Hello! Guest! Please Login or Register! Log Out

Feedback Archive

N.O. Date First Name Last Name Email Institution Subject Webpage Comments
3312006-08-29 21:59:08RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules/PD_browse/expsummary.php?Table for Hybridizations for TA3 has multiple repeats for hybridizations (TA3-H1, TA3-H2, etc.); please inspect and correct the table
3302006-08-28 19:49:59RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules/PD_browse/expsummary.php?Exp. summary info and boxplots, etc. displays the old TA3 (30 hybs); not the new TA3 (39 hybs)
3292006-08-28 19:31:59RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules//PD_probeset/timeplotviewer.php?Probeset_name=Ta.10069.1.S1_at&Analysis;=rma&Scale;=probeset&Experiment;_no=TA1&chipdesign;=WheatExpression of Ta.10069.1.S1_at in This probeset is not on the GeneChip design you have chosen. Please choose the appropriate GeneChip. This is incorrect ; it is a wheat probe set on wheat experiment (TA1)
3282006-08-28 19:28:59RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules/PD_browse/expsummary.php?\"Regular\" version display seems correct. High res dispay has multiple repeats of each hybridization [TA3-H2->H7; TA3-H8 -> H27; etc.] Just inspect and fix
3272006-08-28 02:04:38RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules//PD_probeset/timeplotviewer.php?Probeset_name=Ta.10069.1.S1_at&Analysis;=rma&Scale;=probeset&Experiment;_no=TA3&chipdesign;=WheatSeems just as bad or worse on high-resolution RMA display
3262006-08-28 02:01:18RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules//PD_probeset/timeplotviewer.php?Experiment_no=TA3&Probeset;_name=Ta.10069.1.S1_at&Analysis;=mas&chipdesign;=WheatHigh res time plot viewer has extra dat points on it (TA3-H1, TA3-H8, TA3-H9, etc.)
3252006-08-24 04:23:10RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules//PD_probeset/timeplotviewer.php?Experiment_no=TA3&Probeset;_name=Ta.10069.1.S1_at&Analysis;=mas&chipdesign;=Wheatwheat TA3 expression viewer does not work - can we fix it by next week fort the ITMI meetuing that I will be attending in Adelaide
3242006-08-23 05:12:02daverobertsddervish@hotmail.comscriDead link http://www.plexdb.org/modules//Your_Account/index.php?op=updateDonehi im trying to download the datafile for the experiement \"Barley cv Morex inoculated with Fusarium graminearum and water as mock control\" Accession NO BB9 but its a dead link, can you help please? thanks dave
3232006-08-11 08:34:03RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/index.php?Under Data Submission: expriments is misspelled Why Log in? Submit an experiment through Barley/PLEXExpress View your private expriments and group protected experiments Create and modify groups Update your personal information Login ID: Password:
3222006-08-08 03:31:27JanetHigginsJanet.Higgins@bbsrc.ac.ukJohn Innes Centredata analysis - no results http://www.plexdb.org/modules//PD_dataSelection/genelist_analysis.php?I have created 2 gene lists BB3 and BB4 flowering (hordeumjah_D33 and D32) and have tried to analysis the gene lists using hierachical clustering but I do not get any results
3212006-08-05 16:39:23lingzhanglzhang1@wsu.eduwashington state universityproblem submitting microarray data http://barleybase.org/index.phpHello: I would like to deposit a Barley1 microarray data, I submitted one experiment successfully before, but this time I just could not upload my data. What could be the problem? My data is contained in 8 CDs, each CD contains a CAB file, so I tried to upload one at a time, but it just did not upload. Pls give me detailed instructions, Thank you. Ling
3202006-08-03 15:19:15RicoCaldoracaldo@iastate.eduISUData download error http://www.plexdb.org/modules/PD_general/download_exp.php?exp_no=BB10I downloaded the CEL files from BB10 but they were not the right files. I have gotten 4 files from a different experiment instead of 144 files from the BB10 experiment.
3192006-08-02 11:30:59RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules//PD_probeset/timeplotviewer.php?Experiment_no=TA3&Probeset;_name=Ta.10069.1.S1_at&Analysis;=mas&chipdesign;=WheatTA3 shows old expression plots - or are you still working on this?
3182006-07-31 18:50:52DonaldGardinerdonald.gardiner@csiro.auCSIROProblem searching BarleyBase http://www.plexdb.org/modules//PD_probeset/contig_fusarium.php?Hi, Thanks for fixing yesterday\'s problem. I now am looking at fusarium genes and although I can find the genes I am looking for, there does not appear to be any expression details links under the probe sets section. I am pretty sure that in the past (maybe at barleybase) I could see information here. Cheers Don
3172006-07-30 21:27:54DonaldGardinerdonald.gardiner@csiro.auCSIROdifficulties with seeing expression data for particular genes http://www.plexdb.org/modules/PD_probeset/probeset.php?Hi, I have been trying to view the expression details for just two genes (Barley1_05994 and Barley1_06992) in experiment BB9. However whenever I find these sequences and click on the link for view expression details and then change the experiment to BB9 I am always shown the expression details for Contig2021_at. Am I doing something wrong? Regards Donald
3162006-07-19 08:37:42RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules/PD_dataSelection/browsesample.php?When I select TA3 under sample infomation I get a Fusarium experiment
3152006-07-19 08:33:11RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules//PD_probeset/timeplotviewer.php?Probeset_name=Contig2021_at&Analysis;=mas&Scale;=probeset&Experiment;_no=BB21&chipdesign;=Barley1High-resolution visualization keeps defaulting to MAS 5; won\'t stay on RMA if it is selected - though the default picture is RMA and thepull-down says MAS 5
3142006-07-13 16:35:33RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=WheatGramene link broken -> http://dev.gramene.org/Oryza_sativa/featureview?type=DnaAlignFeature&id;=Ta.10069.1.S1_at View Exemplar Annotation and Probe Set Details OR EST contig alignment of exemplar at PlantGDB Is NOT present under wheat genechip probe alignments
3132006-07-11 14:43:15RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules/PD_dataSelection/blast2expression2.php?When I Blast Barley1 GeneChip and then click on \"Barley1_05126\" I get error message
3122006-07-10 12:34:12RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules/PD_general/news.php?Walbot V, Wise RP,5 and Buckler ES has been...... should be: Walbot V, Wise RP, and Buckler ES has been
3112006-07-10 09:35:40RogerWiserpwise@iastate.eduISUDatabase improvement http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Barley13. BEST BLASTX PLANTS: 10/14/03 1. S05510 0 pir|| glucan endo-1,3-beta-D-glucosidase (EC 3.2.1.39) II precursor - barley Length = 334; 2. gb|AAA32958.1 0 1,3-beta glucan endohydrolase precursor [Hordeum vulgare] Length = 334; 3. sp|P15737 0 E13B_HORVU Gluca more Is this really based on a 10/14/03 Blast? Also, the top hit is not hyperlinked.
3102006-07-07 16:27:19RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules/PD_dataSelection/experiments.php?class=experiment&expName;=anyWhen you click on \"Available Data\" under \"Accessible\" experiments, a lot of junk appears at the top of the page
3092006-07-06 02:14:16PatrickSchweizerschweiz@ipk-gatersleben.deIPKProblem searching BarleyBase http://www.barleybase.org/index.phpHi, A few weeks ago I batch downloaded RMA data from experiment BB9 (Fusarium-infected barley). Some of these data went into a paper that is now in press in Plant Physiology. Unfortunately BB9 data are currenty not available, which produces a problem for our paper. Why are these data not accessible at the moment? Best wishes, Patrick Schweizer
3082006-07-04 11:32:42Jian-Minzhoujianmzho@alcor.concordia.caPlant Biochemistry LabNone http://www.barleybase.org/people.phpI am very interested in studying one barley gene. Would you please tell me where and how I can order this gene (full-length cDNA clone)? Thanks.
3072006-06-23 15:45:07RogerWiserpwise@iastate.eduISUDatabase improvement http://www.plexdb.org/modules//PD_probeset/probeset.php?chipdesign=Barley1&probeset;=HVSMEm0003C15r2_s_atLow-resolution gene expression plot is not working Eliminate this picture and replace with high-resolution plot on same page with: Probe-Level Intensities View, download probe values, and draw barplots Expression Statistics Estimation Min. 1st Qu. Median Mean 3rd Qu. Max HVSMEm0003C15r2_s_at and Co-expressed Genes in AT4: Expression View (rma) and Details etc. AT4 for barley probeset?? Make MAS 5.0 the default
3062006-06-22 08:44:20RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules/PD_dataSelection/expsummary.php?experiment=ZM1Wrong data release poicy statement under PLEX express upload: ie., BarleyBase Current Working Policy for Data Submission and Release: BarleyBase is committed to making data from the Barley1 GeneChip publicly available to researchers world-wide. The default assumption is that all submissions to BarleyBase are public unless you advise us otherwise during the submission process. Data submissions can be designated as private to the submitter for a period of 90 days. This means that only a user with the proper password can access the data. At the end of the 90 day period, the submitter will be automatically contacted to see if the data can be made public or if additional time is needed due to publication or manuscript preparation delays. If approval for public release has not been received within one year of initial submission, the data will be deleted from BarleyBase. The submission will be checked for structure and content during curation and only BarleyBase curators have access to the submission during this time. Submissions will be prioritized in the following order: 1. Submissions that are to be made public immediately regardless of publication status. 2. Submissions that require database accession information in page proof. 3. Private submissions that are related to a paper that has not yet been accepted. 4. Private submissions that are related to a paper that has not been submitted. Data will not be added to the database until a submission is complete and has been examined by a data curator. If we need to contact you about your submission, please respond as quickly as possible so that there will be no delays in making your data available on BarleyBase. The estimated release time is seven days to make a submitted dataset available on the public BarleyBase database.
3052006-06-21 14:31:25RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Maize18kTIGR Maize 18K Gene Index should be TIGR Maize Gene Index
3042006-06-19 09:24:12JanetHigginsjanet.higgins@bbsrc.ac.ukJohn Innes CentreProblem searching BarleyBase http://www.barleybase.org/probealign.phpI am having two problems 1. I cannot generate a gene list, I paste the barley1 probe names into the input gene list box but it does not recognise any of them. For example I have tried both Contig5247_at and Barley1_05247. 2. I would like to access the expression plots for BB8 for Barley1_05247 but it return "Error in factor level". I can access the expression plots for the other barley expts
3032006-06-16 11:33:55RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules//PD_probeset/timeplotviewer.php?Probeset_name=Contig12219_at&Analysis;=rma&Scale;=probeset&Experiment;_no=BB16&chipdesign;=Barley1BB16 appears twice in the pull-down menu under expression visualization
3022006-06-01 10:46:29EthalindaCannonethy@a415software.comISUThis is another test http://barleypop.vrac.iastate.edu/plexdb/rebuild/html/xin//modules/PD_general/feedbackcgi.php?Another test. Sorry All!
3012006-06-01 10:41:51EthyCannonethy@a415software.comISUThis is a test http://barleypop.vrac.iastate.edu/plexdb/rebuild/html/xin//modules/PD_general/feedbackcgi.php?This is only a test.
3002006-05-23 12:27:34JulieDickersonjulied@iastate.eduISUSite improvement http://www.plexdb.org/index.php?This is a test to see where the email goes.
2992006-05-23 11:08:28MarkJordanmcjordan@agr.gc.caAAFCDead link http://www.plexdb.org/modules//Your_Account/index.php?op=associateIn trying to associate experiments with groups to grant access to others the \"change\" link is dead. Is there another way to assign groups to experiments?
2982006-05-22 18:32:00DonaldGardinerdonald.gardiner@csiro.auCSIROProblem searching BarleyBase http://www.barleybase.org/myresult.phpHi, I am having trouble seeing my gene lists after I create them. I seem to be given names for them which are a extension of my email address, but when I come to do for example clustering there is no gene lists to choose from in the drop down box or in the gene list management page. Cheers Don
2972006-05-18 09:20:54MarkJordanmcjordan@agr.gc.caAg CanadaReviewer ID http://www.plexdb.org/modules/PD_general/feedbackarchive.php?I see others have created multiple accounts for manuscript reviewers under their email addresses. When I tried to create a reviewer account I got the message \"that email has already been used - try another one\". How do I create reviewer account under my name? On another note I see that someone else asked whether multiple reviewers could use one reviewer account thus avoiding creating several accounts for each manuscript - I would like to know this as well. It might be handy to also post the answers to the feedback questions to avoid answering the same ones over and over.
