Help:Starting a lab wiki

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<font size=1>< [[Help:Contents|Help]]</font>
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This is a help page for starting a lab wiki on [[OpenWetWare]].  It is a work in progress so apologies if not all information is available here.
This is a help page for starting a lab wiki on [[OpenWetWare]].  It is a work in progress so apologies if not all information is available here.
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==FAQ==
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'''See the [[FAQ/Labs|FAQ on hosting a lab wiki on OpenWetWare]].'''
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===Why should I put my lab on OpenWetWare?===
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See [[OpenWetWare:Why join?| reasons to join]].
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===Why shouldn't I host a lab on OpenWetWare?===
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''To be filled in.''
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===Am I surrendering copyright to my lab materials?===
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No, you retain copyright to all materials you upload or write on OpenWetWare.  You can later republish and relicense them in any way you like. However, you can never retract the Creative Commons Atrribution ShareAlike and GFDL licenses for the versions you placed here.
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===What labs are hosted on OpenWetWare?===
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See the [[Labs|list of labs]] hosted on OpenWetWare.
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==How do I start?==
==How do I start?==
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===Learn the basics of wiki editing===
===Learn the basics of wiki editing===
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If you've never used a wiki before, it is helpful to learn some basics of wiki editing via the [[OpenWetWare:Getting started|OpenWetWare introductory tutorial]].
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If you've never used a wiki before, you can learn some basics of wiki editing via the [[OpenWetWare:Getting started|OpenWetWare introductory tutorial]].
In particular, it is helpful if you put at least a couple lines about yourself on [[Special:Mypage|your user page]].
In particular, it is helpful if you put at least a couple lines about yourself on [[Special:Mypage|your user page]].
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Once you're comfortable with the basics of wiki's, continue with these directions.
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Once you're comfortable with the basics of wikis, continue with these directions.
===Set up a lab template===
===Set up a lab template===
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Once you've registered for an OWW account, start by making your lab banner.  Your lab banner will be used on every course page to help identify it as belonging to your course and to enable lab members to navigate through the lab wiki pages.
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#First, go to [[Template:LabName|the lab template page]] (open this in a new browser window if you want to keep reading this text).
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'''Note: We're building a new method of creating a lab. The documentation is still in progress. As a matter of fact, we're still adding more support to the new method. We think it's already as easy to use as the current method. To take a look, [[OWW-LabMaker:Projects/Horizontal Navigator/version 2|click here]].'''
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#Click [[Image:EditButton.jpg]] and copy all the wiki markup on that page.
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#In the search box on the lefthand side navigation bar, type <code>Template:<Your PI's last name></code> (be sure and replace <code><Your PI's last name></code> with your course's number like <code>Knight</code> or <code>Smolke</code>.  [[Image:Searchbox.png|right]]
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Once you've registered for an OWW account, start by making your lab banner.  Your lab banner will be used on every lab page to help identify it as belonging to your lab and to enable lab members to navigate through the lab wiki pages.
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#You should see a page come up with a message saying '''"There is no page titled "Template:<Your PI's last name>".''' You can create this page." If you don't see this message then that means a page with that name already exists.  You'll need to choose a different lab wiki name.  [[Image:NoPage.png|450px|left]] <br style="clear:both" />
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#First, go to [[Template:LabName|the lab template page]] (open it in a new browser window if you want to keep reading this text).
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#Click on the create this page link.
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#Click [[Image:view-source.jpg]] and copy all the wiki markup on that page.
