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:[email protected] send mail]
  
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This Wiki is in a VERY 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 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>'''New: Subtiwiki is now on [http://www.facebook.com/pages/SubtiWiki/201847669864806 Facebook] - please give it a +1!'''</big>
  
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* [[gltA]]
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* [[gltB]]
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<br/>
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* [[gltC]]
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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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* [[rocG]]
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<pubmed> 24178028 </pubmed>
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* [[rocR]]
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* [[ahrC]]
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* [[ccpA]]
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<big>'''Paper of the month: August 2015'''</big>
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* [[crh]]
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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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* [[glcT]]
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* '''Relevant ''Subti''Wiki pages:''' [[Gürol M. Süel]], [[glutamate metabolism|glutamate consumption and ammonium production]], [[biofilm formation]]
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* [[ptsG]]
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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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* [[ptsH]]
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<pubmed>26200335</pubmed>
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* [[ptsI]]
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* [[Previous papers of the month]]
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* [[pckA]]
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* [[rny]]
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<br/>
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* [[ymdB]]
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<big>'''New procedure for account creation:'''</big>
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* [[sigL]]
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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:[email protected] 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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* [[pgi]]
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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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* [[pfkA]]
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<br/><br/>
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* [[fbaA]]
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<big>'''News in ''Subti''Wiki:'''</big>
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* [[tpi]]
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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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* [[gapA]]
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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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* [[gapB]]
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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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* [[pgk]]
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* '''October 2012''': the [[essential genes]] have been categorized
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* [[pgm]]
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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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* [[eno]]
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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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* [[pyk]]
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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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* [[cggR]]
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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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* [[sr1]]
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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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* [[ccpN]]
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* [[yqfL]]
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* [[spx]]
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<br/>
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* [[Alessandra Albertini]]
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{| border="0" cellpadding="1"
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* [[Arthur Aronson]]
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|width="300"|<big>'''Genes''' (examples)</big>
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* [[Stephane Aymerich]]
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|width="300"|<big>'''Additional pages'''</big>
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* [[Imrich Barak]]
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|- style="height:20px"
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* [[David Bechhofer]]
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| ''[[spo0A]]'' || '''[[template]]'''
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* [[Sabine Brantl]]
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|-
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* [[Richard Brennan]]
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| ''[[glnA]]'' ||  '''[[the people behind SubtiWiki|the people behind ''Subti''Wiki]]'''
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* [[Ciaran Condon]]
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|-
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* [[Simon Cutting]]
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| ''[[rny]]'' ||  '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
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* [[Isabel de Sa-Nogueira]]
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|-
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* [[Nathalie Declerck]]
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| ''[[psdA]]'' || '''[[Regulons]]'''
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* [[Kevin Devine]]
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|-
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* [[Susan Fisher]]
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| ''[[pckA]]'' || '''[[methods]]'''
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* [[Elisabeth Härtig]]
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|-
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* [[Josef Deutscher]]
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| ''[[dnaA]]'' ||  '''[[metabolism]]'''
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* [[Yasutaro Fujita]]
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|-
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* [[Anne Galinier]]
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| ''[[rnpA]]'' ||  '''[[categories]]'''
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* [[Boris Görke]]
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|-
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* [[Leendert Hamoen]]
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| ''[[sigB]]'' || '''[[genome-wide analyses]]'''
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* [[Colin Harwood]]
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|-
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* [[Michael Hecker]]
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| ''[[ptkA]]'' || '''[[list of plasmids]]'''
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* [[Wolfgang Hillen]]
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|-
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* [[Laurent Janniere]]
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| ''[[mreC]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
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* [[Mark J. Jedrzejas]]
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|-
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* [[Oscar Kuipers]]
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|  ||
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* [[Rick Lewis]]
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|}
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* [[Thorsten Mascher]]
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<br>
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* [[Ivan Mijakovic]]
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<big>'''Publications describing ''Subti''Wiki and ''Subti''Pathways:'''</big>
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* [[Philippe Noirot]]
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<div style="width:73%"><pubmed>20157485 19959575 22096228 24178028 </pubmed></div>
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* [[Harald Putzer]]
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<br><br><br><br><br><br>
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* [[Milton H. Saier]]
 
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* [[Linc Sonenshein]]
 
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* [[Jörg Stülke]]
 
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* [[Jan Maarten van Dijl]]
 
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* [[Uwe Völker]]
 
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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



Paper of the month: August 2015


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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