evidence_type_acc OD evidence_type Otholog Detection rank 1 color lightblue ribbon_color blue line_type direct evidence_default_display display <aggregated_correspondence_colors> 1 lightblue 20 blue 0 darkblue </aggregated_correspondence_colors> </evidence_type> ------ and then imported a list of the correspondences, a subset of which looked something like this: ------ feature_name1 feature_acc1 feature_name2 feature_acc2 evidence is_enabled g1 Map1-g1 g1a Map1-g3a Ortholog_Detection 1 g2 Map1-g2 g2a Map1-g2a Ortholog_Detection 1 g3 Map1-g3 g3a Map1-g3a Ortholog_Detection 1 ----- I restarted the webserver and purged all the caches using the cmap_admin.pl. I can see both maps, and add them left and right etc, but I can't see any correspondences between them (Ortholog_Detection is selected as 'use' under the correspondence options). If I view the feature details and select 'correspondence details' it shows both corresponding markers. Any idea why it's not drawing lines between them? Any help would be appreciated. Thanks, -Andrew |
From: Ken Youens-C. <ky...@gm...> - 2009-03-30 18:52:26
|
On Mar 29, 2009, at 9:53 AM, Lee Amy wrote: > I have imported the BLAST correspondences into maps by using > tab-delimited file. Anyway, I set up the "connecting_line_type" to > ribbon at the configuration file and set up "ribbon_color" to yellow > at evidence_type part. However, after I purge the cache data entirely > the the line of correspondence is still "direct", and the color is > blue. > > So could you tell me how to enable that by using ribbon? Amy, I'm not sure what the problem is. You might stop and start your server again to make sure the configuration is being read anew. ky |
From: Dave C. G. H. D. <gmo...@go...> - 2009-03-30 04:17:06
|
Hello all, ***The application deadline for both GMOD summer schools is April 6, one week from now.*** GMOD Summer School - Americas will be held 16-19 July at the National Evolutionary Synthesis Center (NESCent), in Durham, NC, USA. Student tuition is free. See http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas GMOD Summer School - Europe will be held 3-6 August at the University of Oxford, in Oxford, UK. This is a part of GMOD Europe 2009, which includes the next GMOD Meeting. Student tuition is £95. See http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe Please contact the GMOD Help Desk (he...@gm...) if you have questions. We hope to see you in Durham or Oxford, Dave C. On Mon, Mar 16, 2009 at 10:55 AM, Dave Clements, GMOD Help Desk <gmo...@go...> wrote: > Hello all, > > GMOD is offering two Summer Schools in 2009, one on each side of the > Atlantic. GMOD Summer Schools > (http://gmod.org/wiki/GMOD_Summer_School) introduce new GMOD users to > the GMOD project and include several days of hands-on training on how > to install, configure and administer GMOD tools. The 2008 GMOD Summer > School was a great success with 25 students from 4 countries in > attendance. > > Americas, 16-19 July > - at the National Evolutionary Synthesis Center (NESCent), Durham, NC, USA > - Student tuition is free, thanks to NIH grant 1R01HG004483-01. > - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas > > Europe, 3-6 August > - at the University of Oxford, Oxford, United Kingdom > - Part of GMOD Europe 2009, which includes the next GMOD Meeting > - Student tuition is £75 > - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe > > The schools will feature training on these GMOD components: > * GBrowse - the most widely installed genome viewer on the web > * Chado - a modular and extensible database schema > * Apollo - genome annotation editor > * BioMart - biological data warehouse system > * GBrowse_syn - a GBrowse based synteny viewer > * JBrowse - a brand new Web 2.0 genome browser > * Artemis-Chado Integration (Europe only) > * MAKER - Genome annotation pipeline (Americas only) > * Tripal - Web front end for Chado (Americas only) > > Applications for the 2009 GMOD Summer Schools are now being accepted. > > ***The deadline for applications is the end of the day, April 6.*** > > Enrollment is limited to 25 participants in each course. If > applications exceed capacity (and we expect they will) then applicants > will be picked based on the strength of their application. Applicants > will be notified of their admission status by mid April. > > Please contact the GMOD Help Desk if you have any questions. > > Thanks, > > Dave Clements > GMOD Help Desk > he...@gm... > > http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas > http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe > http://gmod.org/wiki/GMOD_Europe_2009 > |