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#In the search box on the lefthand side navigation bar, type <code>Template:<Your PI's last name></code> (be sure and replace <code><Your PI's last name></code> with your PI's last name like <code>Knight</code> or <code>Smolke</code>. Click the "Go" button rather than the "Search" button in the search box.  [[Image:Searchbox.png|right]]
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#A page should come up with the message, "You searched for Template:<Your PI's last name>",  where "Template:<Your PI's last name>" is in red. If you don't see this message then that means a page with that name already exists.  You'll need to choose a different lab wiki name.  [[Image:NoPage.png|450px|left]] <br style="clear:both" />
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#Click on the red link ("Template:<Your PI's last name>").
#Paste the code from the LabName template onto this page.
#Paste the code from the LabName template onto this page.
#Replace every instance of <code>LabName</code> with your PI's last name.
#Replace every instance of <code>LabName</code> with your PI's last name.
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[[Image:Uploadfilelink.png|right]]
[[Image:Uploadfilelink.png|right]]
#Click on upload file link on the left side of the screen (under toolbox).
#Click on upload file link on the left side of the screen (under toolbox).
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#Follow the directions from there to upload the file.  In general it is best if your course image is wider than it is tall and if it is in PNG format but JPG also works.
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#Follow the directions shown to upload the file.  In general, it is best if your lab image is wider than it is tall, and in PNG format, but JPG also works.
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#After the picture has been uploaded, you will be taken to the Image page for your course image.   
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#After the picture has been uploaded, you will be taken to the Image page for your lab image.   
#Copy the page title (i.e. '''Image:<What you named your picture>.jpg''').
#Copy the page title (i.e. '''Image:<What you named your picture>.jpg''').
#Return to your lab template.  You can do this quickly by typing <code>Template:<Your PI's last name></code> in the search box on the left.
#Return to your lab template.  You can do this quickly by typing <code>Template:<Your PI's last name></code> in the search box on the left.
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#Click [[Image:EditButton.jpg]] and replace <code>Image:ATempPic.jpg</code> with <code>Image:<What you named your picture>.jpg</code>
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#Click [[Image:EditButton.jpg]] and replace <code>Image:Placeholder.png</code> with <code>Image:<What you named your picture>.jpg</code>
#Check your work by clicking the [[Image:ShowPreviewButton.jpg]] button.
#Check your work by clicking the [[Image:ShowPreviewButton.jpg]] button.
#Save the changes by clicking [[Image:SavePageButton.jpg]].
#Save the changes by clicking [[Image:SavePageButton.jpg]].
===Set up your main lab page===
===Set up your main lab page===
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#First, go to [[LabName|the generic lab wiki page]] (open this in a new browser window if you want to keep reading this text).
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#First, go to [[LabName|the generic lab wiki page]] (open it in a new browser window if you want to keep reading this text).
#Click [[Image:EditButton.jpg]] and copy all the wiki markup on that page.
#Click [[Image:EditButton.jpg]] and copy all the wiki markup on that page.
#[[Image:Searchbox.png|right]] In the search box on the lefthand side navigation bar, type <code><Your PI's last name></code> (be sure and replace <code><Your PI's last name></code> with the last name of the PI for your lab like <code>Silver</code> or <code>Knight</code>.   
#[[Image:Searchbox.png|right]] In the search box on the lefthand side navigation bar, type <code><Your PI's last name></code> (be sure and replace <code><Your PI's last name></code> with the last name of the PI for your lab like <code>Silver</code> or <code>Knight</code>.   
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#You should see a page come up with a message saying '''"There is no page titled "<Your PI's last name>".''' You can create this page." If you don't see this message then that means a page with that name already exists.  You'll need to choose a different lab wiki name (and [[Help:Renaming pages|rename your lab template]]).
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#A page should come up with the message, "You searched for <Your PI's last name>" where "<Your PI's last name>" is in red. If you don't see this message then that means a page with that name already exists.  You'll need to choose a different lab wiki name (and [[Help:Renaming pages|rename your lab template]]).
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#Click on the create this page link.
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#Click on the red link "<Your PI's last name>".
#Paste the code from the LabName wiki homepage onto this page.
#Paste the code from the LabName wiki homepage onto this page.
