FAQ

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How can I help?

You can help EcoliWiki become the online encyclopedia for E. coli, its phages, plasmids, and mobile genetic elements by adding information in your area of expertise. Add information about mutant alleles and phenotypes of your favorite gene. Add links to expression studies. Have you made changes to a published protocol that you want other researchers to know about? These and many other types of information are needed. Don't be shy! become a registered user and start adding information. If you have additional questions, contact the EcoliWiki team at ecoliwiki@gmail.com

How do I find information in EcoliWiki?

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Start with the Search box in the sidebar. Or look at lists of pages in Popular Categories.

What's the difference between Go and Search?

You use Go when you know the name of the item you are searching for. Search is used to search through the text within the pages. Clicking search will generate a list of pages where the item is found. You will just need to click on the link to be taken to the appropriate page. The search box is case-sensitive so that may be the reason for an unproductive search.

How do I find information about a particular gene or its product

Type the gene name into the search box on the left and click Go. You will be taken directly to the Quickview page for that gene. Once there, you may select the specific tab to display the desired information.

If the gene product's name is the same as the gene name,e.g. DnaK and dnaK, typing the product name into the search box and clicking Go will take you directly to the Quickview page. However, when the product and gene names are different, e.g. sigma70 and rpoD, you will be taken to a page of Search Results that lists Article title matches and Page text matches. Scroll through the list to find the page you want, which is usually at or near the top of the list. For example, a search for sigma70 will yield a list of Page text matches where the second item is "rpoD::Gene Product(s)."

How do I find information about a gene product if I don't know the name of the gene that encodes it?

Type the name of the gene product in the search box on the left and click the Search button. This will search for matching text within EcoliWiki and produce a page of Search Results listing the pages that contain the text you searched for. Scroll through the list to find the page you want and click on its link to be taken to that page.

How do I find information about plasmids?

Type the plasmid name in the search box on the left and click the Go button. If the plasmid has been entered in EcoliWiki you will be taken to that page. To browse the plasmids index already entered, try Category:Plasmids.

To enter a new plasmid into EcoliWiki, click on Create new page on the left hand side of the browser window and type the plasmid name into the Plasmid page generator. Click the Edit button and follow the directions.

How do I find information related to Complexes?

To find a list of complexes in EcoliWiki, try Category:Complexes

If the category you want is not listed, you may create one. If you want to create a new category, simply search for Category:xx where xx is the name of the new category. You will be told that the page does not exist. Click the Create the page link and fill in the information.

How do I find information related to Physiological Processes?

To search for a physiological process, type it into the search box. To enter a new physiological process, click the Create new page link in the navigation bar on the left hand side of the page. This will bring you to the Page_Generator. Type in the name of the process you would like to create under the Physiological Process Page heading and click the create button.

How do I view papers already entered into the wiki?

To see if your paper of interest is already in EcoliWiki, type its PubMed ID (e.g. PMID:## where ## is the number part of the PubMed ID) into the search box and click the Go button. If it's not already there, clicking on "Create this page" should create the page for you, using our common template

How do I find information about other Databases?

To search for a specific database, type the name in the search box. If it doesn't come up, you may browse the database index by typing Databases into the search box. If your database is absent, you may add it by using the Database template generator at the top of the index page.

I don't find what I'm looking for. What do I do?

If you're a registered user, you can just add new types of information to existing pages or create new pages.

If you aren't sure what to add, but you would like to see something in EcoliWiki, describe what you want on the EcoliWiki:Wishlist page. Or, email us at ecoliwiki@gmail.com.

How do I edit information in EcoliWiki?

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Click an edit link at the side of a section and use the textbox in the edit form to add or change content. Or click the Edit table link in a table to change the table content. For more detailed information see Category:Editing Help.

How do I make text bold or italic?

The Mediawiki software uses formatting tags to indicate italics, bold, etc. For example, two apostrophes on either side of a word or phrase cause it to be italicized; the text ''rpoD'' will display as rpoD. You won't need to enter the tags by hand, because most of the time there will be a toolbar at the top of the editing box. Just select the word you want formatted and click on the appropriate box in the toolbar. One exception is when entering or editing information in tables. In tables the formatting tags need to be entered by hand.

How do I add references?

For papers in Pubmed, type <ref name=PMID:xxxxxxx/> where the x's are the Pubmed ID. For a more detailed description about how to enter references in EcoliWiki, see Help: References.

How do I add links?

There are two main types of links for EcoliWiki: internal and external.

Adding an internal link to an EcoliWiki page is done using [[link]] wiki mark-up. For example, to link to the lacZ page type [[lacZ]] and the link will appear on the page like this: lacZ.

Adding links that are outside of EcoliWiki is simple. Type [url what you want to appear]. For example, to add a link to Google you would type: [http://www.google.com link to Google] and the usable link will appear on the page looking like link to Google.

How do I add tables?

EcoliWiki does tables differently from Wikipedia. See Help:Tables and Special:TableEdit

How do I get an image to show up in a page?

To add an image to a wiki page, you must first upload the image to the wiki. Click the upload file link in the toolbox on the left hand side of your browser window underneath the search bar. You may type in the file pathway or click browse to find the file. Write a summary of the image, and click the Upload File button.

Once an image is in the wiki, go back to the page where you want to add the image; click Edit and type [[Image:File.jpg]] where File.jpg is the name of the file you uploaded. Click the Save button to save the image to the wiki.

What do I do if someone changes what I wrote?

