Difference between revisions of "Playground"

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<p style="font-size:30pt" align="center"> Welcome to the Playground!</p>
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<p style="font-size:25pt" align="center"> Oksana Palchevska (Kuzmenko)</p>
  
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[[ycbP]] [[yckB]] [[ycsA]] [[gmuB]] [[ydzA]] [[yesL]] [[yfiG]] [[iolX]] [[ykoM]] [[yncC]] [[yqgW]] [[yqgY]] [[yrpD]] [[ysbA]] [[ysfC]] [[ytkA]] [[yugN]] [[yulD]] [[yuxG]] [[yvdG]] [[yvfK]] ''[[yxlH]]'' [[yydK]] [[yyzE]]
 
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__TOC__
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<big>Welcome to '''''Subti''Wiki'''! </big> - ''Bacillus subtilis'' annotation the "wiki" way!<br/>
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[[File:Start_page_small.png|right|link=http://www.subtiwiki.uni-goettingen.de/]]
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[[File:Playground_small.png|right|link=http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Playground]]
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[[File:Wish_List_small.png|right|link=http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Wish_List]]
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<br/>
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<big>'''Contact:'''</big> [http://wwwuser.gwdg.de/~genmibio/stuelke.html General Microbiology, University of Göttingen], [mailto:jstuelk@gwdg.de send mail]
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<br/>
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<big>'''Upcoming events:'''</big>
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* The [http://www.grampositiveconference.org/  7th International Conference on Gram-positive Microorganisms] (17th International Conference on Bacilli) organized by [[Marta Perego]], [[Jim Hoch]], and [[Hendrik Szurmant]] is going to take place from June 23 - 27, 2013, in [http://www.montecatini.it/english/ Montecatini Terme] in lovely Tuscany, Italy, [http://www.grampositiveconference.org/ conference website], [mailto:fchizer@scripps.edu contact]
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* [[Past conferences]]
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<br/>
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<big>'''New: Subtiwiki is now on [http://www.facebook.com/pages/SubtiWiki/201847669864806 Facebook] - please give it a +1!'''</big>
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<br/>
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<big>'''Now online: A description of ''Subti''Wiki, ''Subti''Pathways, and ''Subt''Interact in the [http://nar.oxfordjournals.org/content/40/D1/D1278.full.pdf+html 2012 Database issue of Nucleic Acids Research]'''</big>
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<pubmed> 22096228 </pubmed>
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<br/>
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<big>'''Paper of the month: September 2012'''</big>
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* [http://www.ncbi.nlm.nih.gov/pubmed/22864117 Chiba and Ito] studied how the translation of [[YidC2]], a membrane protein biogenesis factor, is controlled by [[SpoIIIJ]] availability via ribosome stalling of the ''[[mifM]]'' mRNA.
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* '''Relevant ''Subti''Wiki pages:'''  [[Koreaki Ito]], [[translation]], [[YidC2]], [[SpoIIIJ]], ''[[mifM]]''
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<pubmed> 22864117 </pubmed>
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* [[Previous papers of the month]]
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<br/>
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<big>'''New procedure for account creation:'''</big>
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* Due to massive spam attacks, we had to change our policy for the creation of accounts. If you want to create an account, just [mailto:jstuelk@gwdg.de send me a mail]. We will create the account for you as quickly as possible, then you can change your password. This does not affect existing accounts, which remain active. <br/>
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* '''Please remember that all members of the ''Bacillus'' community are invited to create accounts and to contribute to ''Subti''Wiki!'''
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<br/><br/>
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<big>'''News in ''Subti''Wiki:'''</big>
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* '''September 2012''': 300 mutant strains available at the [http://www.bgsc.org BGSC] were added to the corresponding gene pages
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* '''August 2012''': [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express], the new compagnon of ''Subti''Wiki devoted to gene expression is online! Try it out!
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* '''May 2012:''' updated Excel files that map all genes to [[categories]] and [[regulons]] as well as the general updated identity mapping of all genes were uploaded.
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* '''April 2012:''' Links for expression data under 104 different conditions (based on [http://www.ncbi.nlm.nih.gov/pubmed/22383849 Nicolas ''et al''., 2012]) have been added to the expression section of the individual gene pages
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* '''April 2011:''' [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact], a presentation of [[protein-protein interactions]] in ''B. subtilis'', is online!
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* '''December 2010:''' [http://cellpublisher.gobics.de/scp.html SubtiCellPublisher] allows the conversion of CellDesigner diagrams to navigatable presentations in the style of [[SubtiPathways]]
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* '''December 2010:''' all genes are linked to [[regulons]], and the pages of the [[regulons]] provide an overview on all genes that are members of this specific regulon.
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* '''December 2010:''' all genes/proteins are linked to [[categories]], and the pages of the [[categories]] provide an overview on all genes/proteins that are members of this specific category.
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<br/>
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{| border="0" cellpadding="1"
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|width="300"|<big>'''Genes''' (examples)</big>
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|width="300"|<big>'''Additional pages'''</big>
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|- style="height:20px"
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| ''[[spo0A]]'' || '''[http://subtipathways.uni-goettingen.de ''Subti''Pathways]'''
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|-
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| ''[[glnA]]'' ||  '''[[Lists of genes, proteins and RNAs]]'''
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|-
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| ''[[rny]]'' ||  '''[[Categories]]'''
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|-
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| ''[[psdA]]'' || '''[[Regulons]]'''
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|-
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| ''[[pckA]]'' || '''[[methods]]'''
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|-
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| ''[[dnaA]]'' ||  '''[[metabolism]]'''
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|-
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| ''[[rnpA]]'' ||  '''[[protein-protein interactions]]'''
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|-
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| ''[[sigB]]'' || '''[[genome-wide analyses]]'''
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|-
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| ''[[ptkA]]'' || '''[[list of plasmids]]'''
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|-
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| ''[[mreC]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
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|-
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| ''[[ccpA]]'' || '''[[the people behind SubtiWiki|the people behind ''Subti''Wiki]]'''
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|-
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| ''[[sr1]]'' || '''[[template]]'''
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|-
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|  ||
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|}
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<br>
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<big>'''Publications describing ''Subti''Wiki and ''Subti''Pathways:'''</big>
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<div style="width:73%"><pubmed>20157485 19959575</pubmed></div>
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<br><br><br><br><br><br>