#Replace every instance of <code><nowiki>{{Template:LabName}}</nowiki></code> with <code><nowiki>{{Template:<Your PI's last name>}}</nowiki></code>.  This line is responsible for including the lab banner on the page.
#Replace every instance of <code><nowiki>{{Template:LabName}}</nowiki></code> with <code><nowiki>{{Template:<Your PI's last name>}}</nowiki></code>.  This line is responsible for including the lab banner on the page.
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#Click [[Image:EditButton.jpg]] on your lab's homepage.
#Click [[Image:EditButton.jpg]] on your lab's homepage.
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#Between the line that starts <code><nowiki><div ...></nowiki></code> and the line <code><nowiki></div></nowiki></code>, feel free to put any information you want ... like a lab description, an announcements section or anything else that might be helpful there.
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#Between the line that starts <code><nowiki><div ...></nowiki></code> and the line <code><nowiki></div></nowiki></code>, feel free to put any information you want there-- such as a lab description, an announcements section or anything else that might be helpful.
===Set up your contact information page===
===Set up your contact information page===
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===Create a lab webpage from your lab wiki===
===Create a lab webpage from your lab wiki===
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See [[OpenWetWare:Dewikify]] for instructions on how to automatically create a lab website from your lab wiki.  For example, compare [[Synthetic Biology]] and http://syntheticbiology.org or [[Knight]] and http://knight.openwetware.org.
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See [[OpenWetWare:Dewikify]] for instructions on how to automatically create a static lab website from your lab wiki.  For example, compare [[Synthetic Biology]] and http://syntheticbiology.org or [[Knight]] and http://knight.openwetware.org.
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==Other common tasks==
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===Add your lab to the list of OpenWetWare labs===
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Once you've created your lab wiki and included some content, you can go ahead and list your lab on the [[Labs|OpenWetWare list of labs]].  Institutions are listed in alphabetical order and labs are listed under each institution, also in alphabetical order, by PI's last name.  Labs that are just getting started and don't have much content are listed under '''Labs in Development'''.
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===How does the rest of my lab get OpenWetWare accounts?===
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Other lab members can go through the same process that you did to get an account.  Fill out the form at [[OpenWetWare:How to join]].
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==Adding talks and papers to your lab wiki==
===How do I upload my seminar slides?===
===How do I upload my seminar slides?===
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If you both own the copyright to the paper and are willing to license it under the terms listed at [[OpenWetWare:Copyrights]], then follow the directions listed above under '''How do I upload my seminar slides?'''.  Also, any paper published in an open access journal (like one of the PLoS journals) can be freely uploaded to OpenWetWare.  Consult the particular journal's copyright policies for details.
If you both own the copyright to the paper and are willing to license it under the terms listed at [[OpenWetWare:Copyrights]], then follow the directions listed above under '''How do I upload my seminar slides?'''.  Also, any paper published in an open access journal (like one of the PLoS journals) can be freely uploaded to OpenWetWare.  Consult the particular journal's copyright policies for details.
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<font color=red>Remember, all materials posted or uploaded to OpenWetWare are automatically licensed under the terms at [[OpenWetWare:Copyrights]].  Do not post or upload materials to which you do not hold the copyright (like some papers) or don't want licensed under these terms.</font>  If you do need to make papers to which you don't own the copyright (or don't have a license) available to your students, you can do one of the following...
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<font color=red>Remember, all materials posted or uploaded to OpenWetWare are automatically licensed under the terms at [[OpenWetWare:Copyrights]].  Do not post or upload materials to which you do not hold the copyright (like some papers) or don't want licensed under these terms.</font>  If you do need to make papers to which you don't own the copyright (or don't have a license) available, you can do one of the following...
#Link to the publisher's version (for instance, if your institution has a site license then at least people from your institution will still be able to access the paper).
#Link to the publisher's version (for instance, if your institution has a site license then at least people from your institution will still be able to access the paper).