From: Lee A. <ope...@gm...> - 2009-03-29 14:54:00
|
2009/3/25 Lee Amy <ope...@gm...>: > 2009/3/25 Ken Youens-Clark <ky...@gm...>: >> On Mar 25, 2009, at 10:16 AM, Lee Amy wrote: >> >>> I encounter some data import tasks in recent days and I have no idea >>> to deal with it correctly. >>> >>> There are two data sets A and B. I use NCBI BLAST to get results about >>> their identity. So The A data set will be map A and another will be >>> map B. My task is to make correspondence between the A's items and B's >>> items based on E-Vaule. For instance, I could set up a threshold 0.001 >>> so any E-Value of alignment pair between A and B will make a >>> correspondence. >>> >>> I don't know how to solve such problems. So could any one show me >>> some hints? >> >> Amy, >> >> If you have established meaningful feature accessions (in the >> "cmap_feature.feature_acc" field), then you simply need to create a >> tab-delimited file naming "feature_acc1," "feature_acc2," and the >> correspondence type to relate each of the A-B pairs that are above >> your threshold. >> >> ky >> >> ------------------------------------------------------------------------------ >> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are >> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and >> easily build your RIAs with Flex Builder, the Eclipse(TM)based development >> software that enables intelligent coding and step-through debugging. >> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com >> _______________________________________________ >> gmod-cmap mailing list >> gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-cmap >> > Thanks, Ken. I read mails at the list before I post. It seems there > are some similar problems I ever asked. Thank you very much. I could > use this way to process the results fast. > > Regards, > > Amy > Ken, I have imported the BLAST correspondences into maps by using tab-delimited file. Anyway, I set up the "connecting_line_type" to ribbon at the configuration file and set up "ribbon_color" to yellow at evidence_type part. However, after I purge the cache data entirely the the line of correspondence is still "direct", and the color is blue. So could you tell me how to enable that by using ribbon? Thanks very much. Amy |
From: Lee A. <ope...@gm...> - 2009-03-28 01:57:30
|
2009/3/28 Ken Youens-Clark <kyc...@gm...>: > On Mar 27, 2009, at 11:24 AM, Lee Amy wrote: > >> Thanks. I tried but still failed. However, I find something weird. >> When I set the map type is Physical map I cannot see the maps by such >> errors; if set up a sequence or genetics map I can see the map. > > Amy, > > I can't recall exactly how this works, but perhaps you don't have any > physical maps loaded? Can you send me the query output for the following: > > select count(*) from cmap_map_set > > select sp.species_acc, sp.species_full_name, ms.map_set_name > from cmap_species sp, cmap_map_set ms > where ms.species_id=sp.species_id > > ky > Ken, Sorry for late. Actually I don't know how to type your query SQL syntax properly. MySQL always shows errors. Could you write them in order? Thank you very much. Amy |
From: Lee A. <ope...@gm...> - 2009-03-27 16:25:18
|
2009/3/27 Ken Youens-Clark <kyc...@gm...>: > On Mar 27, 2009, at 9:51 AM, Lee Amy wrote: > >> Hi, I import two maps into a species named Y. But when I am going to >> change the data source to the database H who holds Y, CMap notices me >> that following errors. >> >> Ref. Species: No Data In This Data Source. >> >> So what happened? How do I fix that? >> >> Thank you very much. > > Amy, > > You may need to use the "cmap_admin.pl" tool to purge the data cache. > CMap tries to not look up information more than once if it can. > > ky > > ------------------------------------------------------------------------------ > _______________________________________________ > gmod-cmap mailing list > gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-cmap > Ken, Thanks. I tried but still failed. However, I find something weird. When I set the map type is Physical map I cannot see the maps by such errors; if set up a sequence or genetics map I can see the map. Amy |
From: Ken Youens-C. <kyc...@gm...> - 2009-03-27 15:39:20
|
On Mar 27, 2009, at 9:51 AM, Lee Amy wrote: > Hi, I import two maps into a species named Y. But when I am going to > change the data source to the database H who holds Y, CMap notices me > that following errors. > > Ref. Species: No Data In This Data Source. > > So what happened? How do I fix that? > > Thank you very much. Amy, You may need to use the "cmap_admin.pl" tool to purge the data cache. CMap tries to not look up information more than once if it can. ky |
