Difference between revisions of "User talk:Girlwithglasses"

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==GMOD website feedback extension==
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| http://agripestbase.org || Agripestbase || Agricultural pests || || 2013
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===In brief===
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| http://agripestbase.org/hessianfly || Hessian fly || part of Agripestbase || || 2013
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A tool to allow anyone to submit a comment or feedback on any page of the GMOD wiki.
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| http://agripestbase.org/manduca || Manduca sexta || part of Agripestbase || || 2013
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===Possible plug in uses===
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| http://amoebadb.org || AmoebaDB || Amoeba (part of EupathDB) || || 2013
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*Rate this page - give feedback on how easy/difficult a tutorial or piece of documentation is to follow
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*Geographic location - two possible uses:
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| http://aphidbase.com/ || AphidBase || Pea aphid genome || Yes || 200x || +www
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##Express interest in having a GMOD workshop/meeting in a certain area
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##Add your DB and location to the [[GMOD Users]] list
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| http://arabidopsis.org || [[:Category:TAIR|TAIR]] ||  ||  || 200x || +www
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*Generic feedback - send a message to GMOD help if something is broken (e.g. OpenID login!) or a mistake is found
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| http://arpcard.mcmaster.ca/ || The Comprehensive Antibiotic Resistance Database ||  || Yes || 200x
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===Details===
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| http://atidb.org || ATIDB || Arabidopsis ||  || 200x
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*clicking a link/button/icon brings up a form for submitting feedback
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**use jQuery to bring up form as a modal dialogue box
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| http://banana-genome.cirad.fr/ || Banana Genome Hub ||  || Tripal || 2013
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*the extension should allow anyone, whether they are a member of the wiki or not, to give feedback
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| http://beetlebase.org/ || BeetleBase || ''Tribolium castaneum''<br>Gbrowse, JBrowse || Yes || 2013
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**if the person is a logged-in wiki member, record their name
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**ask for name/email otherwise
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| http://biocomp.dfci.harvard.edu/tgi/ || TGI || The Gene Index Project ||  || 200x
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*form should be configurable
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| http://biohealthbase.org/GSearch/ || BioHealthBase || BioDefense Public Health Database ||  || 200x || +www
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**store the form in a Template page on the wiki? Or in its own namespace? See Mediawiki Widgets for examples of widgets in their own namespace
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**embed a locally-stored form (i.e. store the form html on the server and present it in an iframe)?
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| http://bioinf.scri.sari.ac.uk/ || SCRI Plant Bioinformatics Group ||  || Yes || 200x
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**have the form content dynamically created from some sort of shorthand specification? e.g.
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  <feedback>
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| http://bioinfo.ccbusm.edu.my/cgi-bin/gb2/gbrowse/Rubber/ || Rubber Genome Browser ||  ||  || 200x
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  [{ label = 'Name',
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    name = username,
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| http://bovinegenome.org/ || BGD || Bovine Genome Database ||  || 200x
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    type = text,
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    value = '',
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| http://bovineqtl.tamu.edu || Bovine QTL Viewer ||  ||  || 200x
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    required = true,
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  },
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| http://cacaogenomedb.org || Cacao Genome Database || Cacao || Tripal || 2013 || +www
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  { label = 'Rate the contents of this page',
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    name = page_rating,
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| http://candidagenome.org/cgi-bin/gbrowse/candida_20/ || CGD || Candida Genome Database ||  || 200x || +www
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    type = radio,
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    value = ['poor','ok','good'],
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| http://chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2/ || Chromosome 7 Annotation Project ||  ||  || 200x || +www
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    required = true,