#Link to the author's version.  (Some journals allow authors to post preprints on their own website, so you can link to that version.)
#Link to the author's version.  (Some journals allow authors to post preprints on their own website, so you can link to that version.)
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Referencing published books and papers is easy in OpenWetWare.  See [[OpenWetWare:Biblio]] for instructions on how to automatically generate formatted citations from just the ISBN for books and the PMID for papers.
Referencing published books and papers is easy in OpenWetWare.  See [[OpenWetWare:Biblio]] for instructions on how to automatically generate formatted citations from just the ISBN for books and the PMID for papers.
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==Keeping up-to-date on your lab wiki==
===How can I check for the changes to my lab wiki?===
===How can I check for the changes to my lab wiki?===
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===Oh no ... someone made an incorrect edit on one of my lab pages.  How do I undo it?===
===Oh no ... someone made an incorrect edit on one of my lab pages.  How do I undo it?===
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Occasionally, edits to pages in OpenWetWare are made which are incorrect or should not have been done.  Fortunately, undoing edits is simple in a wiki.  Here are some simple instructions on how to undo edits (also called reverting to a previous version of the page).
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Occasionally, edits to pages in OpenWetWare are made that are incorrect or should not have been done.  Fortunately, undoing edits is easy in a wiki.  Here are some simple instructions on how to undo edits (also called reverting to a previous version of the page).
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#Go to the page whose edit you would like to undo.
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#Go to the page with an edit you would like to undo.
#Click on the [[Image:Historytab.png]] tab at the top of the page.
#Click on the [[Image:Historytab.png]] tab at the top of the page.
#You'll now be viewing the revision history of the page.
#You'll now be viewing the revision history of the page.
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#Click the [[Image:Compareselectedversionsbutton.png]] button.
#Click the [[Image:Compareselectedversionsbutton.png]] button.
#You will see the difference between the current version and the selected older version.
#You will see the difference between the current version and the selected older version.
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#Click the [[Image:Rollbacklink.png]] link on the current version column to rollback to the older version.
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#Click the [[Image:Rollbacklink.png]] link on the current version column to roll back to the older version.
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==More help with editing==
===How do I format a picture?===
===How do I format a picture?===
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Again, Wikipedia has a pretty thorough page on [[MetaWikiPedia:Table|editing tables]].
Again, Wikipedia has a pretty thorough page on [[MetaWikiPedia:Table|editing tables]].
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===How does the rest of my lab get OpenWetWare accounts?===
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===I don't like the standard lab template?  Can I use something else?===
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Of course.  Feel free to design your site however you wish.  Below is a small selection of possible templates you could use.
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#Click on the link below image
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#Copy + Paste onto your lab page
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#Modify them to your liking!
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Other lab members can go through the same process that you did to get an account.  Fill out the form at [[OpenWetWare:How to join]]. 
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'''Feel free to create your own unique lab format!'''
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Alternatively, if you prefer to make lab accounts yourself, contant admin AT openwetware DOT org and request administrator privileges. Then you can follow the directions at [[Help:Adding new users]] to create OpenWetWare accounts for your students.
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<gallery>
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Image:Suggs-Like_Template.jpg|[[LabPageTemplate1|Template 1]]
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Image:Endy-Like Template.jpg|[[LabPageTemplate2|Template 2]]
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Image:Template3.jpg|[[LabPageTemplate3|Template 3]]
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</gallery>
===Help!  My question isn't answered here.===
===Help!  My question isn't answered here.===
Check out the [[Help|help pages]] or else post your question at [[Help:Wiki questions|wiki questions forum]].
Check out the [[Help|help pages]] or else post your question at [[Help:Wiki questions|wiki questions forum]].