2962006-05-18 08:19:43RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules/PD_dataSelection/browsesample.php?Complete descriptions - Developmental stage and organism part are missing for the sample descriptions for BB4
2952006-05-17 15:46:54RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Maize8khttp://www.gramene.org/multi/blastview Gramene alignment point to wrong page
2942006-05-15 16:53:54RogerWiserpwise@iastate.eduISUSite improvement http://www.plexdb.org/modules/PD_dataSelection/expsummary.php?experiment=BB3What happened to \"your data folder\" on the left hand side of the page?
2932006-05-13 11:37:36RogerWiserpwise@iastate.eduISUSite improvementwhy are all the experiments in random order here?: http://plexdb.org/modules/PD_dataSelection/experiments.php?class=experiment&expName;=any Its difficult for the user toscan experiments from a particular organism
2922006-05-12 19:11:15RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules//PD_probeset/probeset.php?chipdesign=Wheat&probeset;=Ta.10069.1.S1_atI can\'t access any other wheat exp but Ta1; even when I am logged in
2912006-05-10 13:50:11RogerWiserpwise@iastate.eduISUWhat I don't like about BarleyBase http://www.plexdb.org//modules/PD_general/feedbackcgi.php?Tools menu on left side menu should be expanded as the default. This is the way it used to be; but now a new user (or proposal reviewer) has to work to see the tools
2902006-05-10 13:47:21RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules/PD_general/publications.php?An atlas of gene expression from seed to seed through barley development. Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R Functional & Integrative Genomics. 2006 Mar does not point correctly link should be: http://www.springerlink.com/(fvod2h55uaepr045zs5zfq3e)/app/home/contribution.asp?referrer=nav&backto;=issue,5,10;journal,1,24;linkingpublicationresults,1:105695,1;&nav;_parent_next.x=1
2892006-05-08 11:58:59MarkJordanmcjordan@agr.gc.caAAFCData error http://www.plexdb.org/classic/BarleyExpress/experiment_design/experiment_design_summary.phpI had previously finalized a submission which was given the accession TA5. Eventually all the data was looked at and appeared for analysis and the experiment appeared as \"finalized\" in \"browse my submissions\". Then the experiment disappeared from my experiment list and when I checked \"browse your submissions\" it appeared that it had been un-finalized. I have re-finalized the data and now it has been given the accession AT9. Could it be given TA5 back? Can I get it looked at fairly soon? Thanks.
2882006-05-04 12:18:11RogerWiserpwise@iastate.eduISUSite improvement http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=SoybeanCystNematode&tmva;=0|3|4|8|12|13|19|22|23|63|65|Tools menu on the left of front page should be expanded (as the default) so readers can see it immediately
2872006-05-04 12:15:23RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules/PD_general/publications.php?link does not work for Atlas of Gene Expression Try this: http://www.springerlink.com/(fvod2h55uaepr045zs5zfq3e)/app/home/contribution.asp?referrer=nav&backto;=issue,5,10;journal,1,24;linkingpublicationresults,1:105695,1;&nav;_parent_next.x=1
2862006-05-04 11:31:40RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/index.phpFront page pull down menus do not work on barleybase classic
2852006-05-04 08:47:55RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules/PD_dataSelection/experiments.php?class=experiment&expName;=Mla-specified+Transcriptional+Responses+in+Barley-Powdery+Mildew+InteractionsExperimental access does not work from the rigt side of the front page (for al exps.) e.g., http://www.plexdb.org/modules/PD_dataSelection/experiments.php?class=experiment&expName;=Mla-specified+Transcriptional+Responses+in+Barley-Powdery+Mildew+Interactions
2842006-05-03 16:38:23RogerWiserpwise@iastate.eduISUDatabase improvement http://www.plexdb.org/modules//Your_Account/index.php?op=updateDoneOld PLEX policy at personal data page
2832006-05-03 16:22:35RogerWiserpwise@iastate.eduISUProblem searching BarleyBase http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Maize18kMaize 18K probes not correctly aligned to rice genome browzer
2822006-05-02 12:26:02RogerWiserpwise@iastate.eduISUWhat I like about BarleyBase http://www.plexdb.org/index.php?test of feedback site
2812006-05-02 09:05:17RogerWiserpwise@iastate.eduISU http://www.plexdb.org/modules//Your_Account/index.php?Test
2802006-04-27 13:32:30MarkJordanmcjordan@agr.gc.caAAFCData error http://www.plexdb.org/modules/PD_dataSelection/expsummary.php?experiment=AT21I submiited wheat data but it has an AT# rather than a TA#. In addition it was submitted on March 31 but the data does not yet show up in the experiment visualization.
2792006-04-25 10:15:27EthalindaCannonethy@a415software.comISUThis is a test http://barleypop.vrac.iastate.edu/plexdb/rebuild/html/xin//modules/PD_general/feedbackcgi.php?This is a test. It is only a test.
2782006-04-25 09:18:01EthalindaCannonethy@a415software.comISUThis is a test http://www.plexdb.org/index.php?This is a test. It is only a test.
2772006-04-25 08:18:48RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Maize58kThe Gramene alignment for the Maize 58K array is not consistent with other chips I get this page: http://www.gramene.org/multi/blastview
2762006-04-24 17:52:25ElizabethTattersalleat@unr.nevada.eduUNRProblem searching BarleyBase http://www.barleybase.org/mydataset.phpWhen I compared two gene lists from the same experiment, and tried to save some of the results as a new gene list, it told me I could not be cause they were not the same chip type. yet, I had chosen the same experiment in the field at the bottom. I tried this twice (starting over for 2nd time) with same result. Please fix this problem. Thank you. WARNING: VV1 is not of the same GeneChip type as your starting gene list. Please choose a compatible experiment. I had selected VV1, and lists 278 and 275, both from VV1.
2752006-04-09 17:11:34RogerThilmonythilmony@pw.usda.govUSDA-ARS Western Regional Research Centerdata download problem http://www.plexdb.org/modules.php?name=PD_general&page;=downloadfile.php&exp;_no=BB9Hi I am trying to do a batch download of data from the \"Barley cv Morex inoculated with Fusarium graminearum\" BB9 dataset. Unfortunately, when I click on download a new Explorer page opens without anythin on it. Can you instruct me how to successfully download the data? Thanks
2742006-03-27 17:11:09RicoCaldoracaldo@iastate.eduISUImpot Gene List Error http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=genelists.php&op;=querySingleThe import gene list function is not working, the step-by-step procedure is left hanging in Step 4 without any continuation. The import gene list function is very important in getting annotations, expression analysis, etc. Users usually have their own gene lists from their own analyses, and they need to upload their gene lists to plexdb to utilize available tools.
2732006-03-26 02:49:03MatthewMoscoumoscou@iastate.eduISUData error http://www.plexdb.org/modules.php?name=PD_general&page;=downloadfile.php&exp;_no=BB1The download page is not working. Also... when logging in on the site, I go to a screen that says \"Restricted Area\" etc....
2722006-03-21 14:59:10RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Maize18kAll Gramene - maize alignments do not point to the right location
2712006-03-21 12:12:30RogerWiserpwise@iastate.eduISUDatabase improvement http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=expsummary.php&experiment;=FG3FG1, 2, and 4 are listed at the top of the experiments. FG3 is below Arabidopsis. Why aren\'t they together - it is confusing
2702006-03-16 12:55:20RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Barley1On the Gramene entry page, under the \"Location of hits\" section, select one of the locations to go to the genome browser (ContigView) page, then under \"Detailed view\" section, select \"arrays\" menu and check the platforms to be displayed. This should be the language on the Barley1 annotation page, not what is currently there. Why does the old incoorrect language keep re-appearing?
2692006-03-15 14:07:59MarkJordanmcjordan@agr.gc.caAg CanadaData error http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=queryExperiments.phpI submitted a wheat experiment and received an AT acession number. Further, I received AT9. AT9 is already used by another experiment (Arabidopsis aluminum tolerance). I can\'t access my experiment as the other AT9 only shows up.
2682006-03-10 15:27:09RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_general&page;=news.phpYou can now search your seuences against all species in our PLEXdb. sequences is misspelled; delete the word \"our\"
2672006-03-06 14:34:17RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=expsummary.php&experiment;=BB2Not Found The requested URL /testls/BB2/tmp/boxplot_exprsMASNorm.png was not found on this server. Apache/2.0.52 (Red Hat) Server at www.plexdb.org Port 80 I get this message for BB2; 3. Boxplot of Affymetrix MAS5.0 expression (log2-scale): The distribution of Affymetrix MAS5.0 expression values for different hybridizations. 4. Histogram of raw PM intensities: The raw PM intensity change in distribution for different hybridizations. AND EVERTHING for BB10; BB20; BB21;and BB28
2662006-03-06 13:29:47RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=experiments.phpBB28 has two expriments atached to it. They should be separate accessions
2652006-03-06 11:24:48RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=SoybeanPhytophthoraYou have BarleyBase blast listed on a Phytophthora page Also TIGR soybean gene index?
2642006-03-02 11:20:58RogerWiserpwise@iastate.eduISUDatabase improvement http://plexdb.org/modules.php?name=PD_dataSelection&page;=experiments.php&class;=experiment&expName;=anyWhen the public sees this page, only the submitter\'s name is visible. Should also have the original data generator
2632006-03-01 15:04:23RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=blast2expression.phpBlast to expression not functional
2622006-03-01 14:15:22RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Rice20kGenome Alignment at Gramene and ZmGDB. Shouldn\'t this be Genome Alignment at Gramene and OsGDB. ? For rice NSF 20K array
2612006-03-01 14:14:50RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Rice20kGenome Alignment at Gramene and ZmGDB. Shouldn\'t this be Genome Alignment at Gramene and OsGDB. ? For rice NSF 20K array
2602006-03-01 11:33:52RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Rice57kGenome Alignment at Gramene On the Gramene entry page, under the \"Location of hits\" section, select one of the locations to go to the genome browser (ContigView) page, then under \"Detailed view\" section, select \"arrays\" menu and check the platforms to be displayed. This should be on every \"cereal\" page not the statement currently on the barley page
2592006-03-01 11:23:32RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=Your_Account&op;=experimentsAssociate with the expriments. should be Associate with the experiments.
2582006-03-01 08:53:01RogerWiserpwise@iastate.eduISUData error http://www.plexdb.org/modules.php?name=PD_probeset&page;=timeplotviewer.php&Experiment;_no=BB8&Probeset;_name=HVSMEm0003C15r2_s_at&Analysis;=masError in factor level! is all I get when trying to view the high resolution plot from BB8
2572006-02-28 15:45:30RyanRapprrapp@iastate.eduISUNone http://www.barleybase.org/downloadlog.phpIs there anyway to have the distance matrix from the clustering analysis output as well? That would be most helpful....
2562006-02-28 08:21:20RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=WheatOn the wheat annotation page the Gramene instructions are for barley It should be \"On the Gramene entry page, under the \"Location of hits\" section, select one of the locations to go to the genome browser (ContigView) page, then under \"Detailed view\" section, select \"arrays\" menu and check the platforms to be displayed. \" Check this for all Gramene instructions for maize, barley, wheat, and rice
2552006-02-27 22:24:53JacksonMoellerjacksonr@iastate.eduIowa StateProblem searching BarleyBase http://www.barleybase.org/get_seq.phpi tried to do a bulk download of the barley exemplars. I've done it numerous times before. It did not work in either explorer or firefox the evening of feb 27, 2006. Please test this and let me know if & when it is working. Thank you!
2542006-02-24 16:54:16RicoCaldoracaldo@iastate.eduISUData Submission Error http://www.plexdb.org/modules.php?name=Your_AccountI tried to submit an experiment, but in the uploading page I got this error message below. Failed to open a file /usr/barleypop/www/html/plexdb/html/classic/BarleyExpress/Upload/JUpload_525.php
2532006-02-24 16:29:08EveWurtelemash@iastate.eduISUhelp with login ID http://www.barleybase.org/feedbackarchive.phpHello, isn't my login ID mash@iastate.edu ? I have tried that and every other one I could think of withthe new password BB just sent me. Thanks, Eve
2522006-02-22 08:43:56RogerWiserpwise@iastate.eduISUTypo http://barleybase.org/barley1_probeset.phpMake language consistent with what is posted on PLEX
2512006-02-17 08:37:01RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Maize18kGenome Alignment at Gramene and ZmGDB will be available soon should be on this page
2502006-02-15 08:47:33RogerWiserpwise@iastate.eduISUDead link http://plexdb.org/index.php?tmva=0|4|8|65|Rice Genome Mapper is gone - we need it up right away for grant reviews. Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator, webadm@vrac.iastate.edu and inform them of the time the error occurred, and anything you might have done that may have caused the error. More information about this error may be available in the server error log. Apache/2.0.52 (Red Hat) Server at www.barleybase.org Port 80
2492006-02-11 16:53:00RicoCaldoracaldo@iastate.eduISUGenelist Comparison not working http://barleybase.org/mydataset.phpThe Comparison of two Genelists Tool is not working properly (I used Mac when I tried it).
