Difference between revisions of "Wish List"

From SubtiWiki
Jump to: navigation, search
(Facts that would be nice to have)
 
(37 intermediate revisions by 8 users not shown)
Line 1: Line 1:
 
SubtiWiki is all about making a useful tool for the ''Bacillus'' community. It is thus very important to receive feedback on what the community needs.
 
SubtiWiki is all about making a useful tool for the ''Bacillus'' community. It is thus very important to receive feedback on what the community needs.
  
= Essential facts (what every gene page should have) =
+
We believe that there are many types of users, with different requirements. For example:
  
* Gene name
+
* You could be a molecular biologist wanting to know the sequence of your gene of interest to make a PCR
* Function
+
* You find a reference to a gene in a paper you are reading and are interested to know more about that gene
* Synonyms
+
* You have some hypotheses in mind and want to travel around the wiki, gathering some facts to get inspired
* Summary (for not self-explanatory functions)
+
* You have a piece of information that you need almost daily and want to make it available not only to you, but also your group or to the whole community
* DNA and protein sequence
 
* Essential?
 
* Genetic context
 
* References
 
  
= Facts that would be nice to have =
+
In all of these cases, you will need different kind of information. The way you want it to be presented would differ too.
  
== About the gene ==
+
The wish list below takes into consideration all the possible users. Please add your wishes on what you would like to see.
* Coordinates
 
  
== About the protein ==
+
= Wish list =
* catalyzed reaction
 
** Kinetics
 
* protein family
 
* structure (or should it just be linked to the database?)
 
* domains
 
* Modifications
 
* Effectors of protein activity
 
* Interactions
 
* Localization
 
* MW
 
* pI
 
  
== About the expression of the protein ==
+
* Would it be possible to have a BLAST tool implemented in Subtiwiki?
* Operon
+
* Überarbeitung der [[rsmY]]-Seite, da fehlt fast alles
* Sigma Factor
+
* [[Genes_controlled_by_SigA | Extraseite: Liste der sigA kontrollierten Gene bearbeiten]]
* Regulation
+
* The search should not be case sensitive
** Inducers
+
* It should be possible to get DNA sequences from intergenic regions, not only 200 bp up- and downstream of the gene
** Repressors
+
* For all fused and splitted genes, there should be a description of the fate (history of the annotation procedure). See for example [[YqbL]]
* Regulatory mechanism
+
* Eine Einteilung der Genprodukte in funktionelle Gruppe ähnlich denen in der alten SubtiList wäre schön.
 
 
== About available biological materials ==
 
* Mutants
 
* Expression vectors
 
* lacZ fusions
 
* GFP fusions
 
* Antibodies
 
 
 
== About the conservation of the gene
 
 
 
== Other stuff ==
 
* Groups working on the Gene
 
 
 
= Databases that should be linked to the page =
 
 
 
* PDB (Protein Data Bank) - Structures
 
* Uniprot
 
* KEGG
 
* SubtiList (?)
 

Latest revision as of 12:08, 22 November 2011

SubtiWiki is all about making a useful tool for the Bacillus community. It is thus very important to receive feedback on what the community needs.

We believe that there are many types of users, with different requirements. For example:

  • You could be a molecular biologist wanting to know the sequence of your gene of interest to make a PCR
  • You find a reference to a gene in a paper you are reading and are interested to know more about that gene
  • You have some hypotheses in mind and want to travel around the wiki, gathering some facts to get inspired
  • You have a piece of information that you need almost daily and want to make it available not only to you, but also your group or to the whole community

In all of these cases, you will need different kind of information. The way you want it to be presented would differ too.

The wish list below takes into consideration all the possible users. Please add your wishes on what you would like to see.

Wish list

  • Would it be possible to have a BLAST tool implemented in Subtiwiki?
  • Überarbeitung der rsmY-Seite, da fehlt fast alles
  • Extraseite: Liste der sigA kontrollierten Gene bearbeiten
  • The search should not be case sensitive
  • It should be possible to get DNA sequences from intergenic regions, not only 200 bp up- and downstream of the gene
  • For all fused and splitted genes, there should be a description of the fate (history of the annotation procedure). See for example YqbL
  • Eine Einteilung der Genprodukte in funktionelle Gruppe ähnlich denen in der alten SubtiList wäre schön.