Current revision

< Help

This is a help page for starting a lab wiki on OpenWetWare. It is a work in progress so apologies if not all information is available here.

See the FAQ on hosting a lab wiki on OpenWetWare.

Contents

How do I start?

Get an account

You'll need a user account on OWW to edit pages. Register for an account here.

Learn the basics of wiki editing

If you've never used a wiki before, you can learn some basics of wiki editing via the OpenWetWare introductory tutorial.

In particular, it is helpful if you put at least a couple lines about yourself on your user page.

Once you're comfortable with the basics of wikis, continue with these directions.

Set up a lab template

Note: We're building a new method of creating a lab. The documentation is still in progress. As a matter of fact, we're still adding more support to the new method. We think it's already as easy to use as the current method. To take a look, click here.

Once you've registered for an OWW account, start by making your lab banner. Your lab banner will be used on every lab page to help identify it as belonging to your lab and to enable lab members to navigate through the lab wiki pages.

  1. First, go to the lab template page (open it in a new browser window if you want to keep reading this text).
  2. Click Image:view-source.jpg and copy all the wiki markup on that page.
  3. In the search box on the lefthand side navigation bar, type Template:<Your PI's last name> (be sure and replace <Your PI's last name> with your PI's last name like Knight or Smolke. Click the "Go" button rather than the "Search" button in the search box.
  4. A page should come up with the message, "You searched for Template:<Your PI's last name>", where "Template:<Your PI's last name>" is in red. If you don't see this message then that means a page with that name already exists. You'll need to choose a different lab wiki name.

  5. Click on the red link ("Template:<Your PI's last name>").
  6. Paste the code from the LabName template onto this page.
  7. Replace every instance of LabName with your PI's last name.
  8. Finally, check your work by clicking the Image:ShowPreviewButton.jpg button.
  9. Save the changes by clicking Image:SavePageButton.jpg ... and you're off.

Next you'll probably want to replace the default image with your own.

  1. Click on upload file link on the left side of the screen (under toolbox).
  2. Follow the directions shown to upload the file. In general, it is best if your lab image is wider than it is tall, and in PNG format, but JPG also works.
  3. After the picture has been uploaded, you will be taken to the Image page for your lab image.
  4. Copy the page title (i.e. Image:<What you named your picture>.jpg).
  5. Return to your lab template. You can do this quickly by typing Template:<Your PI's last name> in the search box on the left.
  6. Click Image:EditButton.jpg and replace Image:Placeholder.png with Image:<What you named your picture>.jpg
  7. Check your work by clicking the Image:ShowPreviewButton.jpg button.
  8. Save the changes by clicking Image:SavePageButton.jpg.

Set up your main lab page

  1. First, go to the generic lab wiki page (open it in a new browser window if you want to keep reading this text).
  2. Click Image:EditButton.jpg and copy all the wiki markup on that page.
  3. In the search box on the lefthand side navigation bar, type <Your PI's last name> (be sure and replace <Your PI's last name> with the last name of the PI for your lab like Silver or Knight.
  4. A page should come up with the message, "You searched for <Your PI's last name>" where "<Your PI's last name>" is in red. If you don't see this message then that means a page with that name already exists. You'll need to choose a different lab wiki name (and rename your lab template).
  5. Click on the red link "<Your PI's last name>".
  6. Paste the code from the LabName wiki homepage onto this page.
  7. Replace every instance of {{Template:LabName}} with {{Template:<Your PI's last name>}}. This line is responsible for including the lab banner on the page.
  8. Check your work by clicking the Image:ShowPreviewButton.jpg button.
  9. Save the changes by clicking Image:SavePageButton.jpg.

Next you can customize the rest of the content on your lab's wiki.

  1. Click Image:EditButton.jpg on your lab's homepage.
  2. Between the line that starts <div ...> and the line </div>, feel free to put any information you want there-- such as a lab description, an announcements section or anything else that might be helpful.

Set up your contact information page

Every new wiki page that you create for your lab should be named <Your PI's last name>:Name of the page.

So much in the same way you created your lab wiki main page, you can start a new page titled <Your PI's last name>:Contact to list the contact information for your lab. See Knight:Contact, Smolke:Contact and Endy:Contact for examples.

Create a lab webpage from your lab wiki

See OpenWetWare:Dewikify for instructions on how to automatically create a static lab website from your lab wiki. For example, compare Synthetic Biology and http://syntheticbiology.org or Knight and http://knight.openwetware.org.

Add your lab to the list of OpenWetWare labs

Once you've created your lab wiki and included some content, you can go ahead and list your lab on the OpenWetWare list of labs. Institutions are listed in alphabetical order and labs are listed under each institution, also in alphabetical order, by PI's last name. Labs that are just getting started and don't have much content are listed under Labs in Development.

