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FAQ

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Contents

How can I help?

You can help SubtilisWiki become the online encyclopedia for B. subtilis, its phages, plasmids, and mobile genetic elements by

  • adding information in your area of expertise. For example:
    • 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?
  • Link SubtilisWiki pages to each other
  • Place SubtilisWiki pages in useful categories.
  • Tell us what you think is missing (see Help:Feedback).

These and many other types of information are needed. Don't be shy! become a registered user and start making SubtilisWiki into the resource you want. If you have additional questions, contact the SubtilisWiki team at subtiliswiki@gmail.com

Searching / Finding Information

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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 and G?

  • Clicking the [GO] button when searching will attempt to take you directly to the article you're interested in. It will try and match an article's title, and if it can't it will give you a list of things that matched your search term.
  • Clicking [Search] will take you straight to the list of pages that matched your search-term, showing any matches to titles before any matches to content. You can specify one or more namespaces to search in when using Search. The search box is case-sensitive so that may be the reason for an unproductive search.
  • The Google [G] allows you to search SubtilisWiki using Google, but if you misspell a word, it will offer suggestions just like Google. The Google search works similar to using the [Search] button, but uses their search-engine (which is much more powerful.)

For more information about searching SubtilisWiki, see Help: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?

There are lots of ways you could find it:

  • Type possible words related to the gene product in the search box and click the Search button. This will look for matching text within SubtilisWiki 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.
  • Browse the lists of genes from B. subtilis strains, phage, plasmids, and mobile genetic elements
  • Go to the Template:Gbrowse link and look in the area where you think the gene maps. When you find it, place your cursor over the gene, and a popup menu will include a link back to SubtilisWiki.
  • Browse the Gene Ontology. Start with biological process, molecular function or cellular component, or start with a gene product that you think should have similar GO annotations[1].

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 inSubtilisWiki you will be taken to that page. To browse the plasmids index already entered, try Category:Plasmids.

To enter a new plasmid into SubtilisWiki, 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 about Complexes?

To find a list of complexes in SubtilisWiki, try Category:Complexes[2]

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 about Physiological Processes?

The first release of SubtilisWiki wasn't automatically seeded with existing information about Physiological Processes, so coverage depends on our users.

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 information about papers already entered into the wiki?

To see if your paper of interest is already in SubtilisWiki, 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?

SubtilisWiki has pages describing other online resources. The goal is to provide additional online documentation for sites our users should know about. 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.

How do I find pages that have been edited by my friends/students/competitors?

Go to the User list and find the username you're interested in. Click on the username. A User contributions link will appear in the toolbox in the sidebar. Click it to see everything that user has done in the wiki.

How do I know if the information in SubtilisWiki is correct?

You can't, but then you can't really know that information in a review article is correct either, without looking at other things. One way that reviews and SubtilisWiki get credibility is by having references to the peer-reviewed primary literature. To learn more about references in SubtilisWiki, see Help:References.

Peer review is another assurance of quality. While SubtilisWiki pages are not assigned peer review before appearing, we hope that users of SubtilisWiki will improve the content by editing out errors and omissions. You can see who added (or deleted) different parts of a page by using the History links on every page, and every page in SubtilisWiki is coupled to a discussion page where users can discuss what is there and how it should be organized. For more information, see Help:History and Help:Talk pages.

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 SubtilisWiki, describe what you want on the SubtilisWiki:Wishlist page. Or, email us at subtiliswiki@gmail.com.

Contributing / Editting

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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.

Remember:

  • You can't really break the wiki.
  • If you're unsure of the formatting, markup, etc. someone else can fix it.

If you want to be sure it gets fixed, email the SubtilisWiki staff at subtiliswiki@gmail.com and ask us to take care of it. The staff will then format the page.

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 SubtilisWiki, see Help: References.

How do I add links?

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

Adding an internal link to an SubtilisWiki 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 SubtilisWiki 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?

SubtilisWiki 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' entries. 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 SubtilisWiki staff to edit your entries. But in general, the wiki philosophy is to allow everyone to edit everything. If someone else edits things you wrote, your version isn't lost, every revision is saved in the page history.

If you and another user disagree about something on a page, try to come up with a neutral way of expressing the controversy. You can each then link to new pages where you can elaborate on each point of view. Note that if you want to write something that other people can't edit, you can make your own website and add a link to it on SubtilisWiki.

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

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

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.

Adding Information

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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 SubtilisWiki?

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 SubtilisWiki.

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 SubtilisWiki 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]]. For more about Categories see Help:Categories

Can I add pages about my lab to SubtilisWiki?

As a registered user, you can add new pages to SubtilisWiki. 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 SubtilisWiki 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 into 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 SubtilisWiki staff at subtiliswiki@gmail.com add ask a staffer to create a template for you.

Accounts

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How can I get an account in SubtilisWiki?

If you would like an account to be created for you at SubtilisWiki.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 subtiliswiki@gmail.com and the SubtilisWiki 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 SubtilisWiki?

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 SubtilisWiki staff at subtiliswiki@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 SubtilisWiki Staff at subtiliswiki@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.

Misc. questions

Can I customize SubtilisWiki?

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.

If you know of a Mediawiki skin you'd like to see here, contact us and we'll see if we can install it.

Can SubtilisWiki let me know when pages I'm interested have changed?

Yes, if you are a registered user? Every page has a watch tab at the top. Click on that to add pages to your watchlist. If a page is on your watchlist, SubtilisWiki will email you if anyone else changes the page. It won't email you again until you view the page, so don't worry about being deluged with emails every time someone makes a minor change. For more information, see Help:Watchlist

If the content in SubtilisWiki is constantly changing, how can I refer to the content at a particular time?

Use the Permanent link in the toolbox. That will always point to the version of the page you are viewing at the time you copy the permanent link.

What is the User Contribution link?

Subtiliswiki 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.

How do I make suggestions?

There are two ways to make suggestions to the SubtilisWiki staff. Click on the Suggestions subheading under the main heading and you will be taken to the Suggestions page. Click the + tab or the edit tab at the top of the page and let us have it. The other way to do this is to email the Subtiliswiki staff at subtiliswiki@gmail.com. Either option will get your suggestions to us.

How do I find additional help if I need it?

If you need additional assistance, please email the Subtiliswiki staff at subtiliswiki@gmail.com and we will be happy to answer your questions.

See also

Footnotes and References

  1. GO annotation for B. subtilis needs improvement. Making it more accurate and comprehensive is one of the goals of SubtilisWiki
  2. Complexes in SubtilisWiki are categories, which allows subunits and subcomplexes to be automatically organized on the page.