Getting Started in CBCB: Difference between revisions
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Last update 4/25/13<br> | Last update 4/25/13<br> | ||
* [[Media:CBCB_orientation.pdf]] -- slides from CBCB orientation | |||
==Getting Building Access and Room Keys== | ==Getting Building Access and Room Keys== | ||
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*/fs/wrenhome/yourUserName/ | */fs/wrenhome/yourUserName/ | ||
*/nfshomes/yourUserName/ | */nfshomes/yourUserName/ | ||
nfshomes has a | nfshomes has a limit on available disk space (in the double digit MBs) while wrenhomes allows you the more freedom. Therefore you should use wrenhomes for your personal work files, but should be very mindful of how much space you are using and how much free space remains. For large amounts of data, you should use one of the following (after first checking with your sponsor). | ||
<br> | |||
For a list of our Disk Storage and amount of available space left on each one, see [http://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage wiki.umiacs.umd.edu/cbcb-private/index.php/Storage]<br> | |||
For a list of our Disk Storage | |||
== Configuring Your Home Directory and Shell == | == Configuring Your Home Directory and Shell == | ||
We import common settings files that set our path variables to include commonly shared software repositories. | |||
As a start, add the following line to the top of the file called ".bashrc" located in your home directory (/nfshomes/username/): | As a start, add the following line to the top of the file called ".bashrc" located in your home directory (/nfshomes/username/): | ||
. /fs/sz-user-supported/share/dotfiles/bashrc.cbcb | . /fs/sz-user-supported/share/dotfiles/bashrc.cbcb | ||
This will import the common bashrc.cbcb file into your own bashrc file every time you log in. | This will import the common bashrc.cbcb file into your own bashrc file every time you log in. | ||
Now add this line to your ".bash_profile" file, also located in your home directory: | Now add this line to your ".bash_profile" file, also located in your home directory: | ||
. ~/.bashrc | . ~/.bashrc | ||
This will import your personal bashrc file every time you log in. Now you should have access to most of the locally installed software like "blastall" and "AMOS." | This will import your personal bashrc file every time you log in. Now you should have access to most of the locally installed software like "blastall" and "AMOS." | ||
If you want to add any addition commands to your bashrc file, such as setting your default text editor to "vim" or formatting the output of bash commands (eg. "ls"), add the appropriate commands after the imported common files as shown in this example: | If you want to add any addition commands to your bashrc file, such as setting your default text editor to "vim" or formatting the output of bash commands (eg. "ls"), add the appropriate commands after the imported common files as shown in this example: | ||
. /fs/sz-user-supported/share/dotfiles/bashrc.cbcb | . /fs/sz-user-supported/share/dotfiles/bashrc.cbcb | ||
alias vi='vim' | alias vi='vim' | ||
alias ls='ls --color' | alias ls='ls --color' | ||
If you decide you want to change the settings in the common bashrc.cbcb to better suit your personal needs, then please copy and paste its contents into your personal bashrc file. '''Do not modify the common bashrc.cbcb file as it will affect everyone's environment.''' Also check back periodically as people may add common paths for new software. | If you decide you want to change the settings in the common bashrc.cbcb to better suit your personal needs, then please copy and paste its contents into your personal bashrc file. '''Do not modify the common bashrc.cbcb file as it will affect everyone's environment.''' Also check back periodically as people may add common paths for new software. | ||
If you have any other problems, | If you have any other problems, contact staff [at] umiacs.umd.edu or your PI. <br> | ||
More resources can be found at [https://wiki.umiacs.umd.edu/umiacs/index.php/GettingStarted umiacs wiki] | |||
== Printing == | == Printing == | ||
Go to the umiacs wiki to find [https://wiki.umiacs.umd.edu/umiacs/index.php/Printing system-specific guides for printing], and be sure to [https://wiki.umiacs.umd.edu/umiacs/index.php/PrinterQueueNaming add 'nb' to the end of your print queue] to avoid wasting paper printing banners. | Go to the umiacs wiki to find [https://wiki.umiacs.umd.edu/umiacs/index.php/Printing system-specific guides for printing], and be sure to [https://wiki.umiacs.umd.edu/umiacs/index.php/PrinterQueueNaming add 'nb' to the end of your print queue] to avoid wasting paper printing banners. | ||
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==Publication Database== | ==Publication Database== | ||
Currently Under Construction<br> | |||
I have a new publications system to help better manage our publications. | <!--I have a new publications system to help better manage our publications. | ||
We will no longer need to edit the index.shtml file anymore, but rather | We will no longer need to edit the index.shtml file anymore, but rather | ||
log into the system and add/edit as we please. Here are the specifications: | log into the system and add/edit as we please. Here are the specifications: | ||
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* Access information (passwords and such) provided on the secure wiki: [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Publication_Server https://wiki.umiacs.umd.edu/cbcb-private/index.php/Publication_Server] | * Access information (passwords and such) provided on the secure wiki: [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Publication_Server https://wiki.umiacs.umd.edu/cbcb-private/index.php/Publication_Server] | ||
<br> | <br> | ||
The system is live at [http://www.cbcb.umd.edu/publications http://www.cbcb.umd.edu/publications]. | The system is live at [http://www.cbcb.umd.edu/publications http://www.cbcb.umd.edu/publications].--> | ||
==Adding Your Publications to Your Website== | ==Adding Your Publications to Your Website== | ||
Two pages are useful for this purpose:<br> | Currently Under Construction | ||
<!--Two pages are useful for this purpose:<br> | |||
