Difference between revisions of "Main Page"

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Welcome to Subtiwiki!
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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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This Wiki is in an early stage of development.
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<br/>
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<big>'''Upcoming events:'''</big>
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* The [http://www.bacillus-2017.de/ 19th International Conference on Bacilli & Gram-Positive Bacteria] organized by [[Jörg Stülke]] will take place from June 11 to June 15, 2017, in Berlin, Germany. [http://www.bacillus-2017.de/ Conference website]
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* [[Past conferences]]
  
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To try how it works, go to the [[playground]]!
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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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If you have any suggestions, please add them to the [[Wish List]]!
 
  
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Pages for all genes are now available, but the information is not complete. To get an idea of how it could look like, visit one of the pages below:
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<br/>
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<big>'''Now online: A new description of ''Subti''Wiki and its acompanying modules in the [https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1006 2016 Database issue of Nucleic Acids Research]'''</big>
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<pubmed> 24178028 </pubmed>
  
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* [[gltA]]
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<br/>
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* [[gltB]]
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<big>'''Paper of the month: August 2015'''</big>
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* [[gltC]]
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* The cells in a biofilm experience very different conditions: While the inner cells are well protected from any harm from the environment, they have on the other hand only poor access to nutrients. For the cells on the edge of the biofilm, it is just the other way round. Now, [http://www.ncbi.nlm.nih.gov/pubmed/26200335 Liu et al.] from the lab of [[Gürol M. Süel]] have discovered oscillation in the [[biofilm formation|growth of the biofilm]]. These oscillations serve to provide the inner cells with access to nutrients. These oscillations are caused by metabolic co-dependence between cells in the biofilm periphery and interior that is driven by [[glutamate metabolism|glutamate consumption and ammonium production]], respectively.
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* [[rocG]]
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* '''Relevant ''Subti''Wiki pages:''' [[Gürol M. Süel]], [[glutamate metabolism|glutamate consumption and ammonium production]], [[biofilm formation]]
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* [[rocR]]
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* see [http://microbepost.org/2015/08/05/conflict-and-co-operation-in-bacterial-communities/ a blog presenting this paper]
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* [[ahrC]]
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<pubmed>26200335</pubmed>
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* [[ccpA]]
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* [[Previous papers of the month]]
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* [[crh]]
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* [[glcT]]
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<br/>
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* [[ptsG]]
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<big>'''New procedure for account creation:'''</big>
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* [[ptsH]]
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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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* [[ptsI]]
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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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* [[pckA]]
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<br/><br/>
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* [[rny]]
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<big>'''News in ''Subti''Wiki:'''</big>
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* [[ymdB]]
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* '''August 2014:''' The first mobile application for ''Subti''Wiki is now available for users of Android phones: Go for SubtiWiki in Google Play! IPhone users, please be patient! You will be served next! [https://play.google.com/store/apps/details?id=de.goettingen.uni.genmibio.subtimobile&hl=en Click here to install!]
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* [[sigL]]
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* '''April 2013:''' SubtiWiki uses a new, faster Mediawiki platform! The times for page access are significantly reduced. Enjoy!
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* [[pgi]]
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* '''March 2013:''' updated Excel files that map all genes to [[categories]] and [[regulons]] as well as the general updated [http://www.subtiwiki.uni-goettingen.de/wiki/index.php/File:SubtiWiki_id_mapping.xls identity mapping] of all genes were uploaded.
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* [[pfkA]]
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* '''October 2012''': the [[essential genes]] have been categorized
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* [[fbaA]]
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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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* [[tpi]]
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* '''August 2012''': [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express], the new compagnon of ''Subti''Wiki devoted to gene expression is online! Try it out!
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* [[gapA]]
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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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* [[gapB]]
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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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* [[pgk]]
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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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* [[pgm]]
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* [[eno]]
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* [[pyk]]
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<br/>
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* [[cggR]]
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{| border="0" cellpadding="1"
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* [[sr1]]
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|width="300"|<big>'''Genes''' (examples)</big>
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* [[ccpN]]
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|width="300"|<big>'''Additional pages'''</big>
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* [[yqfL]]
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|- style="height:20px"
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* [[spx]]
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| ''[[spo0A]]'' || '''[[template]]'''
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* [[Alessandra Albertini]]
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|-
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* [[Arthur Aronson]]
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| ''[[glnA]]'' ||  '''[[the people behind SubtiWiki|the people behind ''Subti''Wiki]]'''
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* [[Stephane Aymerich]]
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|-
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* [[Imrich Barak]]
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| ''[[rny]]'' ||  '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
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* [[David Bechhofer]]
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|-
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* [[Sabine Brantl]]
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| ''[[psdA]]'' || '''[[Regulons]]'''
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* [[Richard Brennan]]
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|-
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* [[Ciaran Condon]]
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| ''[[pckA]]'' || '''[[methods]]'''
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* [[Simon Cutting]]
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|-
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* [[Isabel de Sa-Nogueira]]
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| ''[[dnaA]]'' ||  '''[[metabolism]]'''
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* [[Nathalie Declerck]]
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|-
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* [[Kevin Devine]]
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| ''[[rnpA]]'' ||  '''[[categories]]'''
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* [[Susan Fisher]]
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|-
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* [[Elisabeth Härtig]]
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| ''[[sigB]]'' || '''[[genome-wide analyses]]'''
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* [[Josef Deutscher]]
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|-
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* [[Jan Maarten van Dijl]]
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| ''[[ptkA]]'' || '''[[list of plasmids]]'''
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* [[Yasutaro Fujita]]
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|-
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* [[Anne Galinier]]
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| ''[[mreC]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
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* [[Boris Görke]]
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|-
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* [[Leendert Hamoen]]
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|  ||
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* [[Colin Harwood]]
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|}
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* [[Michael Hecker]]
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<br>
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* [[Lars Hederstedt]]
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<big>'''Publications describing ''Subti''Wiki and ''Subti''Pathways:'''</big>
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* [[John Helmann]]
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<div style="width:73%"><pubmed>20157485 19959575 22096228 24178028 </pubmed></div>
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* [[Tina Henkin]]
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<br><br><br><br><br><br>
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* [[Adriano Henriques]]
 