2482006-02-11 16:48:22RicoCaldoracaldo@iastate.eduISUGO tool not working http://barleybase.org/funcstat4.phpI tried the GO classification tool (Expression2Function) but it is not working.
2472006-02-10 16:21:14RogerWiserpwise@iastate.eduISUData error http://plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Barley1You show the PUT assemblies for the Affy contigs. The Affy contigs are the original archive pages for Barley1 in BarleyBase with contigs from HarvEST
2462006-02-10 16:18:55RogerWiserpwise@iastate.eduISUSite improvement http://plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=WheatOnly 1/2 of the PUT assemblies for wheat. How about for e.g., http://www.plantgdb.org/search/display/data.php?Seq_ID=PUT-151a-Triticum_aestivum-10069 for part A
2452006-02-10 14:42:35RogerWiserpwise@iastate.eduISUSite improvement http://plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Maize58kNeed \"PUT\" assemblies for NSF maize and rice arrays. I know Qunfeng has them for Maize.
2442006-02-10 12:26:45RogerWiserpwise@iastate.eduISUSite improvement http://www.plexdb.org/modules.php?name=PD_probeset&page;=barley1_probeset.php&chipdesign;=Poplar&probeset;=Ptp.1088.1.S1_s_atI don\'t get the statement \"No matching chip design has your input probe set. Or no expression data is available for the probe set yet. Please verify your input and try again.\" This was a direct link from \"expression details\" from the probe page - this is not possible. Use the statement we agreed upon.->> We apologize, but you do not have access to expression data from experiments of this array design type before they are published or released by the contributors. You can obtain access by requesting to join a suitable group [please see: http://www.plexdb.org/modules.php?name=Your_Account&op;=groups.]
2432006-02-09 10:07:55RogerWiserpwise@iastate.eduISUDatabase improvement http://plexdb.org/index.php?still need the user log on back on the front page
2422006-02-07 11:28:40RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=timeplotviewer.php&Probeset;_name=Zm.10134.1.A1_at&Analysis;=mas&Scale;=probeset&Experiment;_no=ZM1The probeset does not exists in the experiment. Should be: This probeset is not on the GeneChip design you have chosen. Please choose the appropriate GeneChip.
2412006-02-03 10:37:15RogerWiserpwise@iastate.eduISUDatabase improvement http://plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Wheat \"Please input chip designator.\" Should be: Please input probe set designator. on ALL annotation pages
2402006-01-26 09:17:30RogerWiserpwise@iastate.eduISUTypo http://plexdb.org/modules.php?name=PD_probeset&page;=barley1contig.phpPlease input chip designator. should be: Please input probe set designator.
2392006-01-24 14:14:11RogerWiserpwise@iastate.eduISUSite improvement http://plexdb.org/modules.php?name=PD_probeset&page;=barley1_probeset.php&chipdesign;=Grape&probeset;=1607001_atSorry, your seem don\'t have access to any experiment of this array design type, so no expression data will be shown. Please obtain access by requesting joining a suitable group should be: We apologize, but you do not have access to expression data from experiments of this array design type before they are published or released by the contributors. You can obtain access by requesting to join a suitable group [see http://plexdb.org/modules.php?name=Your_Account&op;=groups].
2382006-01-23 17:08:02RogerWiserpwise@iastate.eduISUTypo http://plexdb.org/index.php?Legume Information Service (LIS) should be: Legume Information System (LIS),
2372006-01-23 09:00:58RogerWiserpwise@iastate.eduISUSite improvement http://plexdb.org/index.php?tmva=0|1|3|4|6|8|12|17|20|21|27|Both the user login and the News section describing how many experiments have been submitted are missing from the front page. This is a reminder to put them back.
2362006-01-18 12:13:11RogerWiserpwise@iastate.eduISUDead link http://plexdb.org/modules.php?name=PD_dataSelection&page;=runsetup4.php&inputfile;=_ZM18K1_probevalues.txt&experiment;=ZM18K1Probe-Level Intensity Visualization for _ZM18K1 Barplots don\'t show up
2352006-01-13 19:36:29RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Medicago_mtrMediacgo is spelled \"Medicago\"
2342005-12-29 17:26:42sheng lidingshengli@purdue.edupurdue universityProblem searching BarleyBase http://www.barleybase.org/loginpage.phpDear web manager: This is Sheng-Li Ding from Purdue university. Mr. Corby let us to download their infection data at their ftp. site. But we could not get the data. So I have to download FG1, FG2, and FG3 from Barleybase. I will great appreciate your helps! Best Regards! Sheng-Li Ding
2332005-12-22 15:54:44LaurentDelucdelucl@unr.eduUNRData error http://www.barleybase.org/geneexpression.phpHi, I've tried to do some statistical on my data by using the expression profile window. (Vv5 Cabernet and Chardonnay's berries development). But I'm not able to select any of my data, they don't appear at the bottom of the window. Thank you in advance for answering me Laurent Deluc
2322005-12-18 00:10:39GrantCramercramer@unr.eduUNRrequest http://www.barleybase.org/request.phpElizabeth Tattersall is listed as the owner of the UNRgrape group. She is my graduate student and will be leaving soon. I wish to take over the ownership. Could you please switch this? Thanks, Grant Cramer
2312005-12-17 18:49:08GrantCramercramer@unr.eduUniversity of Nevada, Renolpe reference http://www.barleybase.org/filtertut.phpI have a couple of questions concerning the local pooled error test. Is this based upon the Jain et al paper in Bioinformatics 2003 19:1-7? Are there any papers published using barleybase or plexdb using this lpe method? Thanks, Grant
2302005-12-17 15:53:06GrantCramercramer@unr.eduUniversity of Nevada, RenoData errorHi, I tried to delete some of my old data files, but they were not deleted and I got back an error message "Warning: Delete Gene List grantcramer_D33 failed".
2292005-12-17 11:36:17GrantCramercramer@unr.eduUNRstatistics file problem http://www.barleybase.org/expressionfiltermult.phpHello, I have been selected two-group comparisons for my VV2 files When I select for control day 12, I get this response in my results Hybridizations in group A: VV2_H18, VV2_H23, VV2_H24 Hybridizations in group B: VV2_H25, VV2_H26, VV2_H27 with H18 selected instead of H21. Can you correct this problem? Thanks, Grant
2282005-12-17 09:50:25GrantCramercramer@unr.eduUNRANOVA problem http://www.barleybase.org/myresult.phpI have been trying to do statistical filtering of VV2 data. Using RMA, I have been able to do of t-test of two group, control vs water-deficit, but if I try to do three groups using one-way anova for control, water-deficit and salinity, I get nothing. Am I doing something wrong? or is this part of the analysis not working? Grant
2272005-12-15 15:15:47RogerWiserpwise@iastate.eduISUTypo http://plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=SoybeanCystNematodePlexdb blast should be spelled PLEXdb BLAST
2262005-12-06 09:28:15RogerWiserpwise@iastate.eduISUDead link http://plexdb.orgguide.php?page=ncbiblastNCBI Blast tools do not work - no query sequnce entered
2252005-12-06 09:23:58RogerWiserpwise@iastate.eduISUData error http://plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Medicago_mtrMedicago does not align on rice; why is there a Gramene alignment for Medicago? Annotation page needs editing. Maize, etc. is incorrect for this dicot. Should be links to Soybase and LIS
2242005-11-30 11:51:11RogerWiserpwise@iastate.eduISU http://plexdb.orgguide.php?page=ncbiblastNCBI blast does not function according to menu. Everything seems to be blastn
2232005-11-29 09:25:48RicoCaldoracaldo@iastate.eduISUErrors in Gene List Management http://www.plexdb.org/index.php?There are several errors in managing gene list (Pledb-GeneList-Management). http://www.plexdb.org/modules.php?name=Your_Account&op;=geneLists 1.) Guest gene lists are shown even when I logged in. 2.) \"Rename current gene list\" is not working. 3.) \"Comparing two gene list\" is not working.
2222005-11-28 10:29:46rayxinjqxin@iastate.eduabcWhat I don't like about BarleyBase http://www.plexdb.org/modules.php?name=Your_Account&op;=userinfo&bypass;=1&username;=jiangongthanks
2212005-11-28 10:12:21RicoCaldoracaldo@iastate.eduISUDead link http://www.plexdb.org/modules.php?name=Your_Account&op;=geneListsThe import function (http://www.plexdb.org/query_probeset.php?import=yes) is still not working. I pasted 500 probe sets in the text box and selected experiment and estimation method, but nothing happened when I clicked the query button.
2202005-11-28 09:46:10testtestsqwu@iastate.edutestData error http://www.barleybase.org/feedbackcgi.phptese
2192005-11-28 09:35:30TestTesttest@test.eduTestData error http://www.barleybase.org/viz_probeset.phpTest
2182005-11-24 23:38:03orrinna Content-Type: text/plas3996@barleybase.orgas3996@barleybase.orgas3996@barleybase.orgas3996@barleybase.orgas3996@barleybase.orgas3996@barleybase.org
2172005-11-24 18:36:02then Content-Type: text/plainh3330@barleybase.orgh3330@barleybase.orgh3330@barleybase.orgh3330@barleybase.orgh3330@barleybase.orgh3330@barleybase.org
2162005-11-23 15:14:56RogerWiserpwise@iastate.eduISUDead link http://plexdb.org/modules.php?name=PD_dataSelection&page;=runsetup3Bmult.php&lastspecies;=&experiment;=BB4&experiment2;=BB4&exprsMethod;=mas&species;=barleybase&treat1;=1&treat2;=2&whatToPlot;=plottreat&hyb1;=BB4_H1&hyb2;=BB4_H1&treat3;=1&scaletype;=log2&species;=barlScatter plots link is broken Not Found The requested URL /testls/R_PHP/tmp/6244692_FCmasTreatment1and2_2to4.txt was not found on this server. Apache/2.0.52 (Red Hat) Server at www.barleybase.org Port 80
2152005-11-23 08:37:24RogerWoiserpwise@iastate.eduISUDead link http://plexdb.org/modules.php?name=PD_dataSelection&page;=blast2expression.phpPlatform translator link broken Not Found The requested URL /platformtranslator.php was not found on this server. Apache/2.0.52 (Red Hat) Server at www.plexdb.org Port 80
2142005-11-22 08:33:32RexNelsonnelsonrt@iastate.eduUSDA-ARS AmesProblem searching BarleyBase http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=blast2expression2.phpTried to BLAST one sequence against the Soybean 61k exemplars. Pasted in one sequence (fasta format) into window. Checked BLASTN. Clicked \"Blast\" and nothing happend. The form went away leaving a blank frame and a \"Done\" at the bottom of the window. I don\'t know if it is thinking or crashed. refering page is: http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=blast2expression2.php
2132005-11-11 08:25:27RogerWoiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules.php?name=PD_general&page;=presentations.phpMost links to presentations on this page are broken. Not Found The requested URL /help_pages/BBflow.ppt was not found on this server. Apache/2.0.52 (Red Hat) Server at www.plexdb.org Port 80
2122005-11-01 09:37:27RicoCaldoracaldo@iastate.eduISUDead link http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=genelists.php&userChosen;=yes&action;=analysisThe Data Access- Gene Lists- Analysis link from the home page is dead. Can we link it to the log-in page, and then to \"analyze gene list\" page just like in BarleyBase where users can directly select from the saved gene lists?
2112005-10-31 16:37:10RicoCaldoracaldo@iastate.eduISUdownload sequences http://www.plexdb.org/modules.php?name=PD_general&page;=download.php&tmva;=0|1|3|4|8|24|39|43|51|The download sequences tool is not working. It is not retrieving any sequences. I tried a single probe set and still it didn\'t work.
2102005-10-20 14:46:13RogerWiserpwise@iastate.eduISUSite improvement http://plexdb.org/modules.php?name=PD_general&page;=news.php&tmva;=0|1|3|4|5|8|9|11|17|19|23|38|81|Webalizer statistics ended in May2005. What happened?
2092005-10-20 14:22:57RogerWiserpwise@iastate.eduISUData error http://plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Maize8kno data for CornChip0 on annotation page
2082005-10-19 13:19:37RicoCaldoracaldo@iastate.eduISUImport Gene List http://www.plexdb.org/query_probeset.php?import=yesImpot Gene List in plexdb is not working.
