Home.md
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@@ -21,31 +21,31 @@ The Structural Biology Grid at Harvard Medical School (SBGrid) is a computing co
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See the [SBGrid Website](https://www.sbgrid.org/)
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## Help
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-* [Getting Help & Support](faqs/getting-help)
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+* [Getting Help & Support](faq-getting-help)
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-## [FAQ](faqs/)
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+## [FAQ](faqs)
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Frequently Answered Questions
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### Account Related
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-* [Change Your Unix Password](faqs/changing-your-account-password)
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-* [Backups Using Crashplan](faqs/crashplan-backups)
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-* [SBGrid/CMCD VPN](faqs/connecting-to-cmcd-vpn)
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-* [NE CAT Data Collection](faqs/data-collection-at-ne-cat)
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-* [Requesting an Account](faqs/new-accounts)
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+* [Change Your Unix Password](faq-changing-your-account-password)
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+* [Backups Using Crashplan](faq-crashplan-backups)
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+* [SBGrid/CMCD VPN](faq-connecting-to-cmcd-vpn)
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+* [NE CAT Data Collection](faq-data-collection-at-ne-cat)
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+* [Requesting an Account](faq-new-accounts)
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### Software & Linux/Mac/UNIX
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-* [Access Remote Filesystems using SSHFS](faqs/sshfs)
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-* [Firefox Problems on Network Account](faqs/troubleshooting-firefox-on-a-network-account)
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-* [How to Forward Email](faqs/forwarding-mail-to-crystal)
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-* [Linux Remote Access](faqs/remote-access-to-linux-computers)
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-* [OS X (Apple): Find MAC Address](faqs/how-to-find-mac-address-on-os-x-gui)
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-* [Running jobs after you logged off (using Screen)](faqs/running-remote-jobs-after-disconnecting)
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-* [SSH Without a Password](faqs/setting-up-passwordless-ssh)
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-* [SBGrid Software](faqs/using-sbgrid-programs)
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-* [Using Crystal Email](faqs/using-your-crystal-harvard-edu-email-address)
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-* [Other Resources](faqs/other-resources)
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+* [Access Remote Filesystems using SSHFS](faq-sshfs)
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+* [Firefox Problems on Network Account](faq-troubleshooting-firefox-on-a-network-account)
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+* [How to Forward Email](faq-forwarding-mail-to-crystal)
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+* [Linux Remote Access](faq-remote-access-to-linux-computers)
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+* [OS X (Apple): Find MAC Address](faq-how-to-find-mac-address-on-os-x-gui)
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+* [Running jobs after you logged off (using Screen)](faq-running-remote-jobs-after-disconnecting)
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+* [SSH Without a Password](faq-setting-up-passwordless-ssh)
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+* [SBGrid Software](faq-using-sbgrid-programs)
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+* [Using Crystal Email](faq-using-your-crystal-harvard-edu-email-address)
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+* [Other Resources](faq-other-resources)
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faq-forwarding-mail-to-crystal.md
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@@ -6,23 +6,25 @@ To setup mail forwarding on Linux, you should have a .forward file configured in
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Add a .forward file to your home directory:
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- 1. cd <your network home directory>    
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- * example:
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- * ``` cd ~; touch .forward; ```
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+`cd <your network home directory>`
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+
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+Example:
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+
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+`cd ~; touch .forward;`
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Add the following to the .forward file that your just created(using your favorite text editor):
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- 1. &lt;username&gt;@crystal.harvard.edu
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- 2. \&lt;username&gt;
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+* `<username>@crystal.harvard.edu`
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+* `<username>`
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Make sure the permissions are set correctly on the file:
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- 1. chmod 644 .forward;
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+`chmod 644 .forward;`
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Test the setup and check your inbox on crystal email with this command or by sending and email to it from a different account:
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- 1. mailx -s 'my test email' &lt;username&gt; &lt; /dev/null
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+`mailx -s 'my test email' <username> < /dev/null`
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For questions, please contact SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org?Subject=Forward_Email_Help)
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faq-how-to-find-mac-address-on-os-x-gui.md
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* Step 1
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-![](../images/how-to-find-mac-address-on-os-x-gui-1.png)
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+![](images/how-to-find-mac-address-on-os-x-gui-1.png)
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* Step 2
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-![](../images/how-to-find-mac-address-on-os-x-gui-2.png)
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+![](images/how-to-find-mac-address-on-os-x-gui-2.png)
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* Step 3
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-![](../images/how-to-find-mac-address-on-os-x-gui-3.png)
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+![](images/how-to-find-mac-address-on-os-x-gui-3.png)
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faq-new-accounts.md
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## Account Creation
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-Requests for user accounts **must** come from a PI or from someone a PI has authorized to perform requests of this nature. In order for SBGrid to create your account, please have your PI send the request to [help@sbgrid.org](mailto:help@sbgrid.org) with the following information:
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+Requests for user accounts **must** come from a PI or from someone a PI has authorized to perform requests of this nature.