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* [[Wolfgang Hillen]]
 
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* [[Laurent Janniere]]
 
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* [[Mark J. Jedrzejas]]
 
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* [[Oscar Kuipers]]
 
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* [[Rick Lewis]]
 
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* [[Thorsten Mascher]]
 
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* [[Ivan Mijakovic]]
 
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* [[Philippe Noirot]]
 
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* [[Naotake Ogasawara]]
 
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* [[Harald Putzer]]
 
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* [[Milton H. Saier]]
 
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* [[Margarita Salas]]
 
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* [[Wolfgang Schumann]]
 
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* [[Linc Sonenshein]]
 
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* [[Jörg Stülke]]
 
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* [[Uwe Völker]]
 
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* [[Claes von Wachenfeldt]]
 
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* [[Wade Winkler]]
 
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* [[Peter Zuber]]
 
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* [[pGP380]]
 
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* [[pGP382]]
 
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* [[pBQ200]]
 
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* [[pAC5]]
 
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* [[pAC6]]
 
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* [[pAC7]]
 
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* [[pGP172]]
 
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* [[pGP570]]
 
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* [[pGP574]]
 
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* [[pWH844]]
 
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* [[BACTH]]
 
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* [[template]]
 
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* [[templatelab]]
 
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* [[templatelit]]
 
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* [[templateplasmid]]
 

Latest revision as of 10:15, 22 February 2017

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 new description of SubtiWiki and its acompanying modules in the 2016 Database issue of Nucleic Acids Research

Raphael H Michna, Fabian M Commichau, Dominik Tödter, Christopher P Zschiedrich, Jörg Stülke
SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information.
Nucleic Acids Res: 2014, 42(Database issue);D692-8
[PubMed:24178028] [WorldCat.org] [DOI] (I p)



Paper of the month: August 2015

Jintao Liu, Arthur Prindle, Jacqueline Humphries, Marçal Gabalda-Sagarra, Munehiro Asally, Dong-yeon D Lee, San Ly, Jordi Garcia-Ojalvo, Gürol M Süel
Metabolic co-dependence gives rise to collective oscillations within biofilms.
Nature: 2015, 523(7562);550-4
[PubMed:26200335] [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:

  • August 2014: The first mobile application for SubtiWiki is now available for users of Android phones: Go for SubtiWiki in Google Play! IPhone users, please be patient! You will be served next! Click here to install!
  • April 2013: SubtiWiki uses a new, faster Mediawiki platform! The times for page access are significantly reduced. Enjoy!
  • March 2013: updated Excel files that map all genes to categories and regulons as well as the general updated identity mapping of all genes were uploaded.
  • October 2012: the essential genes have been categorized
  • 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!
  • 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



Genes (examples) Additional pages
spo0A template
glnA the people behind SubtiWiki
rny labs working on Bacillus
psdA Regulons
pckA methods
dnaA metabolism
rnpA categories
sigB genome-wide analyses
ptkA list of plasmids
mreC labs working on Bacillus


Publications describing SubtiWiki and SubtiPathways:

Raphael H Michna, Fabian M Commichau, Dominik Tödter, Christopher P Zschiedrich, Jörg Stülke
SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information.
Nucleic Acids Res: 2014, 42(Database issue);D692-8
[PubMed:24178028] [WorldCat.org] [DOI] (I p)

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)

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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