2072005-10-13 16:52:51RicoCaldoracaldo@iastate.eduISUData Uploading error http://barleybase.org/bbexperiment.phpJava uploading is not working in DAT file(s).
2062005-10-13 10:58:40LISHUANGSHENlshen@iastate.eduIOWA STATE UNIVERISITYNonetest
2052005-10-13 10:54:48LISHUANGSHENlshen@iastate.eduIOWA STATE UNIVERISITYNonetest
2042005-10-13 10:25:59RogerWiserpwise@iastate.eduISUsubmission errors http://www.barleybase.org/feedbackcgi.phpDelete treatments function does not work Also, Feedback should open in new window
2032005-10-13 10:03:15RogerWiserpwise@iastate.eduISUsubmission errors 2. Experiment factors/levels 3. Treatment design When I click these, I get the wrong page
2022005-10-13 09:57:18RogerWiserpwise@iastate.eduISUData error http://barleybase.org/bbexperiment.phpProblems with upload "Could not execute group seletion"
2012005-10-12 16:42:14RicoCaldoracaldo@iastate.eduISUData Submission http://www.plexdb.org/modules.php?name=Your_AccountJava Applet uploading is not functioning in PlexdbExpress. I tried to upload wheat data files, it went immediately to uploading complete page (with just 5 seconds of uploading time) but when I checked in the association page no data were uploaded.
2002005-10-11 10:34:24RogerWiserpwise@iastate.eduISUTypo http://plexdb.org/modules.php?name=PD_dataSelection&page;=blast2expression.phpDescritpions is spelled incorrectly on Advanced BLAST options Should be Descriptions
1992005-10-10 11:04:29RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/index.phpRice mapper in BarleyBase is not the same as rice mapper in PLEX. No display in BarleyBase
1982005-10-06 09:50:52RogerWiserpwise@iastate.eduISUTypo http://barleybase.org/experiment_dataquery.phpHead of Laborotary: should be spelled: Head of Laboratory:
1972005-10-05 08:13:44RogerWiserpwise@iastate.eduISUDatabase improvement http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=SoybeanSoybean, soybean - Heterodera, soybean - Phytophthora, and Fusarium show up under \"probe set info\" in BarleyBase classic, but are not on the menu in Plex. Every new chip/update should be mirrored in both BB classic and PLEX
1962005-10-04 12:06:04RpogerWiserpwise@iastate.eduISUDead link http://plexdb.org/modules.php?name=PD_dataSelection&page;=platformtranslator.phpMPT help file dead Not Found The requested URL /MPT_help.htm was not found on this server. Apache/2.0.52 (Red Hat) Server at www.plexdb.org Port 80
1952005-09-23 15:20:35lingzhanglzhang1@wsu.eduwashington state universityabout submitting data http://www.barleybase.org/index.phpHello, I just submitted a Barley1 genechip data in the database. I also have created 4 experiment names when I was trying to submit data. I did not finalize them and want to delete them. Only one "Morex and rrp1" was finalized. I do not know how to delete the 4 tests, pls delete it for me. Thank you, ling
1942005-09-23 13:18:44AnneFennellanne.fennell@sdstate.eduSouth Dakota State UniversityNone http://www.barleybase.org/bbexperiment.phpI am trying to associate data files with hybridizations and I am very confused when I look at this it has six lines labeled the same for each of the samples that I am trying to associate? Do I do all 6 or just one of each of those?? Fennella8 V. riparia photoperiod control of growth.
1932005-09-08 07:52:43JanetHigginsjanet.higgins@bbsrc.ac.ukJohn Innes CentreProblem interpreting data http://www.barleybase.org/loginpage.phpPlease can you explain the scale in the hierarchical clustering dendrogram. I have used Clustering method: complete linkage Distance method: Correlation-Centered Pearson The scale is from 0 to 1.5. What do these units mean?
1922005-08-24 15:55:09MatthewMoscoumoscou@iastate.eduISUData error http://www.plexdb.org/classic/bbgroup.phpWhen submitting information, a number of strange, small errors occurred. After uploading the data, you could only associate files if you select the asssociate tool later on, the first prompt screen would not work. When trying to update a title on an experiment, a group error was given, and the name could not be changed. Also, it looks as if a maize experiment was given an accession AT, rather then ZM. Thanks!
1912005-07-06 10:49:50GrantCramercramer@unr.eduUniversity of Nevada, RenoNone http://plexdb.org/modules.php?name=Your_Account&op;=edituserHi, I have tried to update my information several times using Safari and then Explorer. Each time I try to update the information by clicking on the button, the interface asks me to login (I have already done so to get to my info) and reenter my password. When I do so, it brings me back to my personal window, I click my info link and nothing has been updated.
1902005-06-29 10:11:31JanetHigginsjanet.higgins@bbsrc.ac.ukJohn Innes CentreData error http://www.barleybase.org/barley1contig.phpThe CDS prediction for Barley1_40738 and Barley1_07360 are incorrect.
1892005-06-22 14:31:35RogerWiserpwise@iastate.eduISUTypo http://plexdb.org/modules.php?name=PD_general&page;=publications.phpBarleyBase�an expression profiling database for plant genomics should be: BarleyBase - an expression profiling database for plant genomics
1882005-06-22 14:21:02RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Barley1On the Gramene rice genome browser, selcect "Advanced" under "Feature" menu, should be: On the Gramene rice genome browser, select "ESTs" under "Feature" menu, then check the "Barley1 GeneChip exemplars" box and "Close window" to make it a default view option. selcect should be spelled select
1872005-06-22 14:15:19RogerWiserpwise@iastate.eduISUTypo http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=platformtranslator2.php*You maye edit this list if you want to create new gene list from it. should be: *You may edit this list if you want to create new gene list from it.
1862005-06-17 09:31:51RogerWiserpwise@iastate.eduISUTypo http://plexdb.org/modules.php?name=PD_general&page;=publications.phpBarleyBase�an expression profiling database for plant genomics Need colon and space between "BarleyBase" and "An expression ..........."
1852005-05-27 10:39:46RogerWiserpwise@iastate.eduISUDead link http://plexdb.org/modules.php?name=PD_dataSelection&page;=genelistAll.php&tmva;=0|1|4|8|9|14|35|Rice Genome Mapper - dead link Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator, webadm@vrac.iastate.edu and inform them of the time the error occurred, and anything you might have done that may have caused the error. More information about this error may be available in the server error log. Apache/2.0.52 (Red Hat) Server at www.barleybase.org Port 80
1842005-05-23 11:52:29RogerWiserpwise@iastate.eduISUTypo http://plexdb.org/modules.php?name=PD_probeset&page;=annotation.php&genechip;=Barley1 Rice and Cereals Genome Alignment at Gramene On the Gramene rice genome browser, selcect "Advanced" under "Feature" menu, then check the "Barley1 GeneChip exemplars" box to make it a default view option. Selcect is spelled SELECT
1832005-05-20 09:16:43RogerWiserpwise@iastate.eduISUDatabase improvement http://plexdb.org/modules.php?name=PD_general&page;=go_window.phpBarleyBase Gene Ontology Browser Should be: PLEXdb Gene Ontology Browser Also Fungal anatomy browser should be available from the "Your action" menu (as part of an outline form) eg, Plant anatomy, growth, fungal, GO, etc,
1822005-05-19 17:16:16RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/barley1contig.phpPlantGDB link is broken Not Found The requested URL /data.php was not found on this server. Apache/2.0.46 (Red Hat) Server at www.plantgdb.org Port 80
1812005-05-19 07:05:20RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=genelists.phpno links work on this page
1802005-05-18 15:55:36RexNelsonnelsonrt@iastate.eduARSSite improvement http://www.barleybase.org/fao_browser.phpFungal ontology does not have definitions associated with the FAO numbers. Do they exist?
1792005-05-18 15:52:02RexNelsonnelsonrt@iastate.eduARSDead link http://barleybase.org/blast2expression.phpVmatch dead on pull down menu 404 http://www.plantgdb.org/cgi-bin/BarleyBase/BarleyGeneChipProbeMatch
1782005-05-18 15:47:18RogerWiserpwise@iastate.eduISUDead link http://www.plexdb.org/modules.php?name=PD_dataSelection&page;=selectExp.phpData folder not functional
1772005-05-18 15:46:07RexNelsonnelsonrt@iastate.eduARSDead link http://barleybase.org/index.phpplantgdb blast link dead http://www.plantgdb.org/cgi-bin/PlantGDBblast
1762005-05-18 15:35:45RexNelsonnelsonrt@iastate.eduARSTypo http://barleybase.org/runsetup4.phpin agree with Affymetrix for all different hybridizations and probe pairs (drop different)
1752005-05-18 15:35:03RogerWiserpwise@iastate.eduISUDead link http://plexdb.org/modules.php?name=PD_general&page;=bbsubmission.phpData Submission: Object not found! The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author of that page about the error. If you think this is a server error, please contact the webmaster Error 404 www.plexdb.org Wed May 18 15:34:24 2005 Apache/2.0.49 (Unix)
1742005-05-18 15:09:53RexNelsonnelsonrt@iastate.eduARSData error http://barleybase.org/po_browser.phpThis error is in the http://barleybase.org/feedback.php page. The first time I sent in a feedback request I got a nice confirmation page. But after that I get just the input values as a confirmation. Browser = Firefox 1.0 on OS X 10.2.8
1732005-05-18 14:59:58RexNelsonnelsonrt@iastate.eduARSDead link http://barleybase.org/probealign.php http://barleybase.org/probealign.php EST contig alignment of exemplar at PlantGDB Not Found The requested URL /data.php was not found on this server. Apache/2.0.46 (Red Hat) Server at www.plantgdb.org Port 80
1722005-05-18 12:29:31jianqiangxinjqxin@iastate.eduisuData error http://www.barleybase.org/probevalue.phphttp://www.barleybase.org/probevalue.php?probeset=Ta.10069.1.S1_at&experiment;=TA2&plot;=yes http://www.barleybase.org/runsetup4.php?inputfile=_TA2_probevalues.txt&experiment;=TA2 Is it because no data in TA2 or what else reason?
1712005-05-18 11:50:19RogerWiserpwise@iastate.eduISUDead link http://plexdb.org/modules.php?name=PD_general&page;=tools.phpDedicated VMATCH - Search for Barley1 probes that match the sequence you provide. Dead
1702005-05-18 10:52:01RogerWiserpwise@iastate.eduISUData error http://plexdb.org/modules.php?name=PD_probeset&page;=probealign_soybean.php&exemplar;=Gma.1.1.S1_at&exemplartext;=&ProbeImageWidth;=977Probe numbering format is 0 -> 10, 0->14, etc. (for all Affy chips NOT 1-11)
1692005-05-18 07:53:27RogerWiserpwise@iastate.eduISUData error http://plexdb.org/modules.php?name=PD_general&page;=news.phpMPT link from "News" points to old version
1682005-05-17 09:33:54JulieDickersonjulied@iastate.eduISUData error http://barleybase.org/modules.php?name=PD_dataSelection&page;=genelists.phpThere must be a problem with the new directory structure, the figures from expression analysis are all broken links and the pdf directory cannot be found.
1672005-05-17 08:02:07RogerWiserpwise@iastate.eduISUData error http://plexdb.org/index_m.php?database=BarleyOld phylogenetic tree appeared on the front page today
1662005-05-12 10:54:37RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/modules.php?name=PD_dataSelection&page;=editFolder.phpShould be able to add to data folder where it says "Edit data folder" Not just remove - Not convenient to add additional expts?
1652005-05-12 09:47:29RogerWiserpwise@iastate.eduISU http://plexdb.org/modules.php?name=PD_general&page;=publications.phpThere are 2 #6 publications for the same paper. Delete the second one
1642005-05-12 09:02:19RogerWiserpwise@iastate.eduISUSite improvement http://barleybase.org/modules.php?name=PD_general&page;=quicktour.phpBarleyBase Quick Tour This is a quick tour of the major functions of Barleybase. Please click the links, and corresponding pages will pop-up. Do not close this page during your tour. Some of the popup pages may need further action at the page to try out functions on that page. You may download our Power Point tutorial on data analysis and submission work flow. Should be: PLEXdb Quick Tour and "major functions of PLEXdb
1632005-05-11 14:57:00RogerWiserpwise@iastate.eduISUData error http://barleybase.org/platformtranslator2.phpWheaqt to barley probe set traslator does not function
1622005-05-11 12:39:34RogerWiserpwise@iastate.eduISUTypo http://barleybase.org/modules.php?name=PD_dataSelection&page;=genelists.phpYou have chosen to create a gene list by co expressed. Should be: You have chosen to create a gene list by co-expressed probe sets. or: You have chosen to create a gene list by co-expression. Same for Step 4.
