Try the new EcoliHub and let us know what you'd like to see.
What's new?
From EcoliWiki
What's new in EcoliWiki is now a category in the EcoliHub blog
E. coli B strain REL606
Information pertaining to the E. coli B strain known as REL606 (RefSeq NC_012967) is now available from EcoliWiki, so please add information about the strain or genes of interest. Click here to see the gene list for REL606. We're still working on a few things, but if you see a problem please email us at ecoliwiki@gmail.com. We are also working on another B strain, E. coli BL21(DE3), so keep an eye on the News Feed for that.
RefGenome Genes for November
The RefGenome project is working on a list of genes relevant to early lung development in November. Thus, EcoliWiki is looking to catch up on other genes that are on our list from previous months. Please help us annotate these or others genes on the RefGenome Gene List: cysQ, gfcB, hemF, hemH, add, gntY, gpmA, cutC, gpmA
RefGenome Genes for the month of October
Here are the genes were are annotating this month with our participation in the Reference Genomes project: plsB, cysQ, suhB, lipA, aceF, sucB, birA, eno. We need the community's help to complete these, so feel free to add your own annotations. Thanks!!
Proposed Gene Name Changes
EcoliWiki has 11 genes (htrL, rzpQ, ydhA, tbpA, nohB, lar, sgbH, sgbU, sgbE, htrG, yjgK) that we need input from our community as to which gene name is preferred. To provide your input, please log in and edit the information on this page. Thanks for your input!
Reactome User Survey
From our friends at Reactome:
Reactome Pathway Database User Survey
Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.
You can access the survey at: http://tinyurl.com/l48zzq
Thank you for taking part.
Robin Haw
Manager of Reactome Outreach
Outreach [at] reactome.org
[1]
More Genomes
We now have 20 Phage Genomes available on EcoliWiki. We are working on the addition of several E. coli genomes that recently became available. Check back soon for updates.
Updated Databases Pages
We've contacted and updated information on the Databases pages.
RefGenome Genes
We are annotating the following genes: lepB, secY, rpoB, caiC, fadD, menE, aas
Download meeting presentations
We've made some of our presentations at scientific meetings available for download. See: Category:Meeting presentations.
New EcoliHub BBS
A new discussion forum and bug/feature request tracker system for EcoliHub 2.0 is now available.
EcoliHub 2.0
The EcoliHub project has a new team for the new round of NIH funding starting on Aug 1, 2009. The new team adds new expertise from the PANTHER and Stanford Microarray Databases to two key components of the original EcoliHub project, EcoCyc and EcoliWiki.
RefGenome Genes for the Month of July
We have lots of targets to annotate this month: secA, phoU, yjbB, yggS, cspA, cspB, cspC, cspD, cspE, cspF, cspG, cspH, cspI, cysK, cysM, dcyD/yedO, dsdA, ygeX, tdcB, ilvA, thrC, trpA, trpB
RefGenome Genes for the month of June
EcoliWiki needs help annotating the following genes this month: serB, yidA, ybhA, cof, yigL, yjbF, gfcB
New MainPage
The MainPage has gotten a face-lift! Please leave your comments on the discussion page, we'd love to hear what you think. Also, the wiki recently underwent a software upgrade. If you find something broken or out-of-place, please email us at ecoliwiki@gmail.com with a description of the problem.
RefGenome Genes for the month of May
EcoliWiki needs help annotating the following genes this month: allB, yeiN, rimI, garL, yafU, yejH, tauD, cof, yigL, ybhA, yidA
Textpresso
EcoliWiki now offers Textpresso literature searches. Textpresso searches the entire body for your search term, rather than just the title and abstract like PubMed.
Textpressso allows you to search for exact matches to your terms, and even matches case sensitive searches. You can choose to add a category to your search, which will identify a group of terms related to the category. You can also sort and organize your results by a number of different mechanisms, including score (hits of your search terms), author, or year. If you still want to narrow a search, enter another term into the Filter box in the format of described and click on "Filter!"
Protein Interactions
EcoliWiki has added the interactions data from Arifuzzaman et al.(2006) and Butland et al.(2005) into the Interactions tables on the Gene Product pages and includes links to IntAct. You can click on the EBI numbers to go directly to a description of the experiment, or click on the partner name to see the corresponding EcoliWiki page for that protein. Feel free to add other interactions your lab has characterized to the Interactions table on your favorite gene product!
Cis-Elements
EcoliWiki is accumulating information on all of the Cis Elements in E. coli. See Cis Elements for the current list and click on any name for information on the location, sequence, synonyms, accessions in various other databases, and so forth. Please contribute by adding other Cis Elements you know of, or by changing or deleting information on the list!
