Difference between revisions of "Main Page"

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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]
 
<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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<big>'''[http://subtiwiki.uni-goettingen.de/wiki/images/3/3d/AMBER.pdf Open positions]'''</big>
 
  
 
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<big>'''Upcoming events:'''</big>  
 
<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/registration.html conference website], [mailto:fchizer@scripps.edu contact]
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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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* The [http://www.sporesconference.com/ 6th European Spores Conference] will be held in London from April 9 to April 11, 2014. The meeting will be organized by [[Simon Cutting]] and [[Imrich Barak]], [http://sporesconference.com/ website], [mailto:S.Cutting@rhul.ac.uk contact]
 
 
* [[Past conferences]]
 
* [[Past conferences]]
  
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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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<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> 22096228 </pubmed>
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<pubmed> 24178028 </pubmed>
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<big>'''New: Website of the month: June 2013: [http://sporeweb.molgenrug.nl/  SporeWeb]'''</big>
 
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* [http://sporeweb.molgenrug.nl/  SporeWeb] is a dynamic web-based platform describing all stages of [[sporulation]] in ''B. subtilis'' from a gene regulatory point of view. The website is intended for all microbial researches interested in bacterial [[sporulation]] and/or gene regulatory networks and contains useful information for both [[sporulation]] experts and non-experts.
 
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* You can find:
 
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** detailed review-like descriptions of all [[sporulation]] stages,
 
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** schematic representations of regulatory events during every stage,
 
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** links to specific regulators and their [[regulons]],
 
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** access to detailed Excel sheets of all sporulation-specific [[regulons]],
 
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** Cytoscape-generated layouts of regulon interactions during a specific stage,
 
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** a tool to generate your own Cytoscape interaction figure for specific genes of interest,
 
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** heat maps showing expression values of all [[sporulation]] genes during the sporulation cycle (derived from [http://www.ncbi.nlm.nih.gov/pubmed/22383849  Nicolas ''et al''., 2012]),
 
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** direct links to other knowledge platforms, such as ''Subti''Wiki,
 
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** an extensive list of references for further detailed information.
 
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* The website is self explanatory, but you can also take a quick look at [http://youtu.be/XSTpU80o4t0 the short introduction video].
 
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* Importantly, the website is database driven: it can (and will) be updated as new exciting insights become available in literature.
 
  
 
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<big>'''Paper of the month: June 2013'''</big>  
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<big>'''Paper of the month: August 2015'''</big>  
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* DNA transfer across membranes is important in many fundamental processes. However, the molecular mechanisms behind this transport are only poorly understood. Now, [http://www.ncbi.nlm.nih.gov/pubmed/23667326 Fiche et al.] analysed the assembly and molecular architecture of the [[SpoIIIE]] DNA translocation complex. This study reveals that in contrast to previous model, DNA transfer occurs through an aqueous DNA-conducting pore that could be structurally maintained by the divisional machinery, with [[SpoIIIE]] acting as a checkpoint preventing membrane fusion until completion of chromosome segregation.  
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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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* '''Relevant ''Subti''Wiki pages:''' [[sporulation]], [[SpoIIIE]], [[DNA condensation/ segregation]]
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* '''Relevant ''Subti''Wiki pages:''' [[Gürol M. Süel]], [[glutamate metabolism|glutamate consumption and ammonium production]], [[biofilm formation]]
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<pubmed> 23667326 </pubmed>
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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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<pubmed>26200335</pubmed>
 
* [[Previous papers of the month]]
 
* [[Previous papers of the month]]
  
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<big>'''News in ''Subti''Wiki:'''</big>  
 
<big>'''News in ''Subti''Wiki:'''</big>  
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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!]
 
* '''April 2013:''' SubtiWiki uses a new, faster Mediawiki platform! The times for page access are significantly reduced. Enjoy!
 
* '''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 [http://www.subtiwiki.uni-goettingen.de/wiki/index.php/File:SubtiWiki_id_mapping.xls identity mapping] of all genes were uploaded.
 
* '''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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* '''April 2011:''' [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact], a presentation of [[protein-protein interactions]] in ''B. subtilis'', is online!  
 
* '''April 2011:''' [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact], a presentation of [[protein-protein interactions]] in ''B. subtilis'', is online!  
 
* '''December 2010:''' [http://cellpublisher.gobics.de/scp.html SubtiCellPublisher] allows the conversion of CellDesigner diagrams to navigatable presentations in the style of [[SubtiPathways]]
 
* '''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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|width="300"|<big>'''Additional pages'''</big>
 
|width="300"|<big>'''Additional pages'''</big>
 
|- style="height:20px"  
 
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| ''[[spo0A]]'' || '''[http://subtipathways.uni-goettingen.de ''Subti''Pathways]'''  
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| ''[[spo0A]]'' || '''[[template]]'''  
 
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| ''[[glnA]]'' ||  '''[[Lists of genes, proteins and RNAs]]'''
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| ''[[glnA]]'' ||  '''[[the people behind SubtiWiki|the people behind ''Subti''Wiki]]'''
 
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| ''[[rny]]'' ||  '''[[Categories]]'''
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| ''[[rny]]'' ||  '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
 
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| ''[[psdA]]'' || '''[[Regulons]]'''  
 
| ''[[psdA]]'' || '''[[Regulons]]'''  
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| ''[[dnaA]]'' ||  '''[[metabolism]]'''  
 
| ''[[dnaA]]'' ||  '''[[metabolism]]'''  
 
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| ''[[rnpA]]'' ||  '''[[protein-protein interactions]]'''  
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| ''[[rnpA]]'' ||  '''[[categories]]'''  
 
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| ''[[sigB]]'' || '''[[genome-wide analyses]]'''
 
| ''[[sigB]]'' || '''[[genome-wide analyses]]'''
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| ''[[mreC]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
 
| ''[[mreC]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]'''
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| ''[[ccpA]]'' || '''[[the people behind SubtiWiki|the people behind ''Subti''Wiki]]'''
 
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| ''[[sr1]]'' || '''[[template]]'''
 
 
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<big>'''Publications describing ''Subti''Wiki and ''Subti''Pathways:'''</big>
 
<big>'''Publications describing ''Subti''Wiki and ''Subti''Pathways:'''</big>
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<div style="width:73%"><pubmed>20157485 19959575 22096228</pubmed></div>
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<div style="width:73%"><pubmed>20157485 19959575 22096228 24178028 </pubmed></div>
 
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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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