Difference between revisions of "Main Page"
| (75 intermediate revisions by 2 users not shown) | |||
| Line 5: | Line 5: | ||
<br/> | <br/> | ||
<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] | ||
| − | |||
| − | |||
| − | |||
<br/> | <br/> | ||
<big>'''Upcoming events:'''</big> | <big>'''Upcoming events:'''</big> | ||
| − | * The [http://www. | + | * 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] |
| − | |||
* [[Past conferences]] | * [[Past conferences]] | ||
| Line 20: | Line 16: | ||
<br/> | <br/> | ||
| − | <big>'''Now online: A description of ''Subti''Wiki | + | <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> |
| − | <pubmed> | + | <pubmed> 24178028 </pubmed> |
<br/> | <br/> | ||
| − | <big>'''Paper of the month: | + | <big>'''Paper of the month: August 2015'''</big> |
| − | * | + | * 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. |
| − | * '''Relevant ''Subti''Wiki pages:''' | + | * '''Relevant ''Subti''Wiki pages:''' [[Gürol M. Süel]], [[glutamate metabolism|glutamate consumption and ammonium production]], [[biofilm formation]] |
| − | <pubmed> | + | * see [http://microbepost.org/2015/08/05/conflict-and-co-operation-in-bacterial-communities/ a blog presenting this paper] |
| + | <pubmed>26200335</pubmed> | ||
* [[Previous papers of the month]] | * [[Previous papers of the month]] | ||
| Line 36: | Line 33: | ||
<br/><br/> | <br/><br/> | ||
<big>'''News in ''Subti''Wiki:'''</big> | <big>'''News in ''Subti''Wiki:'''</big> | ||
| + | * '''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. | ||
* '''October 2012''': the [[essential genes]] have been categorized | * '''October 2012''': the [[essential genes]] have been categorized | ||
* '''September 2012''': 300 mutant strains available at the [http://www.bgsc.org BGSC] were added to the corresponding gene pages | * '''September 2012''': 300 mutant strains available at the [http://www.bgsc.org BGSC] were added to the corresponding gene pages | ||
| − | * '''August 2012''': [http:// | + | * '''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! |
* '''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 | * '''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 | ||
* '''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]] | ||
| − | + | ||
| − | |||
<br/> | <br/> | ||
| Line 52: | Line 49: | ||
|width="300"|<big>'''Additional pages'''</big> | |width="300"|<big>'''Additional pages'''</big> | ||
|- style="height:20px" | |- style="height:20px" | ||
| − | | ''[[spo0A]]'' || '''[ | + | | ''[[spo0A]]'' || '''[[template]]''' |
|- | |- | ||
| − | | ''[[glnA]]'' || '''[[ | + | | ''[[glnA]]'' || '''[[the people behind SubtiWiki|the people behind ''Subti''Wiki]]''' |
|- | |- | ||
| − | | ''[[rny]]'' || '''[[ | + | | ''[[rny]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]''' |
|- | |- | ||
| ''[[psdA]]'' || '''[[Regulons]]''' | | ''[[psdA]]'' || '''[[Regulons]]''' | ||
| Line 64: | Line 61: | ||
| ''[[dnaA]]'' || '''[[metabolism]]''' | | ''[[dnaA]]'' || '''[[metabolism]]''' | ||
|- | |- | ||
| − | | ''[[rnpA]]'' || '''[[ | + | | ''[[rnpA]]'' || '''[[categories]]''' |
|- | |- | ||
| ''[[sigB]]'' || '''[[genome-wide analyses]]''' | | ''[[sigB]]'' || '''[[genome-wide analyses]]''' | ||
| Line 71: | Line 68: | ||
|- | |- | ||
| ''[[mreC]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]''' | | ''[[mreC]]'' || '''[[labs working on Bacillus|labs working on ''Bacillus'']]''' | ||
| − | |||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| || | | || | ||
| Line 80: | Line 73: | ||
<br> | <br> | ||
<big>'''Publications describing ''Subti''Wiki and ''Subti''Pathways:'''</big> | <big>'''Publications describing ''Subti''Wiki and ''Subti''Pathways:'''</big> | ||
| − | <div style="width:73%"><pubmed>20157485 19959575</pubmed></div> | + | <div style="width:73%"><pubmed>20157485 19959575 22096228 24178028 </pubmed></div> |
<br><br><br><br><br><br> | <br><br><br><br><br><br> | ||
Latest revision as of 10:15, 22 February 2017
Welcome to SubtiWiki! - Bacillus subtilis annotation the "wiki" way!
Contact: General Microbiology, University of Göttingen, send mail
Upcoming events:
- The 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. Conference website
- Past conferences
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
- 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, Liu et al. from the lab of Gürol M. Süel have discovered oscillation in the 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 consumption and ammonium production, respectively.
- Relevant SubtiWiki pages: Gürol M. Süel, glutamate consumption and ammonium production, biofilm formation
- see a blog presenting this paper
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)
