Getting Started in CBCB

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Revision as of 16:05, 25 April 2013 by Dcross (talk | contribs)
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Last update 4/25/13

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 steep limit on available disk space (in the double digit MBs) while wrenhomes allows you the freedom to be wrecklessly inconsiderate and fill up all of the remaining free disk space. 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):

  • /fs/szdata/
  • /fs/szasmg/
  • /fs/szasmg2/
  • /fs/szasmg3/
  • /fs/szasmg4/

For more information on resources available through CBCB, see www.cbcb.umd.edu/intranet/resources.shtml
For a list of our Disk Storage, with mount points 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

The CBCB setup is complicated and constantly changing. To simplify things for the research staff, 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, as you undoubtedly will, just ask around. Chances are the first person you ask will have no idea how to help you, but they will probably be able to point you to someone who can.

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

(from kunmi)

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 log into the system and add/edit as we please. Here are the specifications:

  • Any logged in user for add/edit
  • Import publications manually, or fetch by PubMed ID, EndNote format(also supports EndNote XML), RIS format, and Bibtex
  • Export to Bibtex, EndNote or RIS formats.
  • Search publications by author, keywords or PubMed ID
  • Better ordering of publications (by date, journal or title ... I'm

working on sorting by author)


The system is live at http://www.cbcb.umd.edu/publications.

Adding Your Publications to Your Website

Two pages are useful for this purpose:
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.

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.

Adding one of these pages within your website can be done with an iframe, e.g.:

<iframe src="http://www.cbcb.umd.edu/publications/authorRecent?n=pop&num=5" 
  width="100%" height=300>
</iframe>


There might be an easier/prettier way but I don't know it.
Note that the pages I mention above automatically add an "et al." after the first 10 authors in any publication with more than 10 authors. Right now this is hardcoded behaviour, though it shouldn't be super-hard to create a more flexible policy.

Also useful: http://www.cbcb.umd.edu/publications/author.php?n=pop
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.

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