This is a wiki and so the information you add to the wiki may be changed by other users, just as you may change other users' enties. If you find the correction to be inaccurate, you may discuss the subject with other users in the Notes section available below each main section, or on the Discussion page. To add a note on the same page at the bottom of the section, click the Edit link to the right of the Notes heading. To initiate or view a discussion on a particular topic, click the discussion tab located on the top left hand side of the page. To add additional comments, you can click the + to add your comment to the end of the list. OR, you may click the edit tab and type your comments there. As you can see, there are plenty of places to make your voice heard.

Is there any way to keep people from editing my entries?

Only in tables. When you add data to a table, you have the opportunity to select public or private. The public selection allows any registered user to change your entries, whereas the private selection allows only you and the Ecoliwiki staff to edit your entries.

How do I import a large data set into the EcoliWiki?

Contact the EcoliWiki staff at ecoliwiki@gmail.com for options about getting your data set into EcoliWiki.

Can I import data from an Excel spreadsheet?

No. We are working on creating a way to do that, but that option is currently unavailable.

How do I add new information to EcoliWiki?

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Add information to existing pages or make new ones.

Can I make new pages?

Registered users can make new pages.

How do I make new pages?

Use the Create new page link in the Sidebar if you want to make your new page look like one of our predefined templates. Otherwise, just search for a page title and click "Create this page".

How do I make my new page look like the pages that are already in EcoliWiki?

Clicking the Create new page link (found in the navigation bar on the left hand side of the browser window) brings you to the page generator. This tool is beneficial because it automatically formats the information you add using a specific template. The page generator is available when adding Complexes, Strains, Plasmids, Literature, Physiological Processes, Genes, Databases, and Bioinformatic Tools to EcoliWiki.

How do I make a page about a journal article?

If you are citing the paper on a wiki page, add a reference to it, using <ref name ='PMID:xxxxxxx'/>. When you save the page, a citation should show up in the references section of the page (If it has one, if not, see Help:References for how to add one). The citation will have a link to an EcoliWiki page for the article. Click it, and the wiki will grab information from PubMed and create the page for you.

Alternatively, click the Create new page link in the navigation bar on the left hand side of the page. This will bring you to the Page_Generator. Type in the Pubmed ID number under the literature page heading and click the create button.

How do I make my page show up in a category?

Categories are ways of grouping pages together by some common thread. To add a page to a category, you'll need to know name of the Category you want. You can find a list of the categories in the wiki by clicking on the Special pages link in the toolbox below the search bar. Clicking on the Category link will show the list of available categories you can choose from.

Once you know the Category, use the following wiki mark-up to add the category:[[Category:Name of Category]].

Can I add pages about my lab to EcoliWiki?

As a registered user, you can add new pages to EcoliWiki. Note that every user has their own User page, which is automatically linked from the Special:Userlist page, and is linked from your name on the upper right. Please add personalized pages there; it makes searches more useful than if you put them in EcoliWiki as regular pages.

How do I add a new plasmid, strain, gene, bioinformatic tool, etc?

For adding a new item, click on the Create new page link on the left-hand side of the page. Find the appropriate heading for the information you want to add in the Page_Generator and click either the Create or Edit buttons.

What if my information doesn't fit in to any templates?

If you find that the pre-existing categories don't apply to your information, search for the information in the search box at the left and click the Create this page link and you can edit the page however you would like. You may also email the EcoliWiki staff at ecoliwiki@gmail.com add ask a staffer to create a template for you.

I have a question about my account

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How can I get an account in EcoliWiki?

If you would like an account to be created for you at EcoliWiki.org, look for a user who can set up an account for you. Or send us an email with the user name you want to use to ecoliwiki@gmail.com and the EcoliWiki Staff will get you set up. You'll receive an email with a temporary password that you can use to log in. Once you log in, you will be prompted to create a new password. It's also good to go to my preferences, where you can set your timezone, confirm your email address, and adjust other settings.

Can I invite my friends/colleagues/students/postdocs to join EcoliWiki?

Yes, go to the login/create account page. You'll need to know the user name your colleague wants to use. Once you have that, type in the username and the email address of the person you wish to invite and click by email. An email will be sent to the person and they will be able to complete their registration.

What do I do if I forget my username?

Check the list of users. Hopefully, you'll be able to recognize your username and the crisis will be averted. If you can't, email the EcoliWiki staff at ecoliwiki@gmail.com and someone will reply with your username.

What do I do if I forget my password?

Go to Special:Userlogin, type in your username and click the email password button. A temporary password will be emailed to you using the email address we have on file (this is a reason to confirm your email address). Once you log in, you will be prompted to enter a new password.

How do I change my username?

Contact the EcoliWiki Staff at ecoliwiki@gmail.com for changing your username.

How do I change my password?

To change your password, click the my preferences link in the upper right hand corner of the browser window. Under the user profile tab, you will have to enter your old password, then type the new one. You will have to retype the new one to verify spelling, then click the Save button.

Can I customize EcoliWiki?

Yes. You may customize the style in which you display the information by clicking the my preferences link in the upper right hand corner of the browser window. Under the skins tab, you may click the display that best suits you. You may preview these styles by clicking the preview button to the right of the style name. once you have made your selection, click the Save button to apply the new setting.

What is the User Contribution link?

Ecoliwiki keeps track of all the contributions you make to the wiki. Once you've logged in, you can click on this link and see a history of the contributions you've made.

See also

• Category:Help