Cbcb - User contributions [en]

File:CBCB-quick-guide.pdf

2022-02-25T14:34:31Z

Blewis: Blewis uploaded a new version of File:CBCB-quick-guide.pdf

Getting Started in CBCB

2022-02-25T14:32:46Z

Blewis:

You may want to review the following:

[[Media:CBCB-quick-guide.pdf]]

==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 [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] 

== Configuring Your Home Directory and Shell ==

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]]. 

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 [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.

== 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]

== 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.

Getting Started in CBCB

2022-02-25T14:31:49Z

Blewis:

You may want to review the following:

[[Media:CBCB-quick-guide.pdf]]

==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 
blewis[at]umiacs.umd.edu 

==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] 

== Configuring Your Home Directory and Shell ==

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]]. 

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 [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.

== 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]

== 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.

Getting Started in CBCB

2022-02-25T14:30:02Z

Blewis:

You may want to review the following:

[[Media:CBCB-quick-guide.pdf]]

==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 
blewis[at]umiacs.umd.edu 

==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] 

== Configuring Your Home Directory and Shell ==

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]]. 

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 [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.

== 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]

== When You Travel ==

[[Media:CBCB_travel_request_form_oct_2014.pdf‎]] form to fill out to obtain information for travel reimbursement

[[Media:Travel_101_cbcb_revised_4-2013.pdf]] for more detailed travel info

Cbcb:Cloud-Computing

2022-02-25T14:28:12Z

Blewis:

Note: contact info for group members and access information for clusters is available on the project's private page: [[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Cloud_computing https://wiki.umiacs.umd.edu/cbcb-private/index.php/Cloud_computing]]

== People ==
Mailing list: cbcb_cloud_computing at mailman.umiacs.umd.edu 
Faculty:
* Michael Cummings (CBCB Director)

== Software ==
* CloudBurst
* CrossBow

== Hadoop information ==

Cbcb:Cloud-Computing

2022-02-25T14:27:56Z

Blewis:

Note: contact info for group members and access information for clusters is available on the project's private page: [[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Cloud_computing https://wiki.umiacs.umd.edu/cbcb-private/index.php/Cloud_computing]]

== People ==
Mailing list: cbcb_cloud_computing at mailman.umiacs.umd.edu 
Faculty:
* Mihai Pop (UMIACS Director)
* Michael Cummings (CBCB Director)

== Software ==
* CloudBurst
* CrossBow

== Hadoop information ==

Main Page

2022-02-25T14:26:09Z

Blewis:

== CBCB Private Wiki ==
'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!'''
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]
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 [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage 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 ==

* [https://cbcb.umd.edu/research-in-progress Research In Progress (RIPS) schedule] 

== Projects ==

* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Cloud-Computing|Cloud Computing]]
* [https://cbcb.umd.edu/summer-internships CBCB Summer Internship Program] 
* [[Metagenomics Reading Group (Wed 2pm)]]

== 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: 
*[[Getting Started in CBCB]]
*[[CBCB Software Modules]]
*[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]]

Main Page

2022-02-25T14:24:05Z

Blewis:

== CBCB Private Wiki ==
'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!'''
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]
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 [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage 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 ==

* [https://cbcb.umd.edu/research-in-progress Research In Progress (RIPS) schedule] 

== Projects ==

* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Cloud-Computing|Cloud Computing]]
* [[Project:SummerInternships|Summer Internship Projects]]
* [[Metagenomics Reading Group (Wed 2pm)]]

== People ==

* [[User:ayres|Daniel Ayres]]
* [[User:pknut777|Adam Bazinet]]
* [[User:irina|Irina Astrovskaya]]
* [[User:jpaulson|Joseph Paulson]]
* [[User:mpop|Mihai Pop]]
* [[User:nelsayed|Najib El-Sayed]]

== 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: 
*[[Getting Started in CBCB]]
*[[CBCB Software Modules]]
*[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]]

Main Page

2022-02-25T14:23:08Z

Blewis:

== CBCB Private Wiki ==
'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!'''
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]
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 [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage 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 ==
* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] 
* [https://cbcb.umd.edu/research-in-progress Research In Progress (RIPS) schedule] 
* [[short_read_sequencing|Short read sequencing Meeting]] (Fridays at 3pm)

== Projects ==

* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Hcbravo-lab|HCBravo Lab]]
* [[Project:Cloud-Computing|Cloud Computing]]
* [[Project:SummerInternships|Summer Internship Projects]]
* [[Metagenomics Reading Group (Wed 2pm)]]

