Getting Started in CBCB: Difference between revisions

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Latest revision as of 14:32, 25 February 2022

You may want to review the following:

Getting Building Access and Room Keys

CBCB is located on the 3rd floor of The Brendan Iribe Center identified on campus maps as Building #432.

Contact the Center Coordinator, Barbara Lewis, about gaining card access to the building. She will need the following information:

A 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.

Barbara Lewis
Room 3234
Brendan Iribe Center
301.405.5936
blewis12[at]umd.edu

Research In Progress Seminars

These seminars are held throughout the year. For information go to CBCB Research in Progress

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

WARNING: /fs/sz-user-supported/ and /cbcb/software has been deprecated as of March 2015. Please move towards using Red Hat 7 machines and CBCB Software Modules.

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

CBCB Software Modules

To use CBCB Software Modules, see CBCB Software Modules

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

When You Travel

See: https://businessoffice.umiacs.umd.edu/travel for travel guidelines.
Get travel pre-approved by PI and determine funding source.
Read and fill out a Travel Request Form at: https://businessoffice.umiacs.umd.edu/form/travel. Once completed, submit.

 A copy will be sent directly to the Center coordinator. A Travel Request must be completed before every trip per University policy.

See the Miscellaneous Expenses section of http://www.dbs.umd.edu/travel/policy/umtravel/trav_guide.php for allowable and unallowable miscellaneous expenses for reimbursement
Keep all original receipts and give to Barbara for reimbursement after the trip has been completed.
Confirmation emails aren’t acceptable. If paying online with your own credit card, then Barbara will need the electronic receipt. and a copy of the credit card transactions showing the expense.
Barbara will need the amount, date, and description for reimbursable expenses.

Retrieved from "https://wiki.umiacs.umd.edu/cbcb/index.php?title=Getting_Started_in_CBCB&oldid=9066"

@@ Line 1: / Line 1: @@
-Last update 4/25/13<br>
+You may want to review the following:
-* [[Media:CBCB_orientation.pdf]] -- slides from CBCB orientation
+[[Media:CBCB-quick-guide.pdf]]
 ==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.
+CBCB is located on the 3rd floor of The Brendan Iribe Center identified on campus maps as Building #432.
-Contact the Center Coordinator, Denise Cross, about gaining card access to the building.  She will need the following information:
+Contact the Center Coordinator, Barbara Lewis, about gaining card access to the building.  She will need the following information:
-*An notification email from your sponsor/adviser
+*A notification email from your sponsor/adviser
 *Your Name
 *Your 9 Digit University ID number
@@ Line 20: / Line 20: @@
 You must get your key from the coordinator in person.
-Denise Cross<br>
+Barbara Lewis<br>
-Room 3121<br>
+Room 3234<br>
-Biomolecular Sciences Bldg #296<br>
+Brendan Iribe Center<br>
 .405.5936<br>
-dcross[at]umd.edu<br>
+blewis12[at]umd.edu<br>
-==Subscribing to Mailing Lists==
+==Research In Progress Seminars==
-There are a number of CBCB mailing lists that you can subscribe to by following the instructions on this page: [https://mailman.umiacs.umd.edu/mailman/listinfo mailman.umiacs.umd.edu/mailman/listinfo] <br>
-(note: you may have to add a security exception to your browser to view the list)
+These seminars are held throughout the year.  For information go to [https://cbcb.umd.edu/research-in-progress CBCB Research in Progress]
-==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).
-<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>
 == Configuring Your Home Directory and Shell ==
+<p style="color: #e70000; font-weight: bold; font-size: medium;">WARNING: <code>/fs/sz-user-supported/</code> and <code>/cbcb/software</code> has been deprecated as of March 2015. Please move towards using Red Hat 7 machines and [[CBCB Software Modules]]. </p>
 We import common settings files that set our path variables to include commonly shared software repositories.
@@ Line 69: / Line 65: @@
 More resources can be found at [https://wiki.umiacs.umd.edu/umiacs/index.php/GettingStarted umiacs wiki]
+== CBCB Software Modules ==
+To use CBCB Software Modules, see [[CBCB Software Modules]]
 == 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.
@@ Line 78: / Line 78: @@
 * [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
-==Publication Database==
+== When You Travel ==
-Currently Under Construction<br>
-<!--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)
-* All publications are stored in a MySQL database.
-* 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>
-The system is live at [http://www.cbcb.umd.edu/publications http://www.cbcb.umd.edu/publications].-->
-==Adding Your Publications to Your Website==
-Currently Under Construction
-<!--Two pages are useful for this purpose:<br>
+* See: https://businessoffice.umiacs.umd.edu/travel for travel guidelines.
-[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>
+* Get travel pre-approved by PI and determine funding source.
-[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>
+* Read and fill out a Travel Request Form at: https://businessoffice.umiacs.umd.edu/form/travel. Once completed, submit.
-Adding one of these pages within your website can be done with an iframe, e.g.:<br>
+   A copy will be sent directly to the Center coordinator. A Travel Request must be completed before every trip per University policy.
-<pre>
+* See the Miscellaneous Expenses section of http://www.dbs.umd.edu/travel/policy/umtravel/trav_guide.php for allowable and unallowable miscellaneous expenses for reimbursement
-<iframe src="http://www.cbcb.umd.edu/publications/authorRecent?n=pop&num=5"
+* Keep all original receipts and give to Barbara for reimbursement after the trip has been completed.
-   width="100%" height=300>
+* Confirmation emails aren’t acceptable. If paying online with your own credit card, then Barbara will  need the electronic receipt. and a copy of the credit card transactions showing the expense.
-</iframe>
+* Barbara will need the amount, date, and description for reimbursable expenses.
-</pre>
-<br>
-There might be an easier/prettier way but I don't know it.
-<br>
-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.
-<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>
-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.-->