How does the rest of my lab get OpenWetWare accounts?

Other lab members can go through the same process that you did to get an account. Fill out the form at OpenWetWare:How to join.

Adding talks and papers to your lab wiki

How do I upload my seminar slides?

PDFs, word docs, powerpoint files or keynote files can all be uploaded to OpenWetWare.

  1. Click on upload file link on the left side of the screen (under toolbox).
  2. Follow the directions from there to upload the file.
  3. OpenWetWare doesn't explicitly support PDF, powerpoint or keynote filetypes. Therefore these files are treated as images and an image page is generated upon upload. To include a link directly to the PDF from your lab wiki, you'll have to use the Media: prefix in your link.

For instance, here is a link to the image page of a PDF that has been uploaded to OpenWetWare: Image:Msb4100025.pdf

Here is a link to the corresponding PDF file itself: Media:Msb4100025.pdf

Note that if your files are in latex, you can actually post the latex source itself and autogenerate the corresponding PDF file via the wiki. Thus, you can collaboratively work via the wiki on latex docs! See OpenWetWare:Feature test/LatexDoc for a sample latex document.

How do I upload papers?

If you both own the copyright to the paper and are willing to license it under the terms listed at OpenWetWare:Copyrights, then follow the directions listed above under How do I upload my seminar slides?. Also, any paper published in an open access journal (like one of the PLoS journals) can be freely uploaded to OpenWetWare. Consult the particular journal's copyright policies for details.

Remember, all materials posted or uploaded to OpenWetWare are automatically licensed under the terms at OpenWetWare:Copyrights. Do not post or upload materials to which you do not hold the copyright (like some papers) or don't want licensed under these terms. If you do need to make papers to which you don't own the copyright (or don't have a license) available, you can do one of the following...

  1. Link to the publisher's version (for instance, if your institution has a site license then at least people from your institution will still be able to access the paper).
  2. Link to the author's version. (Some journals allow authors to post preprints on their own website, so you can link to that version.)
  3. Post them in a password protected directory elsewhere and link to them from OpenWetWare.

How do I include references to published materials?

Referencing published books and papers is easy in OpenWetWare. See OpenWetWare:Biblio for instructions on how to automatically generate formatted citations from just the ISBN for books and the PMID for papers.

Keeping up-to-date on your lab wiki

How can I check for the changes to my lab wiki?

If you've named all your pages as explained above (i.e. in the form <Your PI's last name>, then it is quite easy to check the recent changes to your lab wiki. Just go to Special:Recentchanges/Knight (except replace the Knight with the PI's last name).

Oh no ... someone made an incorrect edit on one of my lab pages. How do I undo it?

Occasionally, edits to pages in OpenWetWare are made that are incorrect or should not have been done. Fortunately, undoing edits is easy in a wiki. Here are some simple instructions on how to undo edits (also called reverting to a previous version of the page).

  1. Go to the page with an edit you would like to undo.
  2. Click on the Image:Historytab.png tab at the top of the page.
  3. You'll now be viewing the revision history of the page.
  4. Click the circle next to the version of the page that you wish to revert back to.
  5. Click the Image:Compareselectedversionsbutton.png button.
  6. You will see the difference between the current version and the selected older version.
  7. Click the Image:Rollbacklink.png link on the current version column to roll back to the older version.

More help with editing

How do I format a picture?

Wikipedia has various examples for formatting pictures.

How do I edit a table?

Again, Wikipedia has a pretty thorough page on editing tables.

I don't like the standard lab template? Can I use something else?

Of course. Feel free to design your site however you wish. Below is a small selection of possible templates you could use.

  1. Click on the link below image
  2. Copy + Paste onto your lab page
  3. Modify them to your liking!

Feel free to create your own unique lab format!

Help! My question isn't answered here.

Check out the help pages or else post your question at wiki questions forum.

Personal tools