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  }]
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| http://chromdb.org/ || ChromDB || Plant Chromatin Database ||  || 200x || +www
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  </feedback>
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| http://ciliate.org/ || TGD || Tetrahymena Genome Database ||  || 2013 || +www
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*how do we stop users from sabotaging the form, either accidentally or deliberately?
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**security risks?
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| http://citrusgenomedb.org || Citrus Genome Database || Citrus || Tripal || 2013 || +www
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*some method for blocking automated submissions is required -- i.e. a captcha
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| http://citrusgreening.org/ || Citrus Greening || pathogens causing citrus greening (Huanglongbing or HLB), esp. ''Liberibacter'' ||  || 2013
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*submitting and storing form data:
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| http://coccidia.icb.usp.br/eimeriatdb/ || ''Eimeria'' transcript database || Annotated transcripts of protozoan parasites of the genus Eimeria ||  || 2013 || +www
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**how/where to store it?
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***in the wiki itself
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| http://comparative-legumes.org/ || LIS || Legume Information System ||  || 2013 || +www
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****investigate how existing ratings extensions store their data
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***in a local text file or database
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| http://cosmoss.org || cosmoss.org || The Bryophyte Genomics Resource - ''Physcomitrella patens'' Annotation ||  || 200x || +www
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***in a remote text file or db, e.g. in Google docs
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***email the data
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| http://cottongen.org/ || Cottongen ||  || Tripal || 2013 || +www
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*can the plugin appear on every page in a category without having to manually add it to each page?
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| http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/ || ANISEED || Ascidian Network for In Situ Expression and Embryological Data ||  || 200x
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| http://cryptodb.org || CryptoDB || Cryptosporidium (part of EupathDB) || GBrowse, Cyc|| 2013
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| http://db.yeastgenome.org/cgi-bin/gbrowse/scgenome/ || [[:Category:SGD|SGD]] ||  ||  || 200x
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| http://db.yeastgenome.org/cgi-bin/gbrowse/scproteome/ || S. cerevisiae Proteome Browser ||  ||  || 200x
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| http://dictybase.org || [[:Category:DictyBase|DictyBase]] ||  || Yes || 200x || +www
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| http://ecocyc.org/ || EcoCyc ||  ||  || 200x
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| http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/ || eQTL browser || eQTLs identified in recent studies in multiple tissues @ [http://pritch.bsd.uchicago.edu/ Pritchard lab, UChicago] || || 2013
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| http://equinegenome.org/ || Equine Genome || Equus caballus ||  || 200x || +www
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| http://eupathdb.org || EupathDB || Eukaryotic pathogens, including Babesia, Crithidia, Cryptosporidium, Edhazardia, Eimeria, Encephalitozoon, Endotrypanum, Entamoeba, Enterocytozoon, Giardia, Gregarina, Hamiltosporidium, Leishmania, Nematocida, Neospora, Nosema, Plasmodium, Theileria, Toxoplasma, Trichomonas, Trypanosoma, and Vivraia || || 2013
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| http://fagaceae.org || Fagaceae Genomics Web || ''Fagaceae'' spp, including oak, beech, chestnut, etc. || Tripal || 2013
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| http://flybase.org || [[:Category:FlyBase|FlyBase]] || A Database of Drosophila Genes & Genomes || Yes || 2013 || +www
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| http://fungal.genome.duke.edu/ || Fungal Comparitive Genomics ||  ||  || 200x
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| http://fungus.kbrin.uky.edu/cgi-bin/gbrowse/A_fumigatus_tigr_tel_100k || A. fumigatus TIGR/Sanger Assembly ||  ||  || 200x
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| http://gabcsfl.org || Cool Season Food Legume Database || Cool season legumes, e.g. pea, lentil, chickpea, fava beans, etc. || Tripal || 2013
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| http://genedb.org || GeneDB || Pathogen Sequenceing Unit || Yes || 200x || +www
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| http://genetics.ucla.edu/labs/nelson/ || ??? || Microarray data, Chado, H. sapiens || Yes || 200x
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| http://genome.kbrin.uky.edu/fungi_tel/browser.html || Fungal Telomere Browser ||  ||  || 200x
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| http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken || Gallus Genome Browser ||  ||  || 200x
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| http://giardiadb.org || GiardiaDB || Giardia (part of EupathDB) || || 2013