1612005-05-09 15:38:51RhondaDeCookrdecook@iastate.eduIowa State UniversitySite improvement http://barleybase.org/modules.php?name=Your_AccountI also can't find a way to completely remove my submission when I know some of my entries are wrong - and I can't seem to edit them either. I could just wipe everything out and start over, but I'm not finding this option.
1602005-05-09 15:10:05RhondaDeCookrdecook@iastate.eduIowa State UniversitySite improvement http://barleybase.org/modules.php?name=Your_AccountI've been trying to describe my experiment and upload CEL files, but I can't figure out how to edit my experiment design page. Is there an e-mail of someone to contact?
1592005-05-05 20:36:52StevenSchmidtschmidt@cshl.eduCold Spring Harbor LabLinking to Wheatplex http://www.barleybase.org/modules.php?name=PD_general&page;=BarleyBaseFAQ.phpGramene is adding Wheat plex hits to our rice genome browser. We want to link from these hits to you. I tried this http://www.barleybase.org/modules.php?name=PD_probeset&page;=contig_wheat.php&probsetnew;=Ta.5589.2.S1_a_at but it just goes to the sample exemplar Ta.10069.1.S1_at. What should we do?
1582005-05-04 14:29:58RogerWiserpwise@iastate.eduISUProblem searching BarleyBase http://barleybase.org/modules.php?name=PD_probeset&page;=barley1_probeset.phpPull down menu of "Expression of Contig1637_at " does not give new expression plot when different experiment is selected
1572005-05-04 06:57:36RogerWiserpwise@iastate.eduISUProblem searching BarleyBase http://www.barleybase.org/index1.php?In WheatPlex I can't get expression details. For eg., using Ta.10069.1.S1_at (the default probe set on the annotation page) I get the following message: No matching chip design has your input probe set. Please varify your input and try again.
1562005-04-26 14:10:35ANthonyLeottatonyl@pillarsoftware.comPSISchema http://www.barleybase.org/schema.phpHave you posted the SQL Table creation statemente needed to recreate the BarleyBase schema mine local machine?
1552005-04-22 13:41:01RogerWiserpwise@iastate.eduISUTypo http://barleybase.org/index1.php?database=Soybean"The Feedback" should be just "Feedback"
1542005-04-22 13:39:23RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/modules.php?name=Your_Accountrpwise@iastate.edu, Welcome to BarleyBase, a community resource for cereal microarrays! I got the above message, even though I was in WheatPLEX. We should change this statement to Welcome to PLEXdb, a community resource for plant and plant pathogen microarrays
1532005-04-22 08:19:51RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/modules.php?name=PD_dataSelection&page;=genelists.php&op;=querySingle"Back" or "next" buttons get blank pages; must use browser controls
1522005-04-22 08:18:15RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/modules.php?name=PD_dataSelection&page;=genelists.php&op;=querySingleDoneSelect your Experiment ..... Click next -> get blank page
1512005-04-22 08:14:45RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/modules.php?name=PD_dataSelection&page;=genelists.php&op;=querySinglePlease choose gene list creation approach: There should be a option here to copy and paste a set of Affy probe set designators. e.g., Contig11969_at Contig12219_at Contig15413_at Contig15515_at Contig15861_at Contig1271_x_at Contig2168_s_at Contig8605_s_at HV_CEb0004O15r2_s_at Contig24175_at Contig4728_at Contig5108_s_at HY07P02u_at HT09O03u_s_at or Ta.10069.1.S1_at, etc.
1502005-04-21 17:08:25RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/modules.php?name=PD_general&page;=feedbackcgi.phpThe confirmation on feedback sites should say PLEXdb user, not BarleyBase user
1492005-04-21 17:06:27RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/modules.php?name=PD_general&page;=bbsubmission.phpData Submisson link on species front page presents a blank page in Mac Explorer. Its works in Safari.
1482005-04-21 10:29:20RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/modules.php?name=PD_general&page;=download.php"Forum" needs to be removed from the menu at the top of the PLEX pages
1472005-04-21 10:28:47RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/modules.php?name=PD_general&page;=download.php"Forum" needs to be removed from the menu at the top of the PLEX pages
1462005-04-21 10:27:00RogerWiserpwise@iastate.eduISU http://barleybase.org/modules.php?name=PD_probeset&page;=hybdetail.php&experiment;=TA3*Visualize hybridizations by scatter plots and MVA plots Check table below for more details on hybridizations. Click a hybridization link for their Full Details Click hyperlink to "hybridizations" -> blank page
1452005-04-21 10:24:10RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/modules.php?name=PD_dataSelection&page;=experiments.phpFeedback should open in a new window (just like it did for BarleyBase classic)
1442005-04-21 10:22:55RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/modules.php?name=PD_dataSelection&page;=experiments.phpProviders: Show details When I click "show details" for TA3 a blank page appears
1432005-04-20 09:57:40RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/modules.php?name=PD_dataSelection&page;=hybdetail.phpWhen you click on available data on the right - hand side of the PLEX front page or species pages, the page comes up blank.
1422005-04-13 13:28:37RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/index.phpWhen clicking My BarleyBase - Submission we get the following message: Object not found! The requested URL was not found on this server. The link on the referring page seems to be wrong or outdated. Please inform the author of that page about the error. If you think this is a server error, please contact the webmaster Error 404 www.barleybase.org Wed Apr 13 13:27:01 2005 Apache/2.0.49 (Unix)
1412005-04-05 08:41:50StacyBarkeloosmturner@iastate.eduISUplant anatomy ontology problem http://www.barleybase.org/browsesample.phpI seem to be unable to expand the "whole plant" portion of the plant anatomy ontology. The other sections, such as tissue, work fine.
1402005-04-01 10:04:25RogerWiserpwise@iastate.eduISUTypo http://barleybase.org/news.phpPlant Ontology Brower added, with updated plant ontology information. Browser is misspelled
1392005-03-16 18:06:29RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/modules.php?name=PD_probeset&page;=annotation.php&database;=RiceRice annotation link is empty
1382005-03-15 16:38:57GregFuerstgsfuerst@iastate.eduUSDA-ARSDownload sequences http://barleybase.org/get_seq.phpIt would be helpful to get a response indicating which inputs were not found to match an examplar name when trying to retrieve multiple sequences. Right now it just retrieves the sequences it can find.
1372005-03-08 14:38:25MattFritzmcfritz@iastate.eduISULogin http://www.barleybase.org/bblogin.phpI recieved an email confirming my login ID and my password and when I try t login it tells me that I have an invalid login ID. How do I enter the site?
1362005-02-28 17:04:49RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/experiment_dataquery.phpProviders [http://barleybase.org/experiment_dataquery.php?showproviders=yes] not shown for experiments
1352005-02-28 16:02:51RogerWiserpwise@iastate.eduISUProblem searching BarleyBase http://barleybase.org/query_experiment.phpMake TA2 public access
1342005-02-28 15:27:26RogerWiserpwise@iastate.eduISUData error http://barleybase.org/index1.php?database=BarleyYou should take North American Barley Genome project off the sponsor list for all PLEX front pages except BarleyBase, and replace it with USDA-NRI. Put the original funding from the live site back on for new site for BarleyBase.
1332005-02-28 09:57:54GregFuerstgsfuerst@iastate.eduUSDA-ARSDead link http://barleybase.org/index.phpThe PlantGDB link on the homepage (under Data Access) does not work.
1322005-02-25 17:01:47RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/documentation.phpAll help files under the hyperlink in #3. Instructions on submission ......) seem to be broken
1312005-02-25 07:56:56RogerWiserpwise@iastate.eduISUDead link http://barleybase.org/query_experiment.phpContent overview is incorrect - no experiments can be seen
1302005-02-09 15:35:00stevewhithamswhitham@iastate.eduISUDatabase improvement http://barleybase.org/platformtranslator2.phpa "clear" button would be good on this page in case you mis-enter data or if you have multiple queries. A good place would be beside the "translate" button?
1292005-02-08 09:25:42RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/get_seq.phpDownload Sequences for a Gene List This should be accessible from the Gene List menu under Analysis and Viz.; it is not clear that "Download sequences" in this pull-down menu is this tool.
1282005-01-24 14:42:21RogerWiserpwise@iastate.eduISUTypo http://barleybase.org/probealign.phpOn a proibe alignment page where there is more than one probe, each probe should be labeled 0 -> 10; not 0-32 for 3 probe sets
1272005-01-21 11:40:04GregFuerstgsfuerst@iastate.eduUSDAdownload sequences http://barleybase.org/get_seq.phpI am unable to retrieve any sequences using the "Probe Set Info / Download Sequences" function. I have tried inputting multiple contigs as well as single contigs. When I click on "Retrieve Sequence", I get a list of the contigs I inputted but no sequence data.
1262005-01-19 14:43:24PeterOlssonPeter.Olsson@tbiokem.lth.seLund UniversityNone http://www.barleybase.org/funcstat.phpHi! First I would like to say that I find this resource excelent! Thank you for creating it! Now to the problem; I am working with som ATH1 gene chip arrays and I very much like to use your function "Analysis & Viz. => FuncExpression => Expression2Function". This function worked very well a couple of days ago. However you seam to have added Barley1 arrays since I last time used the Expression2function. Since then I can not acces my data from Fishers Test anymore. When I click the link to my Fishers test data the document show me data from Barley 1 etc. and not my gene list anymore! I suspect that you have a bug in the software. If I can help in anyway to correct this problem please contact me! Thank you very much! Peter Olsson PhD
1252005-01-18 13:59:14PierreBushelbushel@niehs.nih.govNIEHSNone http://www.barleybase.org/schema.phpIs it possible to have the sql that creates the BarleyBase database schema provided to us? We have a two-color array database which we would like to link to a local instance of the BarleyBase database in order to store Affy single-color data and experiment information.
1242005-01-13 09:24:42RogerWiserpwise@iastate.eduISUDatabase improvement http://barleybase.org/timeplotviewer.phpThe contig box at the bottom with hyperlink to "Expression view" should be available from the High Resolution page as well
1232005-01-12 08:42:30StacyBarkeloosmturner@iastate.eduISUTrouble submitting http://www.barleybase.org/personnel.phpWhen I get to the upload page, it just says "Failed to open file". I"m using Mac 10.3.6 and have tried both Internet Explorer (v. 5.2 for mac) and Safari (1.2.4) and got the same result.
1222005-01-11 15:50:26RicoCaldoracaldo@iastate.eduISUFailed to open site for data uploading http://www.barleybase.org/bbexperiment.phpI was submitting a new experiment and the data uploading site could not be opened.
1212005-01-06 16:20:21JoyRoyroyxx084@umn.eduMinnesota UniversityWhat I like about BarleyBase http://www.barleybase.org/BarleyBaseFAQ.phpI was looking for information that whether microsatellite sequences are present in EST sequences that were used in construction of barley chip.
1202004-12-16 11:27:50RogerWiserpwise@iastate.eduISU http://barleybase.org/contig_wheat.phpadd: Genomic Alignment with Rice and Cereals, GrainGenes in the BLAST and EST alignment section like for barley1 on the wheat exemplar page
1192004-12-14 17:53:22RogerWiserpwise@iastate.eduISUData error http://barleybase.org/browsesample.phpThe first sample for BB4 does not listthe correct Growth Ontologies
1182004-12-10 11:02:16RogerWiserpwise@iastate.eduISUData error http://barleybase.org/browsesample.phpOrganism for the maize smaples should be Zea mays, NOT Hordeum vulgare
1172004-11-09 12:10:34SeunghoChochoxx048@umn.eduUMNID and password http://www.barleybase.org/index.phpI have another stupid question concerning ID and password for reviewers. Can reviewers use identical ID and a password? If it is OK, I would like to give only one of three you sent last time. And to change the password, it seems to be done only by DB manager. Would you help changing each password having a corresponding number, 1, 2, and 3 at the end of each password? I appreciate your help. -Seungho
1162004-09-14 01:02:35TimSawbridgetim.sawbridge@uq.edu.auDepartment of Primary Industries and Fisheries, Queensland, AustraliaData error http://www.barleybase.org/experiment_dataquery.phpHi there, thanks for your site, it is very useful. I have been doing some clustering of data downloaded from your site and have notice the rma files for AT15 and AT16 are the same. I think the AT16 files are possibly the wrong ones because there seems to be high mads box gene expression which would probably be expected for anthers(?) Regards Tim
1152004-09-11 20:48:07DaveMatthewsmatthews@greengenes.cit.cornell.eduUSDA-ARS, Cornell U.Faulty experiment name http://www.barleybase.org/browsesample.phpHmm, the actual page on which I clicked the Feedback link isn't http://www.barleybase.org/browsesample.php, it's http://www.barleybase.org/experiment_dataquery.php. For the experiment "A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning". I was quite interested at first to see this experiment name. Symbiotic nodulation of barley! However I see that this is just the title of the reference cited which is actually about a gene in Medicago truncatula, although it does also deal with transcript-based cloning. - Dave
1142004-09-02 17:11:57RicoCaldoracaldo@iastate.eduISUBB4 publication http://www.barleybase.org/feedbackarchive.phpPlease put this info to the Publication_id in BB4. "Rico A. Caldo, Dan Nettleton, and Roger P. Wise Interaction-Dependent Gene Expression in Mla-Specified Response to Barley Powdery Mildew Plant Cell 2004 16: 2514-2528." And also please link all publications to Pubmed or to the journals.