Coming soon: Cis Elements of Phages and keep an eye out for a list of E. coli Promoters as well. Again, please add, change or delete!!
New Skin
This is a modified version of the Mediawiki skin "Cavendish," originally downloaded here.
If you would like to set this as your skin, click on [My preferences] at the top right and then on [Skin.] Select "Cavendish" and click [Save]. You can customize EcoliWiki to look the way you want. If you are interested in having your skin installed, contact an administrator. We'd love to show off your work!
There are a few known bugs, please send any feedback to Daniel.
Domains, Signal Sequences & Modification Sites
We added domains, modification sites and signal sequences from InterPro & predicted transmembrane domains from TMHMM. The TMHMM images appear directly on the Gene Products pages.
Structures
Now you can view the best E. coli structure and the best homolog structure on the Gene Products page, or get links to other structures available from PDB.
Phages
Looking for a gene or other information about an E. coli-specific phage? Try here - Phages
Search for three letter gene mnemonics
Now you can search for genes that share the same three-letter mnemonic. Try searching for lac or fli
Guided tours
We now have some EcoliWiki guided tours of EcoliWiki online. More are coming. Let us know what other ones you'd like.
Essential genes page
We now have a page for Essential genes for E. coli.
Mutant alleles from CGSC
We now have mutant alleles from the Coli Genetic Stock Center on the pages for each E. coli gene.
Link to GEO profiles added
Jump directly to GEO profiles from the Expression pages to see the pattern of gene expression in different transcriptome experiments.
Contributor listings added
A list of people who contributed edits to each page is now displayed at the bottom, as a way of acknowledging people's contributions to EcoliWiki. Thanks to Jaime Prilusky of Proteopedia for showing us how to do this.
Update Aug 20,2008: Now there's a special page where we can monitor what pages have been edited by community members (excluding EcoliHub staff).
Table Editor updated
We've just installed a new version of the Table Editor. This one should be more resistant to common errors (like forgetting to close a reference tag), and it has several other new features.
Embed video into EcoliWiki pages
We have now installed an extension to allow embedding videos from YouTube or Google Video as figures. See Help:Video for more.
DOI links
The document object identifier (DOI) is a unique id for all kinds of documents, including papers. Creating a new literature page on EcoliWiki now incorporates a DOI link, where available, which should send you to the relevant journal's website. If there is an online fulltext version, it should link there.
Expanding the literature coverage
We are making a large list of papers to enter.
Minor changes
We're working on some minor fixes to things. Links to the InParanoid website were broken and have been fixed. We will be updating the links for PFAM and UniProt in anticipation of changes that will be happening on those sites. We split the putative transcription factors on Are these really transcription factors? into three tables, as the old single table was very slow.
If there are other things you would like to see us work on, please add them to our EcoliWiki:Wishlist. Or contact us via whatever means is convenient to you.
Pages for plasmid cloning vectors being added
A team of TAMU students is entering pages for commercially available cloning vectors, and useful plasmids we're finding from the literature. If you've used these and have commentary about what works and what doesn't, please add it to the appropriate pages.
Virtual sticky notes
Template:Problems has instructions on how you can put notes on specific wiki pages to tell us that there are problems. Leaving a note automatically puts the page in a category called Category: Pages with problems or questions
New features support using EcoliWiki for teaching
See Help:Using EcoliWiki for teaching.
Excess GO category pages removed
It was pointed out to us that having the whole Gene Ontology as part of EcoliWiki leads to too many false positives when searching for terms like "RNA Polymerase". We've now removed the text from the GO pages. We will restore something for those GO terms that have E. coli annotations. Note that you can browse the full ontology at GONUTS, our wiki-based ontology browser.
New editing feature: Shortcuts below the edit box
We've implemented a set of shortcuts that insert Greek letters, misc. symbols, and reference markup when clicked. These tools are below the edit box.
F and λ on EcoliWiki
Annotations were imported from Genbank via GFF; lots of manual curation is needed. See Category:Gene_List:Plasmid_F and Category:Gene_List:Phage_lambda.
Phage meeting workshop 2007
EcoliWiki is getting ready for our first public release at the Phage meeting in Madison (Aug 7-12). We'll be giving a workshop and we'll be available during the poster sessions for one-on-one help.
See Also
- Special:Recentchanges for the most recent changes on the wiki
- EcoliWiki:Wishlist for what the community wants from EcoliWiki, and what we are planning to add or change soon.
- EcoliHub for more E. coli and EcoliHub news.
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