== People ==

* [[User:ayres|Daniel Ayres]]
* [[User:pknut777|Adam Bazinet]]
* [[User:irina|Irina Astrovskaya]]
* [[User:jpaulson|Joseph Paulson]]
* [[User:mpop|Mihai Pop]]
* [[User:nelsayed|Najib El-Sayed]]

== 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: 
*[[Getting Started in CBCB]]
*[[CBCB Software Modules]]
*[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]]

Main Page

2022-02-25T14:21:40Z

Blewis:

== CBCB Private Wiki ==
'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!'''
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]
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 [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage 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 ==
* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] 
* <a href="https://cbcb.umd.edu/research-in-progress">[[CBCB:Research In Progress (RIPS)]] - Research in Progress seminar schedule</a> 
* [[short_read_sequencing|Short read sequencing Meeting]] (Fridays at 3pm)

== Projects ==

* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Hcbravo-lab|HCBravo Lab]]
* [[Project:Cloud-Computing|Cloud Computing]]
* [[Project:SummerInternships|Summer Internship Projects]]
* [[Metagenomics Reading Group (Wed 2pm)]]

== People ==

* [[User:ayres|Daniel Ayres]]
* [[User:pknut777|Adam Bazinet]]
* [[User:irina|Irina Astrovskaya]]
* [[User:jpaulson|Joseph Paulson]]
* [[User:mpop|Mihai Pop]]
* [[User:nelsayed|Najib El-Sayed]]

== 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: 
*[[Getting Started in CBCB]]
*[[CBCB Software Modules]]
*[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]]

Main Page

2022-02-25T14:19:27Z

Blewis:

== CBCB Private Wiki ==
'''You have to be on the UMIACS VPN to view the private wiki if you are not on campus!'''
*[https://wiki.umiacs.umd.edu/cbcb-private/index.php/Main_Page CBCB private wiki]
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 [https://wiki.umiacs.umd.edu/cbcb-private/index.php/Storage 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 ==
* [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] 
* [[CBCB:Research In Progress (RIPS)]] - Research in Progress seminar schedule 
* [[short_read_sequencing|Short read sequencing Meeting]] (Fridays at 3pm)

== Projects ==

* [[Project:Pop-Lab|Pop-Lab]]
* [[Project:Hcbravo-lab|HCBravo Lab]]
* [[Project:Cloud-Computing|Cloud Computing]]
* [[Project:SummerInternships|Summer Internship Projects]]
* [[Metagenomics Reading Group (Wed 2pm)]]

== People ==

* [[User:ayres|Daniel Ayres]]
* [[User:pknut777|Adam Bazinet]]
* [[User:irina|Irina Astrovskaya]]
* [[User:jpaulson|Joseph Paulson]]
* [[User:mpop|Mihai Pop]]
* [[User:nelsayed|Najib El-Sayed]]

== 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: 
*[[Getting Started in CBCB]]
*[[CBCB Software Modules]]
*[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]]

Getting Started in CBCB

2019-06-04T18:45:28Z

Blewis:

You may want to review the following:

[[Media:CBCB-quick-guide.pdf]]

==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 
blewis[at]umiacs.umd.edu 

==Research In Progress Seminars==

These seminars are held throughout the year. For information go to [http://cbcb.umd.edu/node/18625 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] 

== Configuring Your Home Directory and Shell ==

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]]. 

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 [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.

== 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]

== When You Travel ==

[[Media:CBCB_travel_request_form_oct_2014.pdf‎]] form to fill out to obtain information for travel reimbursement

[[Media:Travel_101_cbcb_revised_4-2013.pdf]] for more detailed travel info

Getting Started in CBCB

2018-11-12T21:13:28Z

Blewis:

You may want to review the following:

[[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.

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
*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 3121 
Biomolecular Sciences Bldg #296 
301.405.5936 
blewis[at]umiacs.umd.edu 

==Research In Progress Seminars==

These seminars are held through the year. For information go to [http://cbcb.umd.edu/node/18625 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] 

== Configuring Your Home Directory and Shell ==

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]]. 

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 [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.

== 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]

== When You Travel ==

[[Media:CBCB_travel_request_form_oct_2014.pdf‎]] form to fill out to obtain information for travel reimbursement

[[Media:Travel_101_cbcb_revised_4-2013.pdf]] for more detailed travel info