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== Seminars ==
== CBCB Private Wiki ==
* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] <br>
'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!'''
* [[Cbcb:Works-In-Progress]] - Works in progress seminar schedule (Summer 2008) <br>
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]
* [[short_read_sequencing|Short read sequencing Meeting]] (Fridays at 3pm)
In addition to this wiki there is also the CBCB private wiki. It contains information internal to CBCB, such as information about how to use the cluster.


== Projects ==
== IMPORTANT (Read First) ==


* [[Project:Pop-Lab|Pop-Lab]]
<span style="color: green; font-size: medium; font-weight: bold;">NEW!&nbsp;</span><span style="font-weight: bold">Read about the [[CBCB Software Modules]]</span>
* [[Project:Kingsford-Group|Kingsford Group]]
* [[Project:Cloud-Computing|Cloud Computing]]


== People ==
The CBCB computational infrastructure is a shared resource and we all need to pitch in in order to make sure it works well for all of us. Most importantly, we need to ensure that our disk space and computational resources are used responsibly.  The disk space, in particular, is a valuable commodity and thus it is important to pay attention to the following:
   
* There are two types of disk space available (a full list of volumes is available at [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]) :
* [[User:ayres|Daniel Ayres]]
** Local hard drives (usually mounted as /scratch on the machines that have this resource).  These are not backed up, are quite fast (they live physically close to the processor), but can only be 'seen' by the machine where they are mounted and, thus, require data staging in/out (which can take a while)
* [[User:pknut777|Adam Bazinet]]
** Isilon storage (/fs/cbcb-lab, /fs/cbcb-scratch/*, etc.).  This is very fast and very expensive disk and thus a limited resource.
* [[User:amp|Adam M Phillipy]]
* You should remove any temporary results you don't need in the long term as soon as you've generated them, and compress all of the large files.  Bzip2 works better than gzip but either should dramatically improve the space requirements, especially for text files such as fasta or fastq.
* [[User:adelcher|Arthur L. Delcher]]
* [[User:carlk|Carl Kinsford]]  
* [[User:dpuiu|Daniela Puiu]]
* [[User:dsommer|Dan Sommer]]
* [[User:gpertea|Geo Pertea]]
* [[User:jeallen|Jonathan Edward All]]
* [[User:ayanbule|Kunmi Ayanbule]]
* [[User:mschatz|Michael Schatz]]
* [[User:mpertea|Mihaela Pertea]]
* [[User:mpop|Mihai Pop]]
* [[User:nelsayed|Najib El-Sayed]]
* [[User:nedwards|Nathan Edwards]]
* [[User:niranjan|Niranjan Nagarajan]]
* [[User:saket|Saket Navlakha]]
* [[User:angiuoli|Samuel V Angluoli]]
* [[User:salzberg|Steven Salzberg]]
* [[User:whitej|James Robert White]]


== Getting started ==
For more information on the CBCB resources see [[Getting Started in CBCB]].
(under development)<br>
===Getting building access and room keys===
Talk to 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)


Her 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.
== Seminars ==


===Subscribing to mailing lists===
* [https://cbcb.umd.edu/research-in-progress Research In Progress (RIPS) schedule] <br>
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)


===Understanding the layout of available resources===
== Projects ==
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/
You can check the available disk space by using df from the command line or by visiting (what is this web page?)


Follow the resources link at the bottom of this page for more information on resources available through CBCB.
* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Cloud-Computing|Cloud Computing]]
* [https://cbcb.umd.edu/summer-internships CBCB Summer Internship Program] <br>
* [[Metagenomics Reading Group (Wed 2pm)]]


===Configuring your home directory and shell===


===Other helpful resources===
== Getting started ==
* [[Cbcb:Resources]] (VERY) Useful information on CBCB resources<br><br>
If you have just received a new UMIACS account through CBCB, follow the instructions on this page to get the basic information you'll need to start working:<br>
* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
*[[Getting Started in CBCB]]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
*[[CBCB Software Modules]]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Slurm Slurm]
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage CBCB Storage]
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Compute CBCB Computers]
*[[Communal Software]]

Latest revision as of 14:26, 25 February 2022

CBCB Private Wiki

You have to be on the UMIACS VPN to view the private wiki if you are not on campus!

In addition to this wiki there is also the CBCB private wiki. It contains information internal to CBCB, such as information about how to use the cluster.

IMPORTANT (Read First)

NEW! Read about the CBCB Software Modules

The CBCB computational infrastructure is a shared resource and we all need to pitch in in order to make sure it works well for all of us. Most importantly, we need to ensure that our disk space and computational resources are used responsibly. The disk space, in particular, is a valuable commodity and thus it is important to pay attention to the following:

  • There are two types of disk space available (a full list of volumes is available at CBCB Storage) :
    • Local hard drives (usually mounted as /scratch on the machines that have this resource). These are not backed up, are quite fast (they live physically close to the processor), but can only be 'seen' by the machine where they are mounted and, thus, require data staging in/out (which can take a while)
    • Isilon storage (/fs/cbcb-lab, /fs/cbcb-scratch/*, etc.). This is very fast and very expensive disk and thus a limited resource.
  • You should remove any temporary results you don't need in the long term as soon as you've generated them, and compress all of the large files. Bzip2 works better than gzip but either should dramatically improve the space requirements, especially for text files such as fasta or fastq.

For more information on the CBCB resources see Getting Started in CBCB.

Seminars

Projects


Getting started

If you have just received a new UMIACS account through CBCB, follow the instructions on this page to get the basic information you'll need to start working:

Retrieved from "https://wiki.umiacs.umd.edu/cbcb/index.php?title=Main_Page&oldid=9061"