1132004-08-31 17:36:53RicoCaldoracaldo@iastate.eduISULink Publication ID http://www.barleybase.org/experiment_dataquery.phpIt's better if we can link the publication_id to Pubmed or to the journal so that users can easily get the paper or the abstract. Publication_id: Mitra et al: "A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning" Proc Natl Acad Sci USA. 101(13):4701-5, 30 March 2004.
1122004-08-11 12:36:02SeunghoChochoxx048@umn.eduU. MinnesotaDatabase improvement http://www.barleybase.org/bbexperiment.phpI have some trouble in selecting uploaded files corresponding to each experiment. Although I can see all of my 33 files in the list, I can't see them all when I moved to "selection of files corresponding to 3 replications". It shows only part of the list. Can you help me to resolve this issue? Thanks.
1112004-08-10 15:58:52RicoCaldoracaldo@iastate.eduISUTypo http://barleybase.org/bbexperiment.php Associate groups with the expriments. Should be : Associate groups with the experiments. The word experiment is misspelled.
1102004-08-06 09:09:20RogerWiserpwise@iastate.eduISUSite improvement http://www.barleybase.org/barley1contig.phpIn the "search" pull down menu, can you list contig no., EST name, and GenBank no. as well to help to find a probe set.
1092004-08-05 09:37:42RogerWiserpwise@iastate.eduISUProblem searching BarleyBase http://www.barleybase.org/request.phpATH1 non-host resistance group indicates that i am a member, (+++) but I can not see our experiment
1082004-08-03 09:29:21RogerWiserpwise@iastate.eduISUTypo http://barleybase.org/download.phpThe links between probe set names and new seuqence names of Barley1 GeneChip: A TAB delimited form with the probe set name in the first column and the sequence name (the new name) in the second column. "seuqence" should be sequence
1072004-08-02 14:39:51SeunghoChochoxx048@umn.eduU. Minnesota http://www.barleybase.org/bbexperiment.phpI am trying to input "Number of Factor Levels" which should be 11. But for some reason it is not workin gin that way. I have 11 different genotypes and I think numer 11 should be the "Number of Factor Levels" Am I misunderstaning this?
1062004-07-21 15:16:03RogerWiserpwise@iastate.eduUSDA-ARS / ISUData error http://barleybase.org/expsummary.phpInformation of Hybridizations from ZM1:� The genotype in column 6 does not correspond to the [correct] gentype in column 4
1052004-07-21 07:59:49RogerWiserpwise@iastate.eduUSDA-ARS / ISUData error http://barleybase.org/experiment_dataquery.phpMaize Pioneer GeneChip Experiment name should be: Maize Pilot GeneChip Array Description is not understandable; Table columns do not line up with headings Wf9 should be Wf9-BG (T cytoplasm; Rf1)
1042004-07-21 07:47:57RogerWiserpwise@iastate.eduUDSA-ARSDead link http://barleybase.org/experiment_dataquery.phpProviders: hide details No result is returned from mysql SELECT experiment_design_id from experiment_design where experiment_name='BB3'; Providers aren't listed
1032004-07-15 15:34:38jiangongjiangong@iastate.eduisuTypo http://barleybase.org/blastbarley.phpyou can either enter your query sequence in the textarea change to you can enter your query sequence in the text area
1022004-07-15 15:07:22jiangongjiangong@iastate.eduisu http://barleybase.org/genekeyword.phpIf some example keywords are given, it would encourage users to try this function.
1012004-07-15 14:58:52jiangongjiangong@iastate.eduisuimport gene list http://barleybase.org/query_probeset.phpOr maybe we can allow user upload their own file containing gene list.
1002004-07-14 14:32:03jiangongjiangong@iastate.eduisuNone http://www.barleybase.org/getkegghits.phpIt would be better if user can select all and clear all check boxes by one click instead of click each one to form a gene list.
992004-07-07 16:33:58RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityData error http://barleybase.org/experiment_dataquery.phpThere are 3 hybridization protocols - but 2 of them are blank tests. Delete 2 and 3. Also the 2nd extraction protocol makes no sense; it should be removed. Also the left hand column should be top justified for everything
982004-06-12 18:41:24RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityDatabase improvement http://www.barleybase.org/barley1contig.phpI think it would be more obvious if you including the "Blast Details" (for BLAST against Barley1 exemplars, TIGR Barley Gene Index and all Plant Proteins) button up within the grey highlighted box for the annotations. You will need to lengthen the grey box to include this. The "BLAST TOP HITS" can then be deleted, possibly
972004-06-11 08:46:41RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityData error http://www.barleybase.org/experiment_dataquery.phpThe recipe for Trizol is not fixed yet - It should be: TRIzol-like Reagent: Final Concentration Phenol, pH. 4.3 380 ml 38% Guanidine thiocyanate 118.6 g, 1 M Ammonium thiocyanate 76.12 g, 1 M 3M Sodium Acetate, pH 5.0 33.4, 0.1 M Glycerol 50 ml H2O to 1 liter
962004-06-03 16:09:34RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityDatabase improvement http://www.barleybase.org/experiment_dataquery.phpPlease list the Close et al 2004 Pl Physiology publication under the BB1 experiment data. There is a cell for publications but it is not there. Even better would be to list the publication and also hyperlink to the PubMed id.
952004-05-13 16:42:01RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://www.barleybase.org/timeplotviewer.phpshould be 16 hai, 20 hai, etc. not hai 16, hai 20
942004-05-13 15:20:03RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityData error http://barleybase.org/mydataset.phpCountry usage graph is not working under visitor statistics
932004-05-13 12:43:08jiangongjiangong@iastate.eduisuDead link http://www.barleybase.org/myresult.phpThere is a dead link when I clicked "Result Details".
922004-05-13 11:23:01RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityDatabase improvement http://barleybase.org/mapviewer.phpMagenta/green should added tolist of options or as a repacement for red/green. These are color blind friendly
912004-05-06 09:40:26RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityWhat I don't like about BarleyBase http://www.barleybase.org/mydataset.phpWe need to have a discussion on gene lists also, we should be able to compare conditions for individual probesets from the probe set summary page.
902004-05-06 09:35:00RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityDatabase improvement http://www.barleybase.org/mydataset.phpI. Browse Your Gene Lists and II. Create Gene List from Existing Ones should be reversed in order on the page to make it easier for the user. Also, BarleyBase is storing everyones genelists - it is messy
892004-05-04 12:07:48RogerWiserpwise@iastate.eduISUTypo http://barleybase.org/timeplotviewer.phpIn Netscape (Mac) the label colors are yellow, not black or blue. It is very difficult to see
882004-05-01 11:59:22PengDanhuipandaway1314@sohu.comCAUSite improvement http://www.barleybase.org/bblogin.phpCan not login?Why? Show:"Invalid login ID, please try again" Login ID and Password are correct I swear!
872004-04-28 17:35:35LISHUANGSHENlshen@iastate.eduISUWhat I like about BarleyBase http://www.barleybase.org/index.phpWe have new server to better serve you now.
862004-04-21 12:30:20RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/bblogin.phpSubmit the experiment through BarleyExpress View your private expriment and group protected experiments should be: Submit an experiment through BarleyExpress View your private experiment and group protected experiments Typo on "experiment"; substitute "an" for "the"
852004-04-14 08:25:14RicoCaldoracaldo@iastate.eduISUTypo http://barleypop.vrac.iastate.edu/BarleyBase/membersgrant.phpIn the Request Grant/Deny page, please correct the word "Request" in Your Action: Requst grant/deny.
842004-04-13 13:26:40QunfengDongqfdong@iastate.eduPlantGDBDisplay Error at bottom http://barleypop.vrac.iastate.edu/BarleyBase/barley1contig.phpWarning: Unknown(): Your script possibly relies on a session side-effect which existed until PHP 4.2.3. Please be advised that the session extension does not consider global variables as a source of data, unless register_globals is enabled. You can disable this functionality and this warning by setting session.bug_compat_42 or session.bug_compat_warn to off, respectively. in Unknown on line 0
832004-04-07 08:53:51RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityDead link http://barleypop.vrac.iastate.edu/BarleyBase/index.php306 hybridizations from 11 experiments. "11 experiments" link is broken.
822004-03-24 08:00:09RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase//geneexpression.phpFold Change Filter:�Mean of group A must �� against group B mean by at least��folds (define groups below). folds should be fold; in all places in database
812004-03-24 07:55:27RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpInterconnecting with PlantGDB and Gramene allows users to perform gene predictions using the 21,439 Barley1 exemplar sequences, or cross-species comparison at genome level. Arabidopsis probe sets can also be accessed by pathway or gene family information. Should be: Interconnecting links with PlantGDB and Gramene allows users to perform gene predictions using the 21,439 Barley1 exemplar sequences, or cross-species comparison at genome level. Arabidopsis probe sets can also be accessed by pathway or gene family information. {insert "links" after the word "interconnecting"; hyperlink Gramene}
802004-03-19 07:07:24XiaoyunTangxytang@iastate.eduISUBarleyExpressIn Experiment factor page, two "help" butons are missing
792004-03-05 12:44:59RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityProblem searching BarleyBase http://barleypop.vrac.iastate.edu/BarleyBase//bbexperiment.phpMy request tojoin the Mla network group has been granted by caldo, but I can't get in?!
782004-03-05 12:39:55RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityDead link http://barleypop.vrac.iastate.edu/BarleyBase//bbexperiment.phpWhen I log on and click "Browse experiments ", nothing happens. I should be able tosee 5 experiments. I am using Internet explorer
772004-03-05 08:16:24RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/barleypicindex.phpIf you had beautiful Barley pictures, you are welcome to send them to us. Should be: If you have beautiful Barley pictures, you are welcome to send them to us .
762004-03-04 10:11:44RicoCaldoracaldo@iastate.eduISUTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpYour Action: Requst grant/deny Please correct the word "Requst" to "request" in Request Grant/Deny page.
752004-03-04 09:58:14RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpTotally� 7 experiments and �246 hybridizations submitted. should be: 246 hybridizations from a total of 7 experiments have been submitted.
742004-02-26 15:25:22RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversitySite improvement http://barleypop.vrac.iastate.edu/BarleyBase/content.phpAnnotation information for this new array is hosted on the NetAffx Analysis Center at Affymetrix. Change to: Annotation information for the Barley1 array is hosted on the NetAffx Analysis Center at Affymetrix (http://www.affymetrix.com/support/technical/byproduct.affx?product=barley1)
732004-02-25 11:03:35RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpThere are also slides for� PAGXII poster and a� presentation for analysis work flow. Change to: Download our PAGXII poster [hyperlink] and a Power Point presentation to facilitate your analysis work flow [hyperlink].
722004-02-25 08:36:59RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversitySite improvement http://barleypop.vrac.iastate.edu/BarleyBase/index.phpDocumentation: The FAQ will answer many general questions. The detailed instructions for submission, query and data analysis flow� are provided through the help pages. Add link to PAG12 poster and new ppt presentation for work flow
712004-02-25 08:29:58RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State Universityupdate http://barleypop.vrac.iastate.edu/BarleyBase//content.phpAlign Barley1 exemplar sequences with other cereal genes and genomes on the Gramene Rice Genome Browser (http://www.gramene.org/) for cross-species comparison. (Not active yet). This is incorrect - please update to make consistent with Lishuang's exemplar information page
702004-02-25 08:24:01RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State Universityupdate http://barleypop.vrac.iastate.edu/BarleyBase//links.phpreplace "Affymetrix GeneChips: Affymetrix is a major high-density oligonucleotide GeneChip manufacturer. The designer of Barley1 GeneChip, the first Affymetrix high-density GeneChip for major cereal species. Affymetrix� produces microarray for a wide range of organisms, including barley, human, murine, rat, E. coli, Arabidopsis, yeast and Drosophila. " with: Affymetrix GeneChips: Affymetrix is a high-density oligonucleotide GeneChip manufacturer. The Barley1 GeneChip is the first Affymetrix high-density GeneChip for cereals. Affymetrix� produces GeneChips for a wide range of organisms, including barley, Arabidopsis, C. elegans, yeast, human, rat, Drosophila, and E. coli.