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| http://gmod.mbl.edu/ || JBPC Generic Model Organism Database servers || Huge set of GMOD/GBrowse resources covering many different species ||  || 2013
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| http://gramene.org || [[:Category:Gramene|Gramene]] ||  ||  || 2013 || +www
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| http://hapmap.org/cgi-perl/gbrowse/ || HapMap ||  ||  || 200x || +www
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| http://hardwoodgenomics.org || Hardwood Genomics Project || Hardwood tree spp || Tripal || 2013 || +www
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| http://hcgs.unh.edu/gbrowse/ || UNH HCGS Tetraodon Genome Browser || Gbrowse plus GFF ||  || 200x
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| http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/ || Human Genome Diversity Project || HGDP @ [http://pritch.bsd.uchicago.edu/ Pritchard lab, UChicago] || || 2013
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| http://huref.jcvi.org/browse.html || JCVI || J. Craig Venter Institute || Yes || 200x
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| http://hymenopteragenome.org/beebase/ || BeeBase ||  ||  || 2013
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| http://ich.ciliate.org/ || IchDB || Ichthyophthirius multifiliis genome || || 2013
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| http://influenza.genomics.org.cn/ || IVDB || Influenza Virus Database ||  || 200x
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| http://informatics.jax.org/ || [[:Category:MGI|MGI]] ||  ||  || 200x || +www
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| http://inra.fr/lepidodb || Lepido dB || Lepidoptera database; covers '''Helicoverpa armigera''' and '''Spodoptera frugiperda''' || || 2012 || +www
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| http://insects.eugenes.org/DroSpeGe/ || DroSpeGe ||  ||  || 200x
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| http://irfgc.irri.org/cgi-bin/gbrowse || OryzaSNP ||  ||  || 200x
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| http://jcvi.org || TIGR || The Institute for Genomic Research || Yes || 200x || +www
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| http://knowpulse2.usask.ca/portal/ || KnowPulse: Pulse Crop Genomics & Breeding || Chickpea, lentil, common bean, pea || Tripal || 2013
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| http://livestockgenomics.csiro.au/ || Livestock Genomics || CSIRO Livestock Industries (LI) livestock genomics; covers bovines and ovines || || 2013 || +www
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| http://magi.plantgenomics.iastate.edu/ || MAGI || Maize Assembled Genomic Island ||  || 200x
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| http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=01_azm2bac || AZM-to-BAC Viewer ||  ||  || 200x
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| http://maizeapache.ddpsc.org/cgi-bin/gbrowse.cgi?source=02_azm2gene || AZM-to-Gene Viewer ||  ||  || 200x
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| http://map.lab.nig.ac.jp/cgi-bin/gbrowse/Oryza_chr8/ || Oryza Chromosome 8 ||  ||  || 200x
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| http://marinegenomics.org || Marine Genomics || Multispecies marine organism database || Tripal || 2013 || +www
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| http://me.lzu.edu.cn/yak/ || Yak Genome Database || Yak genome ||  || 2013
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| http://microsporidiadb.org || MicrosporidiaDB || Microsporidia (part of EupathDB) || || 2013
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| http://mips.gsf.de/cgi-bin/proj/plant/gbrowse/synbrowse || PlantsDB || MIPS PlantsDB ||  || 200x
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| http://nypg.bio.nyu.edu/vicogenta/ || Vicogenta || Viewer for Comparing Genomes to Arabidopsis ||  || 200x
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| http://omap.org/ || OMAP || Oryza Map Alignment Project || || 200x || +www
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| http://orygenesdb.cirad.fr/ || OryGenesDB ||  ||  || 200x
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| http://paramecium.cgm.cnrs-gif.fr/ || [[ParameciumDB]] ||  || Yes || 200x
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| http://patricbrc.org || PATRIC  || Pathosystems Resource Integration Center || JBrowse || 2013
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| http://peanutgenetics.tamu.edu/cmap/ || PeanutMap ||  ||  || 200x
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| http://piroplasmadb.org || PiroplasmaDB || Piroplasma (part of EupathDB) || || 2013
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| http://plasmodb.org || PlasmoDB || Plasmodium (part of EupathDB) || || 2013
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| http://popgenie.org/ || PopGenIE || The Populus Genome Integrative Explorer ||  || 200x
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| http://possumbase.org.nz/cgi-bin/gbrowse/mondom4/ || PossumBase ||  ||  || 200x || +www
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| http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b36 || Human Genome Segmental Duplication Database ||  ||  || 200x
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| http://projects.tcag.ca/variation/cgi-bin/gbrowse/hg17 || Database of Genomic Variants ||  ||  || 200x
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| http://projects.tcag.ca/xenodup/gbrowse.php || Non-Human Segmental Duplication Database ||  || ||
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| http://puma.princeton.edu/ || PUMAdb || Princeton Microarray Database, Chado ||  || 200x
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| http://racerx00.tamu.edu/cgi-test/searchCattleDatabase.html || Cattle EST Gene Family Database ||  ||  || 200x
