E. coli is indeed the coolest thing on the planet - Carl Zimmer

What's new?

From EcoliWiki

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.