692004-02-25 08:17:24RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityUpdate for acknowledgement http://barleypop.vrac.iastate.edu/BarleyBase//acknowledge.phpReplace current acknowledgement with text below: Content of the Barley1 probe array benefited greatly from EST sequence chromatograms and/or matching sequence and quality value files generously provided by Dorrie Main (Clemson University Genomics Institute, South Carolina); Andreas Graner, Nils Stein, Winnie Weschke and Hangning Zhang (Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany); Kazuhiro Sato, Daisuke Saisho and Kazuyoshi Takeda (Okayama University, Japan) and Yuji Kohara and Tadasu Shin-I (National Institute of Genetics, Japan); Robbie Waugh, David Marshall, and Linda Cardle (Scottish Crop Research Institute, Dundee, Scotland); Hans Bohnert (University of Illinois); and Alan Schulman, Ari-Matti Sar�n, and Jaakko Tanskanen (Institute of Biotechnology, University of Helsinki, Finland). Thanks also to David Matthews (USDA-ARS, Cornell University, New York) for sequences that were available only from the GrainGenes database and to Shibo Zhang and Peggy Lemaux (University of California, Berkeley) for help with common reporter gene sequences, Warren Krueger (University of Minnesota) for assistance with detection of fungal sequences, and Jan Svensson (University of California, Riverside) for assistance with chimera detection. Special thanks goes to Xiaoqiu Huang (Iowa State University), for providing customized versions of the CAP3 assembly program and answering many questions about the algorithms, Dan Nettleton (Iowa State University) for advice on experimental design, Qunfeng Dong (PlantGDB, Iowa State University) and Doreen Ware (Gramene Database, Cold Spring Harbor, New York) for facilitating linkage with BarleyBase, and the Affymetrix team of Eric Schell, Gene Tanimoto, Alan Williams, Xue Mei Zhou, Lianne McLean, Paul Doran, Mike Mittman, Venu Valmeekam, Sandra Wells, Dawn Kerber, Curtis Fideler, Joe Prosser and Kyle O'Connor.
682004-02-25 08:12:30RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpSubmission: Submission: BarleyBase is committed to making ........... Delete 2nd "Submission"
672004-02-20 16:08:01RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversitySite improvement http://barleypop.vrac.iastate.edu/BarleyBase/index.phpSubmission: Researchers are encouraged to submit their data to the repository through BarleyExpress,� our MIAME-compliant online submission tool. Submitted data can be made public, or held private for up to 180 days until publication. Submitters can also grant access to their private data to designated individuals or groups, including manuscript reviewers.� Change to: Submission: BarleyBase is committed to making data from the Barley1 GeneChip publicly available to researchers world-wide. Researchers are encouraged to submit their data to the repository through BarleyExpress,� our MIAME-compliant online submission tool. Submitted data can be made public immediately, or an Accession no. can be acquired up to 180 days prior to publication. Submitters can also grant access to their data to designated individuals or groups, including manuscript reviewers.�
662004-02-17 17:27:02StacyTurnersmturner@iastate.eduISUProblem searching BarleyBase http://barleypop.vrac.iastate.edu/BarleyBase//blastbarley.phpNo matter what I enter into the barleybase blast, it always gives me the same results, using some sequence named test, that is 1203 characters long, rather than what I put into the window on the barleybase blast page
652004-02-04 11:50:57RicoCaldoracaldo@iastate.eduISUSample preparation page http://barleypop.vrac.iastate.edu/BarleyBase//bblogin.phpIn sample preparation page, there are fields for initial timepoint and genetic variation. But in the Add/Edit sample preparation template, there are no fields associated for the above categories.
642004-02-03 08:58:30RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/barley1contig.phpOn the Gramene genome browse page should state: On the Gramene rice genome browser
632004-01-27 16:12:41jianggongjiangong@iastate.eduisuDatabase improvement http://barleypop.vrac.iastate.edu/BarleyBase//download.phpIt would be very nice if BB can export MAGE-ML files.
622004-01-27 08:59:59RicoCaldoracaldo@iastate.eduISUPlant Ontology Fields http://barleypop.vrac.iastate.edu/BarleyBase//bblogin.phpI am not sure what to do in the Developmental Stage and Organism Part fields in the sample preparation page. The links are okay, they will get you through Gramene plant ontology site, but putting the selected plant parts and stages in the fields is hard. I don't know if it will automatically select or we need to "cut and paste" the selected categories. I tried to "cut and paste" but when I clicked the save button a new window appeared that says "Please fill up the required fields". So I don't think the "cut and paste" is working, what about the automatic select function. Let me know what to do.
612004-01-23 16:05:57jiangongjiangong@iastate.eduisu http://barleypop.vrac.iastate.edu/BarleyBase//expsummary.phpdead link
602004-01-16 09:27:24RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/barley1contig.phpAt Gramene genome browse page, selcect "Advanced" under "Feature" menu, check the "Barley1 GeneChip exemplars" box to make it a default view option. Sould be: On the Gramene genome browser page, select "Advanced" under the "Feature" menu, then check the "Barley1 GeneChip exemplars" box to make it a default view option.
592003-12-11 15:02:08RicoCaldoracaldo@iastate.eduISUTypo http://barleypop.vrac.iastate.edu/BarleyBase/bbexperiment.phpIn the "copy existing sample for edit" in the "sample preparation for treatment X" page, there is a note that says, If you want to copy an existing sample and modify it, please select a sample name from sample list and click 'Copy exsiting sample for edi' button. Once you finish your changes, click 'Save' button and a new sample is saved. Change the word "exsiting" to "existing" and the word "edi" to "edit". Also in the "Associate data files with treatments" page, there is an overview button, if you click it, it will show the experimental design overview window, in this window there is a "close windown" button. Change the word "windown" to "window".
582003-12-04 15:53:12RicoCaldoracaldo@iastate.eduISUError in Treatment Names http://barleypop.vrac.iastate.edu/BarleyBase/experiment_dataquery.phpIn the hybridization details for BB3, there are errors in the treatment names (eg. genotype_Golden20%Promise_tissue20%type_seedling,20%leaf).
572003-11-25 10:52:16DennisHaltermandhalterm@iastate.eduISUDatabase improvement http://barleypop.vrac.iastate.eduguide.php?page=ncbiblastI'd like to be able to blast against the est database in GenBank. Currently, I am not given the option of seaching against only ests when linking from BarleyBase. I can only BLAST against the nr database.
562003-11-25 08:21:30RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/hybvisualization.phpMicroarray Hybridizaion Visualization should be: Microarray Hybridization Visualization
552003-11-24 01:46:13StacyTurnersmturner@iastate.eduISUSite improvement http://barleypop.vrac.iastate.edu/BarleyBase/download.phpJust have a couple of suggestions here. 1. On the "downloads" page, the text in the tables should probably be top aligned. Or perhaps the tables should be reformatted for downloading experiment data, such that the heading bar is on the left side, and the information is in rows instead of columns. I think it would probably save space, and fix the alignment problem. 2. On the Microarray Hybridization Visualization charts need to be checked and the word "folds" should be replaced with "fold" (It should read, "two-fold change", not "two-folds change") 3. In the search function (the one that searches the whole website), would it be possible to block it from finding some things, like the feedback archive for instance?
542003-11-22 07:38:43VolkovichZeevzeev@actcom.co.ilOrt Braude CollegeProblem searching BarleyBase http://barleypop.vrac.iastate.edu/BarleyBase/download.phpDear Sir! I am looking for a Matlab or C implementation of the partitioning around medoid (PAM) clustering algorithm. Maybe you are aware of free versions of these implementations?
532003-11-18 16:49:27RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityDatabase improvement http://barleypop.vrac.iastate.edu/BarleyBase/probesetlist.phpLeft justify "Sequence_Description" column for easier reading.
522003-11-14 16:02:56RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/geneexpression.phpGeneral Filter Option: ������ Single filter -- Use the first checked filter. ������ Multiple filters -- Try all check filters. ������ Composite filters -- All check filters used together. should be: General Filter Option: ������ Single filter -- Use the first checked filter. ������ Multiple filters -- Try all checked filters. ������ Composite filters -- All checked filters used together.
512003-11-13 17:28:26SteveWhithamswhitham@iastate.eduisuDatabase improvement http://barleypop.vrac.iastate.edu/BarleyBase/barley1contig.phpplease do the same thing for this rice genome blast http://riceblast.dna.affrc.go.jp/cgi-bin/robo-blast/blast2.cgi?dbname=all as for TAIR and barley base blast. see previous email from us. steve and roger
502003-11-13 16:59:56SteveWhithamswhitham@iastate.eduISUDatabase improvement http://barleypop.vrac.iastate.edu/BarleyBase/barley1contig.phplink to http://www.arabidopsis.org/Blast/ so that barley sequences can be BLASTed directly against Arabidopsis AGI sequences. Track the contig that you are looking at the same way for barley base blast or ncbi blast. Steve and Roger
492003-11-11 18:59:23RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpCurrently BarleyBase should be:Currently, BarleyBase ...CHP files from 22K Affymetrix Barley1 and Arabidopsis GeneChip, ... should be: ...CHP files from the 22K Affymetrix Barley1 and Arabidopsis GeneChips, ..... ...or individual files through database experiments query. � should be: or individual files through database experiment query.� ...perform gene prediction should be: perform gene predictions
482003-11-11 15:32:19RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpI would encourage BB to correct the front page as soon as possible since manuscript reviewers may get the wrong impression from misuse of proper English terms. Thanks.
472003-11-11 15:06:40jianqiangxinjqxin@iastate.eduisuNone http://barleypop.vrac.iastate.edu/BarleyBase/index.phpIt seems that the link of BarleyExpress is linked to old login pages, it should link to bblogin.php.
462003-11-06 10:39:04RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversitySite improvement http://barleypop.vrac.iastate.edu/BarleyBase/index.phpUnder the caption "Thanks to ----------- for providing the photo ", we should put a note - "Click on picture to go the photo gallery" In additon you can hyperlink the word "photo gallery"
452003-11-06 07:41:27RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityProblem searching BarleyBase http://barleypop.vrac.iastate.edu/BarleyBase/barley1contig.php1. Feedback link should pop up in a new window. As it is now if you go back to look at the problem page, all form data is erased. This is inconvenient and deters people from providing thoughtful feedback. 2. Under "View exemplar annotation" BarleyBase blast should automatically paste the chosen sequence in the box. 3. Under NCBI Blast, you should not have to reselect your chosen exemplar; it should stay on the path you are following. Also there isno text box to see what your searching. 4. Under PlantGDB Blast, every thing works (if you know how to use PlantGDB) 5. Still problems with header in expression viewer
442003-11-05 10:05:31RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityProblem searching BarleyBase http://barleypop.vrac.iastate.edu/BarleyBase/geneexpression.phpIt would be excellent if you could query across experiments, for example, all the genes expressed in BB1 and BB3, or chips 1 and 2 from BB1 "and" chips 5-50 from BB3. Eventually we could do this for multiple experiments, say for BB3, BB4, and BB5, etc. Right now you can only query an individual experiment, correct?
432003-11-05 07:14:54RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityProblem interpreting data http://barleypop.vrac.iastate.edu/BarleyBase/geneexpression.phpwhat's going on here. if youare working on the interface, please do it off line as we have a manuscript in review right now. Reviewers may access the site and reject the manuscript because of things they do not understand.
422003-11-04 14:47:08RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/hybvisualization.phpMicroarray Hybridizaion Visualization should be: Visualization of GeneChip probe array hybridizations
412003-10-09 15:33:25RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTemporary delete http://barleypop.vrac.iastate.edu/BarleyBase/index.php( read more about Barley1 GeneChip development and history). Please delete this link from the front or any other other page (pull down History link from Project overview). We cannot have the history page available while we go through manuscript review. After the manuscript goes through review, we can restore it.