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| http://rgd.mcw.edu || [[:Category:RGD|RGD]] || Rat Genome Database ||  || 200x
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| http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice || MSU Rice Genome Browser ||  ||  || 200x
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| http://rosaceae.org || Genome Database for Rosaceae || Rosaceae species || Tripal || 2013 || +www
+
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| http://rulai.cshl.edu/cshlmpd/credit.html || CSHLmpd || Mammalian Promoter Database ||  || 200x
+
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| http://sgdlite.princeton.edu/ || SGD Lite ||  ||  || 200x
+
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| http://smedgd.neuro.utah.edu/ || SmedGD || Planaria ESTs || Yes || 200x
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| http://solgenomics.net/ || [[:Category:SGN|Sol Genomics Network]] ||  || Yes || 200x
+
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| http://soybase.org/ || SoyBase || USDA Soybean Genetics and Genomics Database || No || 200x
+
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| http://soybeangenome.siu.edu/ || Soybean [[GBrowse]] Database ||  ||  || 200x
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| http://spbase.org || SpBase || Genome sequence and annotations produced by the [http://www.hgsc.bcm.tmc.edu/ Baylor College of Medicine Human Genome Sequencing Center] and the sea urchin research community. ||  || 200x
+
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| http://t1dbase.cimr.cam.ac.uk/cgi-bin/gbrowse/2q33/ || Human 2q33 ||  ||  || 200x
+
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| http://t1dbase.org/cgi-bin/dispatcher.cgi/Welcome/display || T1DBase || Type 1 Diabetes Database ||  || 200x
+
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| http://tigr.org/tigr-scripts/medicago/gbrowse_bacs.pl || TIGR Medicago BACs ||  ||  || 200x || +www
+
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| http://toxodb.org || ToxoDB || Toxoplasma (part of EupathDB) || || 2013
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| http://treetfdb.bmep.riken.jp/index.pl || TreeTFDB || transcription factors (TF) of papaya (''Carica papaya''), jatoropha (''Jatropha curcas''), cassava (''Manihot esculenta''), poplar (''Populus trichocarpa''), castor bean (''Ricinus communis'') and grape vine (''Vitis vinifera'') ||  || 2013
+
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| http://trichdb.org || TrichDB || Trichomonas (part of EupathDB) || || 2013
+
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+
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| http://tritrypdb.org || TriTrypDB || Kinetoplastids (part of EupathDB) || || 2013
+
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+
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| http://tropgenedb.cirad.fr/ || TropGENE DB || genetic and genomic information about tropical crops studied by [http://www.cirad.fr/ Cirad]. ||  || 200x
+
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| http://uclaaccess.ucla.edu/UCLAACCESS/Web/Faculty.aspx?ri=58 || ??? || Trichomona vaginalis || Yes || 200x || +www
+
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|-
+
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| http://urgi.infobiogen.fr/projects/TriAnnot/GBrowse.php || TriAnnot BAC Viewer ||  ||  || 200x
+
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+
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| http://v2.pseudomonas.com/whats_new.jsp || PseudoCAP || Pseudomonas Genome Database ||  || 200x
+
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+
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| http://vaccinium.org/ || Genomic DB for Vaccinium || Blueberry, cranberry, lingonberry, other Vaccinium spp. || Tripal || 2013 || +www
+
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|-
+
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| http://vectorbase.org || VectorBase || Chado, DAS, Apollo || Yes || 2013 || +www
+
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|-
+
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| http://wfleabase.org/ || wFleaBase || Daphnia || Yes || 200x
+
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|-
+
−
| http://wheat.pw.usda.gov/ || GrainGenes ||  ||  || 200x
+
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|-
+
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| http://wheatgenome.info/ || Wheat Genome || Wheat || || 2013 || +www
+
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|-
+
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| http://wormbase.org || [[:Category:WormBase|WormBase]] ||  ||  || 200x || +www
+
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|-
+
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| http://xanthusbase.org/ || XanthusBase ||  || Yes || 200x || +www
+
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|-
+
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| http://xenbase.org/ || Xenbase ||  ||  || 200x || +www
+
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|-
+
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| http://xmap.ftdna.com/ || Xmap || Human X chromosome map for SNP and STR markers used in genetic genealogy and anthropology || No || 2009
+
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|-
+
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| http://yandell-lab.org/cgl/ || CGL || Comparative Genomics Library ||  || 200x || +www
+
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|-
+
−
| http://ymap.ftdna.com/ || Ymap || Human Y chromosome map for SNP and STR markers used in genetic genealogy and anthropology || No || 2009
+
−
|}
+