From: Ken Youens-C. <kyc...@gm...> - 2009-03-27 15:37:55
|
On Mar 25, 2009, at 10:43 PM, Lee Amy wrote: > How to cite CMap at paper? Thanks very much. Amy, This has been a long-standing problem as there's never been a CMap paper. Just reference the GMOD website: http://gmod.org/cmap ky |
From: Lee A. <ope...@gm...> - 2009-03-27 14:51:54
|
Hi, I import two maps into a species named Y. But when I am going to change the data source to the database H who holds Y, CMap notices me that following errors. Ref. Species: No Data In This Data Source. So what happened? How do I fix that? Thank you very much. Amy |
From: Lee A. <ope...@gm...> - 2009-03-26 03:43:09
|
Hi, How to cite CMap at paper? Thanks very much. Amy |
From: Lee A. <ope...@gm...> - 2009-03-25 15:40:27
|
2009/3/25 Ken Youens-Clark <ky...@gm...>: > On Mar 25, 2009, at 10:16 AM, Lee Amy wrote: > >> I encounter some data import tasks in recent days and I have no idea >> to deal with it correctly. >> >> There are two data sets A and B. I use NCBI BLAST to get results about >> their identity. So The A data set will be map A and another will be >> map B. My task is to make correspondence between the A's items and B's >> items based on E-Vaule. For instance, I could set up a threshold 0.001 >> so any E-Value of alignment pair between A and B will make a >> correspondence. >> >> I don't know how to solve such problems. So could any one show me >> some hints? > > Amy, > > If you have established meaningful feature accessions (in the > "cmap_feature.feature_acc" field), then you simply need to create a > tab-delimited file naming "feature_acc1," "feature_acc2," and the > correspondence type to relate each of the A-B pairs that are above > your threshold. > > ky > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > gmod-cmap mailing list > gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-cmap > Thanks, Ken. I read mails at the list before I post. It seems there are some similar problems I ever asked. Thank you very much. I could use this way to process the results fast. Regards, Amy |
From: Ken Youens-C. <ky...@gm...> - 2009-03-25 15:33:18
|
On Mar 25, 2009, at 10:16 AM, Lee Amy wrote: > I encounter some data import tasks in recent days and I have no idea > to deal with it correctly. > > There are two data sets A and B. I use NCBI BLAST to get results about > their identity. So The A data set will be map A and another will be > map B. My task is to make correspondence between the A's items and B's > items based on E-Vaule. For instance, I could set up a threshold 0.001 > so any E-Value of alignment pair between A and B will make a > correspondence. > > I don't know how to solve such problems. So could any one show me > some hints? Amy, If you have established meaningful feature accessions (in the "cmap_feature.feature_acc" field), then you simply need to create a tab-delimited file naming "feature_acc1," "feature_acc2," and the correspondence type to relate each of the A-B pairs that are above your threshold. ky |
From: Lee A. <ope...@gm...> - 2009-03-25 15:16:24
|
Hi, I encounter some data import tasks in recent days and I have no idea to deal with it correctly. There are two data sets A and B. I use NCBI BLAST to get results about their identity. So The A data set will be map A and another will be map B. My task is to make correspondence between the A's items and B's items based on E-Vaule. For instance, I could set up a threshold 0.001 so any E-Value of alignment pair between A and B will make a correspondence. I don't know how to solve such problems. So could any one show me some hints? Thanks very much. Regards, Amy Lee |
From: Dave C. G. H. D. <gmo...@go...> - 2009-03-16 17:55:24
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Hello all, GMOD is offering two Summer Schools in 2009, one on each side of the Atlantic. GMOD Summer Schools (http://gmod.org/wiki/GMOD_Summer_School) introduce new GMOD users to the GMOD project and include several days of hands-on training on how to install, configure and administer GMOD tools. The 2008 GMOD Summer School was a great success with 25 students from 4 countries in attendance. Americas, 16-19 July - at the National Evolutionary Synthesis Center (NESCent), Durham, NC, USA - Student tuition is free, thanks to NIH grant 1R01HG004483-01. - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas Europe, 3-6 August - at the University of Oxford, Oxford, United Kingdom - Part of GMOD Europe 2009, which includes the next GMOD Meeting - Student tuition is £75 - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe The schools will feature training on these GMOD components: * GBrowse - the most widely installed genome viewer on the web * Chado - a modular and extensible database schema * Apollo - genome annotation editor * BioMart - biological data warehouse system * GBrowse_syn - a GBrowse based synteny viewer * JBrowse - a brand new Web 2.0 genome browser * Artemis-Chado Integration (Europe only) * MAKER - Genome annotation pipeline (Americas only) * Tripal - Web front end for Chado (Americas only) Applications for the 2009 GMOD Summer Schools are now being accepted. ***The deadline for applications is the end of the day, April 6.