402003-10-07 14:31:14jianqiangxinjqxin@iastate.eduisuaSite improvement http://barleypop.vrac.iastate.edu/BarleyBase/index.phpComplete data sets made public by submitter will be open to all registered users at download center. The public data sets is accessible to all users no matter whether they registered or not.
392003-10-03 07:20:26jiangongjiangong@iastate.eduisuTypo http://barleypop.vrac.iastate.edu/BarleyBase/BarleyBaseFAQ.php 1.1 What is a BarleyBase? What is BarleyBase. BarleyBase is a MIAME-compliant, MySQL relational database, (Which )serves as a public repository for raw and normalized expression data from the Affymetrix Barley1- and ATH1-121501-GeneChips. 1.2 Where does the Funding for BarleyBase come from? BarleyBase is funded by USDA-NRI grant no. 2002-35300-12619 1.3 Does BarleyBase stores(store) only barley microarray data?
382003-09-23 12:19:21RicoCaldoracaldo@iastate.eduISUIncorrect help files http://barleypop.vrac.iastate.edu/BarleyBase/index.phpThe help files in the protocol binding and sample provider information in the overview of the sample preparation page are all the same and are all for growth condition help file description.
372003-09-21 06:26:13EveWurtelemash@iastate.eduISUwebbrowser quitsHi Lishuang, Barleybase looks great, but Mozilla quit on me three times when I tried to look at my data after entering it. This last time it didn't quit. I am not sure if its Mozilla, my computer or Barleybase, but I havent had previous problems. Also, there is some part of Barleybase information to enter (I see it for a second just before Mozilla quits) that looks interesting, but I cant get to it. Are all our fields filled in? Also, I would like to form a consortium, but am not sure how to register as such. Finally, there are two types of publications, those using the microarray data and those needed to interpret the data (for example information about the mutant used). I just entered the later in "commments". Not sure if "publications" is a better place. thanks much, Eve
362003-09-19 09:56:22RicoCaldoracaldo@iastate.eduISUcomputer problemThe URL and sample preparation date "fields" in the sample preparation page are not working in Mac but work in PC. We tried several browsers in Mac but still the same. I used PC just to finish the submission.
352003-09-19 08:00:12RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityData error http://barleypop.vrac.iastate.edu/BarleyBase/downloadpage.phpThe Barley Exemplar download files (txt) do not work. Try downloading and open the file to see.
342003-09-18 08:16:55RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.php probe sets names. should be: probe set names.
332003-09-18 08:11:36RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/test/downloadfile.phpChange to:->> Thanks for your interest in the BarleyBase download center. Raw data is generously provided by Barley1 GeneChip users. Use of these data from BarleyBase should cite the Accession number, original author, and the BarleyBase URL, http://barleybase.org/. Please supply your e-mail address to continue with the download.
322003-09-17 15:46:51RogerWiserpwise@iastate.eduUSDA-ARS / Iowa State UniversityTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.php"Thanks for Dr. Julie Dickerson providing the barley photo" should be worded "Thanks to Dr. Julie Dickerson for providing the barley photo" The same would apply to Dr. Pat Hayes or Dr. Roger Wise
312003-09-16 16:35:26RicoCaldoracaldo@iastate.eduISUProtocol submission pages http://barleypop.vrac.iastate.edu/BarleyBase/guide.php?page=usage_200309The "protocol resource field" is not working for all protocol submission pages. I couldn't save the item "Affymetrix manual" in the resource.
302003-09-16 15:26:54juliedickersonjulied@iastate.eduISUProblem searching BarleyBase http://barleypop.vrac.iastate.edu/BarleyBase/test/download.phpBatch Download list should contain the BB experiment number and the experiment summary should also contain this number
292003-09-15 17:52:28RicoCaldoracaldo@iastate.eduISUSample preparation page http://barleypop.vrac.iastate.edu/BarleyBase/index.phpThe field on sample preparation date is not working.
282003-09-11 14:50:37RogerWiserpwise@iastate.eduISUSite improvement http://barleypop.vrac.iastate.edu/BarleyBase/index.phpUse http://www.plantgdb.org/hordeum_vulgare.html as the link to Plant GDB instead of http://www.plantgdb.org/ on home page description eg. hrough collaboration with PlantGDB, multiple BLAST tools are provided to link users own sequences to BarleyBase
272003-09-11 13:12:41RogerWiserpwise@iastate.eduISUTypo http://barleypop.vrac.iastate.edu/BarleyBase/dataquery.phpThis experiement is kindly made public experiment !!! Spell check before you publish on the WWW!
262003-09-11 12:31:08RogerWiserpwise@iastate.eduISUTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpAll researchers are welcomed [welcome] to deposit their data from Barley1 GeneChip or Arabidopsis ATH1-121501 GeneChip through BarleyExpress,� our MIAME-compliant online submission tool based on ArrayExpress. Submitted data can be made public immediately, or hold as private for up to 270 days [180 days] at users designation. Submitters can make their private data accessible to designated groups or peoples, including manuscript reviewers.� [designated individuals or groups, including ....]
252003-09-09 06:33:59RicoCaldoracaldo@iastate.eduIowa State UniversityHelp Files in Protocol Submission http://barleypop.vrac.iastate.edu/BarleyBase/index.phpSome of the "Help files" got mixed-up in the different fields in the labelling, hybridization, scanning, washing and hybridization submission pages.
242003-09-04 21:45:31jiangongjiangong@iastate.eduisuTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.phpIn the banner of BarleyExpress: 'aray' should be 'array'
232003-09-02 21:54:25jiangongjiangong@iastate.eduisuTypo http://barleypop.vrac.iastate.edu/BarleyBase/test/feedbackcgi.phpAfter sending feedback, user can see a page that saying an email have been sent..., should be 'has'.
222003-09-02 21:51:49jiangongjiangong@iastate.eduisuTypo http://barleypop.vrac.iastate.edu/BarleyBase/test/query_probeset.phpRadio button at the bottom doesn't work
212003-08-27 10:22:06RicoCaldoracaldo@iastate.eduIowa State UniversitySubmission Page http://barleypop.vrac.iastate.edu/BarleyBase/index.phpI was trying to submit the cross-species experiment but an error showed up when I clicked the Save/Continue button in the Experimental Design page (It says "the page is outdated").
202003-08-26 14:45:00RogerWiserpwise@iastate.eduISUTypo http://barleypop.vrac.iastate.edu/BarleyBase/index.php"A community resource for cereal microarrays" should be A community resource for cereal GeneChip probe arays This is more accurate. Technically, a chip is not the same as a microarray.
192003-08-14 20:27:49jianqiangxinjqxin@iastate.eduisuWhat I like about BarleyBase http://barleypop.vrac.iastate.edu/BarleyBase/index.phpThis is a test.
182003-08-13 05:16:50jianqiangxinjqxin@iastate.eduisuWhat I like about BarleyBase http://barleypop.vrac.iastate.edu/BarleyBase/barleypic.phpThese pics are very beatiful.
172003-06-19 16:04:31RogerWiserpwise@iastate.eduISUProblem searching BarleyBasehttp://barleypop.vrac.iastate.edu/BarleyBase/guide.php?page=toolsThe tools link points to an old barley base page. What hapened to the new tools page?
162003-06-16 23:02:13LishuangShenlshen@iastate.eduISUData errorhttp://barleypop.vrac.iastate.edu/BarleyBase/guide.php?page=submissionsMy input on radiobox and several textboxes lost when I hit the "Help" button, or when I submit the unfinished submission and was asked to go back.
152003-06-13 10:25:25RogerWiserpwise@iastate.eduISUSite improvementhttp://barleypop.vrac.iastate.edu/BarleyBase/guide.php?page=submissionsExtract Protocol should be spelled Extraction Protocol Replace funny font (for titles) in BarleyExpress
142003-06-13 10:22:15RogerWiserpwise@iastate.eduISUDatabase improvementhttp://barleypop.vrac.iastate.eduguide.php?page=diagramSearch drop down list ends at Barley1_8017 on MACs
132003-06-12 12:33:05RogerWiserpwise@iastate.eduISUhttp://barleypop.vrac.iastate.edu/BarleyBase/guide.php?page=diagramMy mistake - Mouse over probes does NOT function in Safari
122003-06-12 12:20:41RogerWiserpwise@iastate.eduISUWhat I like about BarleyBasehttp://barleypop.vrac.iastate.eduguide.php?page=diagramOK - Probe aligment diagram is runnning great on Mac Explorer and Safari. Mouse over probes does function in Safari Mouse over in Explorer is cool!
112003-06-12 11:48:09RogerWiserpwise@iastate.eduISUTypohttp://barleypop.vrac.iastate.edu/BarleyBase/guide.php?page=submissionsBarleyExpress:� A tool for Barley Microarray Experiment Submission. (based on ArrayExpress should be: BarleyExpress:� A tool for Barley Microarray Experiment Submission (based on ArrayExpress).
102003-06-11 19:21:01RogerWiserpwise@iastate.eduisuhttp://barleypop.vrac.iastate.edu/BarleyBase/guide.php?page=fundingBarleyExpress: A tool for Barley Microarray Experiment Submission (based on ArrayExpress) GOES UNDER DATA SUBMISSION; NOT FUNDING!
92003-06-11 11:06:11RogerWiserpwise@iastate.eduISUProblem searching BarleyBaseOn the probe alignment diagram, there is no blast search available anymore, at least on Mac Explorer and Mac Safari Mouse over of probes (green bars) does not work for either browser Make probe entry such that a typed in entry has precedence over a drop down entry if both are entered; do not make user choose only one Also, put in a reset button for drop down or type-in fields
82003-06-11 09:06:13RogerWiserpwise@iastate.eduISUDatabase improvementFinancial support This database is supported by * USDA Initiative for Future Agriculture and Food Systems (IFAFS) #01-52100-11346 9/1/01 - 8/31/04; ?An integrated physical and expression map of barley for Triticeae improvement? to Andris Kleinhofs, Roger P. Wise, Rod A. Wing, Timothy J.Close, Gary J. Muehlbauer. * USDA-NRI/CGP #2002-03582 9/15/02 - 9/31/05; "BarleyBase, a prototype online database for cereal microarrays with integrated tools for data visualization and statistical analysis" to J. Dickerson, Computer and Electrical Engineering; V. Brendel, Zoology & Genetics; R. Wise, Plant Pathology; D. Cook and D. Nettleton, Statistics; Dan Ashlock, Mathematics. * USDA-CSREES North American Barley Genome Project funds to Roger P. Wise, Daniel A. Ashlock and Julie A. Dickerson. Also under submission: BarleyExpress: A tool for Barley Microarray Experiment Submission (based on ArrayExpress; http://www.ebi.ac.uk/arrayexpress/)
72003-06-11 05:51:44juliedDickersonjulied@iastate.eduISUProblem searching BarleyBaseThe probe alignment page does not work with IEv5.2 on the Mac. It loads very slowly as reported by Roger. The mouse over effect does not work on the table either. I will check safari later.
62003-06-03 15:16:57RogerWiserpwise@iastate.eduISUAdd links to http://www.plantgdb.org/hordeum_vulgare.html under news for 6/3/03 with note: BLAST the Barley1 GeneChip.
52003-05-21 11:46:03RogerWiserpwise@iastate.eduISUDatabase improvementPull down menu under DB overview has subjects in dark blue on a blue background (Mac Explorer) When I try to sign up for a Barley express password, it says "error"
42003-05-20 10:05:02RogerWiserpwise@iastate.eduISUDead linkBarleyBase is a public repository for barley microarray expression data, including experiment descriptions, array design and analysis. "barley microarray" link is broken
32003-05-14 10:04:54RogerWiserpwise@iastate.eduISUDatabase improvementBarleyBase is featured as a MIAME-compliant, relational database. It is based on the MAGE-OM object model and currently implemented in MySQL at Iowa State University. Hyperlink "Iowa State University" on the home page In PGDB, feedback has a new function to let the DB adminstrator know where user was when they clicked "feedback" Please incorporate this.
22003-05-07 11:51:05RogerWiserpwise@iastate.eduISUData errorhttp://www.barleybase.org is actually http://barleybase.org; no www
12003-05-07 11:48:10RogerWiserpwise@iastate.eduISUTypoArabidopsis thaliana should have a lower case t in thaliana Feedback should pop up a new window, not come up inthe same window
02003-05-05 13:35:55DennisHaltermandhalterm@iastate.eduIowa StateDead linkFirst link in text of home page: "barley microarray" expression data does not work. Link should be http://barleypop.vrac.iastate.edu/BarleyBase/barleychip.htm

 
Copyright@2001-2005 The BarleyBase Group
All rights reserved.

For problems with the webpages, contact barleybasewebmaster