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+
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+In order for SBGrid to create your account, please have your PI send the request to [help@sbgrid.org](mailto:help@sbgrid.org) with the following information:
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* Your first and last name.
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* Your primary email address
faq-troubleshooting-firefox-on-a-network-account.md
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properly (because of a crash or network interruption.)
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##On Mac OS X
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-**To fix this issue on OS X, please log out, and log back in.
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-You may also need to delete your parentlock file, located at
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-~/Library/Application Support/Firefox/Profiles/*.default/.parentlock
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+To fix this issue on OS X, please log out, and log back in. You may also need to delete your parentlock file, located at:
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+
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+`~/Library/Application Support/Firefox/Profiles/*.default/.parentlock`
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##On Linux
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-**Before attempting the following steps, please make sure that you are currently logged into only one computer.
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+Before attempting the following steps, please make sure that you are currently logged into only one computer. Often times Linux users have multiple Firefox session running, each session use the same lock file which causes Firefox to get confused.
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+
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Here are some steps to use Firefox, if it becomes locked by mistake:
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* Remove any application lock files. Typically, these lock files are found in the browser home directory. Just run the following to delete the locks:
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> rm -f ~/.mozilla/firefox/*.default/.parentlock
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-
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->
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-
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+>
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> rm -f ~/.mozilla/firefox/*.default/lock
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After you do so, try to run firefox one more time.
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- * In the worst case scenario, you could do this: mv /.mozilla/firefox /.mozilla/firefox_hold (Note: this will completely reset Firefox.) Then start your browser, which will create a new profile. After you do this, you may wish to restore your bookmarks. You can do this via the Firefox menu path Bookmarks/Organize Bookmarks/File/Import (your old bookmarks would be in ~/.mozilla/firefox_hold/…)
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+ In the worst case scenario, you could do this:
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+
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+ `mv /.mozilla/firefox /.mozilla/firefox_old`
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+
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+(*Note*: this will completely reset Firefox.)
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+
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+Then start your browser, which will create a new profile. After you do this, you may wish to restore your bookmarks. You can do this via the Firefox menu path `Bookmarks/Organize Bookmarks/File/Import` (your old bookmarks would be in `~/.mozilla/firefox_old/…`)
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faq-using-crystal-google-apps.md
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From the web interface you can switch Applications by clicking on the 3x3
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square pattern near your email address (top right):
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-![](../images/using-crystal-google-apps-1.png)
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+![](images/using-crystal-google-apps-1.png)
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## Crystal Google Calendar:
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* [<https://support.google.com/calendar/answer/99358>](https://support.google.com/calendar/answer/99358)
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-![](../images/using-crystal-google-apps-2.png)
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+![](images/using-crystal-google-apps-2.png)
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## Share Calendar
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To share your calendars with other users, please refer to this page:
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* [<https://support.google.com/calendar/answer/37082>](https://support.google.com/calendar/answer/37082)
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-![](../images/using-crystal-google-apps-3.png)
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+![](images/using-crystal-google-apps-3.png)
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-![](../images/using-crystal-google-apps-4.png)
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+![](images/using-crystal-google-apps-4.png)
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To remove shared calendars, please refer to this page:
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[<https://support.google.com/calendar/answer/40802>](https://support.google.com/calendar/answer/40802)
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-![](../images/using-crystal-google-apps-5.png)
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+![](images/using-crystal-google-apps-5.png)
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## Calendar Import
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Instead of importing calendars into iCal, etc, go to the manage page:
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* [<https://www.google.com/calendar/syncselect>](https://www.google.com/calendar/syncselect)
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-![](../images/using-crystal-google-apps-6.png)
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+![](images/using-crystal-google-apps-6.png)
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## Crystal Google Drive/Docs:
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You can also set permissions for read only, comment, and edit.