*** Enrollment is limited to 25 participants in each course. If applications exceed capacity (and we expect they will) then applicants will be picked based on the strength of their application. Applicants will be notified of their admission status by mid April. Please contact the GMOD Help Desk if you have any questions. Thanks, Dave Clements GMOD Help Desk he...@gm... http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe http://gmod.org/wiki/GMOD_Europe_2009 |
From: Ken Youens-C. <kc...@cs...> - 2009-01-20 23:51:40
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On Jan 20, 2009, at 11:14 AM, Chantal Hamelin wrote: > Hi, > > We have created a map in CMAP where there are features such as > markers and QTLs. QTLs were first named with a number but we changed > our mind and decided to rename them by concatening the trait name > and the number. For instance the QTL n°1195 for the trait Days to > flowering became Days_to_flowering_1195. We changed directly the > feature_name in the cmap_feature table in CMAP but the result is the > following (see below), only one map (no 10) over 12 displays the > QTLs with their new names, the others maps still displays the QTLs > with their old feature_name (a number). We saw also that if we > change the total magnification on map 10 (for instance we choose 2) > the QTLs are displayed with their old name (a number). Afterwards if > we use the previous magnification the old QTL names (numbers) are > still displayed, we cannot display again the QTLs with their new > names. > A detail is that the map 10 is the one which has the fewer number of > markers and QTLs. > It seems that the feature_name displayed varies with the > magnification of the map but we don't understand why at the original > magnification one map only (no 10) if displayed as we want. > > > Can you help us ? Chantal, Have you reset the cache? If not, use "cmap_admin.pl" on the server where CMap is running and choose "[10] Purge the cache to view new data." I believe that should help. > Another problem is the length varchar(32) of the feature_name in > table cmap_feature, can we increase this length ? Yes, just use the "ALTER TABLE" command in MySQL. It shouldn't hurt anything, but remember to do this again in the future should you move to a new db. ky |
From: Chantal H. <cha...@ci...> - 2009-01-20 17:15:06
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Hi, We have created a map in CMAP where there are features such as markers and QTLs. QTLs were first named with a number but we changed our mind and decided to rename them by concatening the trait name and the number. For instance the QTL n°1195 for the trait Days to flowering became Days_to_flowering_1195. We changed directly the feature_name in the cmap_feature table in CMAP but the result is the following (see below), only one map (no 10) over 12 displays the QTLs with their new names, the others maps still displays the QTLs with their old feature_name (a number). We saw also that if we change the total magnification on map 10 (for instance we choose 2) the QTLs are displayed with their old name (a number). Afterwards if we use the previous magnification the old QTL names (numbers) are still displayed, we cannot display again the QTLs with their new names. A detail is that the map 10 is the one which has the fewer number of markers and QTLs. It seems that the feature_name displayed varies with the magnification of the map but we don't understand why at the original magnification one map only (no 10) if displayed as we want. Another problem is the length varchar(32) of the feature_name in table cmap_feature, can we increase this length ? Can you help us ? Best regards. ?cmap -- Chantal HAMELIN CIRAD - Département Systèmes Biologiques UMR Développement et Amélioration des Plantes - Equipe Intégration des données TA A96/03 Avenue Agropolis 34398 Montpellier Cedex 5 FRANCE Tél : (33) 4 67 61 59 75 Fax : (33) 4 67 61 56 05 mailto:cha...@ci... |