Getting Started in CBCB: Difference between revisions

From Cbcb

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: @@
-(under development)<br>
+You may want to review the following:
+[[Media:CBCB-quick-guide.pdf]]
 ==Getting Building Access and Room Keys==
-Talk to the coordinator (Denise Cross) about gaining card access to the building and a key to your lab. She will need the following information:
-*An endorsement email from your sponsor/adviser
-*9 Digit University ID number
-*Name
-*Contact (email/phone)
-*Room number (for keys only)
-Denise's office is 3120D in the Biomolecular Sciences Bldg or you can email her at dcross@umd.edu. For further questions her office number is 301.405.5936.
+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<br>
+Room 3234<br>
+Brendan Iribe Center<br>
+.405.5936<br>
+blewis12[at]umd.edu<br>
+==Research In Progress Seminars==
+These seminars are held throughout the year.  For information go to [https://cbcb.umd.edu/research-in-progress CBCB Research in Progress]
+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.
+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'
-==Subscribing to Mailing Lists==
+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.
-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)
-==Understanding the Layout of Available Resources==
+If you have any other problems, contact staff [at] umiacs.umd.edu or your PI. <br>
-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 [http://www.cbcb.umd.edu/intranet/resources.shtml www.cbcb.umd.edu/intranet/resources.shtml]<br>
+More resources can be found at [https://wiki.umiacs.umd.edu/umiacs/index.php/GettingStarted umiacs wiki]
-For a list of our Disk Storage, with mount points and amount of space 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==
+== CBCB Software Modules ==
-Ask around if you have any problems, as you undoubtedly will
+To use CBCB Software Modules, see [[CBCB Software Modules]]
-==Publication Database==
+== 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.
-(from kunmi)<br>
+== Using the Wiki ==
+* [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Wiki Formatting Cheatsheet]
+* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
+* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
+* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
-I have a new publications system to help better manage our publications.
+== When You Travel ==
-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 Just Your Publications to Your Website==
+* See: https://businessoffice.umiacs.umd.edu/travel for travel guidelines.
-Two pages are useful for this purpose:<br>
+* Get travel pre-approved by PI and determine funding source.
-[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>
+* Read and fill out a Travel Request Form at: https://businessoffice.umiacs.umd.edu/form/travel. Once completed, submit.
-[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>
+   A copy will be sent directly to the Center coordinator. A Travel Request must be completed before every trip per University policy.
-Adding one of these pages within your website can be done with an iframe, e.g.:<br>
+* 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
-<pre>
+* Keep all original receipts and give to Barbara for reimbursement after the trip has been completed.
-<iframe src="http://www.cbcb.umd.edu/publications/authorRecent?n=pop&num=5"
+* 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.
-   width="100%" height=300>
+* Barbara will need the amount, date, and description for reimbursable expenses.
-</iframe>
-</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.