Latest revision as of 14:08, 19 September 2012

Oksana Palchevska (Kuzmenko)

ycbP yckB ycsA gmuB ydzA yesL yfiG iolX ykoM yncC yqgW yqgY yrpD ysbA ysfC ytkA yugN yulD yuxG yvdG yvfK yxlH yydK yyzE


Welcome to SubtiWiki! - Bacillus subtilis annotation the "wiki" way!

Start page small.png
Playground small.png
Wish List small.png


Contact: General Microbiology, University of Göttingen, send mail


Upcoming events:


New: Subtiwiki is now on Facebook - please give it a +1!



Now online: A description of SubtiWiki, SubtiPathways, and SubtInteract in the 2012 Database issue of Nucleic Acids Research

Ulrike Mäder, Arne G Schmeisky, Lope A Flórez, Jörg Stülke
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis.
Nucleic Acids Res: 2012, 40(Database issue);D1278-87
[PubMed:22096228] [WorldCat.org] [DOI] (I p)



Paper of the month: September 2012

Shinobu Chiba, Koreaki Ito
Multisite ribosomal stalling: a unique mode of regulatory nascent chain action revealed for MifM.
Mol Cell: 2012, 47(6);863-72
[PubMed:22864117] [WorldCat.org] [DOI] (I p)


New procedure for account creation:

  • Due to massive spam attacks, we had to change our policy for the creation of accounts. If you want to create an account, just send me a mail. We will create the account for you as quickly as possible, then you can change your password. This does not affect existing accounts, which remain active.
  • Please remember that all members of the Bacillus community are invited to create accounts and to contribute to SubtiWiki!



News in SubtiWiki:

  • September 2012: 300 mutant strains available at the BGSC were added to the corresponding gene pages
  • August 2012: SubtiExpress, the new compagnon of SubtiWiki devoted to gene expression is online! Try it out!
  • May 2012: updated Excel files that map all genes to categories and regulons as well as the general updated identity mapping of all genes were uploaded.
  • April 2012: Links for expression data under 104 different conditions (based on Nicolas et al., 2012) have been added to the expression section of the individual gene pages
  • April 2011: SubtInteract, a presentation of protein-protein interactions in B. subtilis, is online!
  • December 2010: SubtiCellPublisher allows the conversion of CellDesigner diagrams to navigatable presentations in the style of SubtiPathways
  • December 2010: all genes are linked to regulons, and the pages of the regulons provide an overview on all genes that are members of this specific regulon.
  • December 2010: all genes/proteins are linked to categories, and the pages of the categories provide an overview on all genes/proteins that are members of this specific category.


Genes (examples) Additional pages
spo0A SubtiPathways
glnA Lists of genes, proteins and RNAs
rny Categories
psdA Regulons
pckA methods
dnaA metabolism
rnpA protein-protein interactions
sigB genome-wide analyses
ptkA list of plasmids
mreC labs working on Bacillus
ccpA the people behind SubtiWiki
sr1 template


Publications describing SubtiWiki and SubtiPathways:

Lope A Flórez, Sebastian F Roppel, Arne G Schmeisky, Christoph R Lammers, Jörg Stülke
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.
Database (Oxford): 2009, 2009;bap012
[PubMed:20157485] [WorldCat.org] [DOI] (I p)

Christoph R Lammers, Lope A Flórez, Arne G Schmeisky, Sebastian F Roppel, Ulrike Mäder, Leendert Hamoen, Jörg Stülke
Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.
Microbiology (Reading): 2010, 156(Pt 3);849-859
[PubMed:19959575] [WorldCat.org] [DOI] (I p)







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