[http://www.cbcb.umd.edu/publications/authorByYear?n=pop&fn=Mihai&nyr=3 http://www.cbcb.umd.edu/publications/authorByYear?n=pop&fn=Mihai&nyr=3] -- this page displays the publications for an author with last name specified in the '''n=''' option, with full name specified in '''fn=''', grouped by year for the first '''nyr=''' years (default 3), after which all remaining publications are listed in reverse chronological order.<br><br> | [http://www.cbcb.umd.edu/publications/authorByYear?n=pop&fn=Mihai&nyr=3 http://www.cbcb.umd.edu/publications/authorByYear?n=pop&fn=Mihai&nyr=3] -- this page displays the publications for an author with last name specified in the '''n=''' option, with full name specified in '''fn=''', grouped by year for the first '''nyr=''' years (default 3), after which all remaining publications are listed in reverse chronological order.<br><br> | ||
[http://www.cbcb.umd.edu/publications/authorRecent?n=pop&num=5 http://www.cbcb.umd.edu/publications/authorRecent?n=pop&num=5] -- this page displays the last '''num=''' publications (default 5) for an author with last name specified in the '''n=''' option.<br><br> | [http://www.cbcb.umd.edu/publications/authorRecent?n=pop&num=5 http://www.cbcb.umd.edu/publications/authorRecent?n=pop&num=5] -- this page displays the last '''num=''' publications (default 5) for an author with last name specified in the '''n=''' option.<br><br> | ||
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<br><br> | <br><br> | ||
Also useful: [http://www.cbcb.umd.edu/publications/author.php?n=pop http://www.cbcb.umd.edu/publications/author.php?n=pop] <br> | Also useful: [http://www.cbcb.umd.edu/publications/author.php?n=pop http://www.cbcb.umd.edu/publications/author.php?n=pop] <br> | ||
if you look at the file, what you need is from line 10 - 21. Everything else is for the look and feel. I did two ways to search for a user and thats by database user id and last name (case-insensitive). Searching by last name gives better results. | if you look at the file, what you need is from line 10 - 21. Everything else is for the look and feel. I did two ways to search for a user and thats by database user id and last name (case-insensitive). Searching by last name gives better results.--> | ||
Revision as of 18:36, 29 April 2013
Last update 4/25/13
- Media:CBCB_orientation.pdf -- slides from CBCB orientation
Getting Building Access and Room Keys
CBCB is located on the 3rd floor of The Biomolecular Sciences Building identified on campus maps as Building #296. The building is secure and access is gained by either using your UM ID card, guest card or entering the 3-digit code of the person you to visit at the call box on the right side of the front door.
Contact the Center Coordinator, Denise Cross, about gaining card access to the building. She will need the following information:
- An notification email from your sponsor/adviser
- Your Name
- Your 9 Digit University ID number
- Your Contact email
Along with your assigned space and phone numbers, the coordinator will send your information to UMIACS Coordinator Edna Walker who will contact campus security to add you into their system. Note: clearance usually takes a number of days, so contact the coordinator as soon as possible.
If you prefer not to send your information through email feel free to contact the coordinator in person.
You must get your key from the coordinator in person.
Denise Cross
Room 3121
Biomolecular Sciences Bldg #296
301.405.5936
dcross[at]umd.edu
Subscribing to Mailing Lists
There are a number of CBCB mailing lists that you can subscribe to by following the instructions on this page: mailman.umiacs.umd.edu/mailman/listinfo
(note: you may have to add a security exception to your browser to view the list)
Understanding the Layout of Available Resources
When you first log into a server (eg. flicker01@umiacs.umd.edu), you will probably be placed in one of the following personalized directories:
- /fs/wrenhome/yourUserName/
- /nfshomes/yourUserName/
nfshomes has a limit on available disk space (in the double digit MBs) while wrenhomes allows you the more freedom. Therefore you should use wrenhomes for your personal work files, but should be very mindful of how much space you are using and how much free space remains. For large amounts of data, you should use one of the following (after first checking with your sponsor).
For a list of our Disk Storage and amount of available space left on each one, see wiki.umiacs.umd.edu/cbcb-private/index.php/Storage
Configuring Your Home Directory and Shell
We import common settings files that set our path variables to include commonly shared software repositories.
As a start, add the following line to the top of the file called ".bashrc" located in your home directory (/nfshomes/username/):
. /fs/sz-user-supported/share/dotfiles/bashrc.cbcb
This will import the common bashrc.cbcb file into your own bashrc file every time you log in.
Now add this line to your ".bash_profile" file, also located in your home directory:
. ~/.bashrc
This will import your personal bashrc file every time you log in. Now you should have access to most of the locally installed software like "blastall" and "AMOS."
If you want to add any addition commands to your bashrc file, such as setting your default text editor to "vim" or formatting the output of bash commands (eg. "ls"), add the appropriate commands after the imported common files as shown in this example:
. /fs/sz-user-supported/share/dotfiles/bashrc.cbcb alias vi='vim'
alias ls='ls --color'
If you decide you want to change the settings in the common bashrc.cbcb to better suit your personal needs, then please copy and paste its contents into your personal bashrc file. Do not modify the common bashrc.cbcb file as it will affect everyone's environment. Also check back periodically as people may add common paths for new software.
If you have any other problems, contact staff [at] umiacs.umd.edu or your PI.
More resources can be found at umiacs wiki
Printing
Go to the umiacs wiki to find system-specific guides for printing, and be sure to add 'nb' to the end of your print queue to avoid wasting paper printing banners.
Using the Wiki
Publication Database
Currently Under Construction
Adding Your Publications to Your Website
Currently Under Construction