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-![](../images/using-crystal-google-apps-7.png)
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+![](images/using-crystal-google-apps-7.png)
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## Crystal Google Mail:
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[<http://mail.crystal.harvard.edu>](http://mail.crystal.harvard.edu)
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-![](../images/using-crystal-google-apps-8.png)
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+![](images/using-crystal-google-apps-8.png)
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### Tabs for inbox
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-![](../images/using-crystal-google-apps-9.png)
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+![](images/using-crystal-google-apps-9.png)
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### IMAP
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the arrow to expand - select 'Manage labels'. From that page for 'All mail'
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setting - uncheck 'show in imap'.
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-![](../images/using-crystal-google-apps-10.png)
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-![](../images/using-crystal-google-apps-11.png)
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+![](images/using-crystal-google-apps-10.png)
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+![](images/using-crystal-google-apps-11.png)
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#### Filters
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you choose what to do with the message. You can select ‘Choose Label’ and that
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is basically a folder.
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-![](../images/using-crystal-google-apps-12.png)
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-![](../images/using-crystal-google-apps-13.png)
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-![](../images/using-crystal-google-apps-14.png)
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+![](images/using-crystal-google-apps-12.png)
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+![](images/using-crystal-google-apps-13.png)
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+![](images/using-crystal-google-apps-14.png)
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faqs.md
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+
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+# FAQ
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+Frequently Answered Questions
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+
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+## Account Related
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+* [Change Your Unix Password](changing-your-account-password)
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+* [Backups Using Crashplan](crashplan-backups)
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+* [SBGrid/CMCD VPN](connecting-to-cmcd-vpn)
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+* [NE CAT Data Collection](data-collection-at-ne-cat)
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+* [Requesting an Account](new-accounts)
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+
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+## Software & Linux/Mac/UNIX
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+
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+* [Access Remote Filesystems using SSHFS](sshfs)
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+* [Firefox Problems on Network Account](troubleshooting-firefox-on-a-network-account)
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+* [How to Forward Email](forwarding-mail-to-crystal)
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+* [Linux Remote Access](remote-access-to-linux-computers)
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+* [OS X (Apple): Find MAC Address](how-to-find-mac-address-on-os-x-gui)
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+* [Running jobs after you logged off (using Screen)](running-remote-jobs-after-disconnecting)
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+* [SSH Without a Password](setting-up-passwordless-ssh)
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+* [SBGrid Software](using-sbgrid-programs)
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+* [Using Crystal Email](using-your-crystal-harvard-edu-email-address)
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+* [Other Resources](other-resources)
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\ No newline at end of file
genzyme.md
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# Storage and Backup:
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The NFS server is backed up to a local external hard drive.
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+This should checked monthly to ensure that backups are working.
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+
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# General IT Support:
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Support for office computing is provided by local Genzyme IT.
hms5-walker.md
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New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.
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# Computers
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-SBGrid supports Linux systems in the Walker Lab. If you need support for Mac systems or printers, please contact HMS-IT support at:
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+SBGrid can provide support for Linux systems in the Walker Lab. If you need support for Mac systems or printers, please contact HMS-IT support at:
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* <http://hms.harvard.edu/departments/hms-information-technology/get-help>
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hu2-kahne.md
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### Linux
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Linux computers authenticate locally and data directories can be accessed only from within the lab. Home directories are located
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-at /home/<username>. The shared data directory is located at /shared. SBGrid's comprehensive collections of structural biology
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-applications is located in the /programs directory.
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+at `/home/<username>`. The shared data directory is located at `/shared`. SBGrid's comprehensive collections of structural biology
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+applications is located in the `/programs` directory.
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If you need remote access, please contact [help@sbgrid.org](mailto:help@sbgrid.org).
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