Latest revision as of 14:15, 1 July 2013

GMOD website feedback extension

In brief

A tool to allow anyone to submit a comment or feedback on any page of the GMOD wiki.

Possible plug in uses

  • Rate this page - give feedback on how easy/difficult a tutorial or piece of documentation is to follow
  • Geographic location - two possible uses:
    1. Express interest in having a GMOD workshop/meeting in a certain area
    2. Add your DB and location to the GMOD Users list
  • Generic feedback - send a message to GMOD help if something is broken (e.g. OpenID login!) or a mistake is found

Details

  • clicking a link/button/icon brings up a form for submitting feedback
    • use jQuery to bring up form as a modal dialogue box
  • the extension should allow anyone, whether they are a member of the wiki or not, to give feedback
    • if the person is a logged-in wiki member, record their name
    • ask for name/email otherwise
  • form should be configurable
    • store the form in a Template page on the wiki? Or in its own namespace? See Mediawiki Widgets for examples of widgets in their own namespace
    • embed a locally-stored form (i.e. store the form html on the server and present it in an iframe)?
    • have the form content dynamically created from some sort of shorthand specification? e.g. 
 <feedback>
 [{ label = 'Name',
    name = username,
    type = text,
    value = ,
    required = true,
  },
  { label = 'Rate the contents of this page',
    name = page_rating,
    type = radio,
    value = ['poor','ok','good'],
    required = true,
  }]
 </feedback>
  • how do we stop users from sabotaging the form, either accidentally or deliberately?
    • security risks?
  • some method for blocking automated submissions is required -- i.e. a captcha
  • submitting and storing form data:
    • how/where to store it?
      • in the wiki itself
        • investigate how existing ratings extensions store their data
      • in a local text file or database
      • in a remote text file or db, e.g. in Google docs
      • email the data
  • can the plugin appear on every page in a category without having to manually add it to each page?
Retrieved from "http://gmod.org/mediawiki/index.php?title=User_talk:Girlwithglasses&oldid=23755"