BioMicroCenter:Computing: Difference between revisions

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The BioMicro Center has developed and manages a computational infrastructure to support our genomics experimentation and [[BioMicroCenter:BioInformaticsStaff|bioinformatics analysis]]. In response to requests from our users, we have expanded these servers to create a new collaborative computational environment at MIT. These public servers are designed to offer CORE labs access to inexpensive analysis and storage systems that piggy-back on the existing infrastructure. These services are built on a full cost recovery model where the total cost of the servers and services is expected to be recovered over three years. Charges for the equipment are billed on an annual basis.
The BioMicro Center has developed and manages a computational infrastructure to support our genomics experimentation and [[BioMicroCenter:BioInformaticsStaff|bioinformatics analysis]]. In response to requests from our users, we have expanded these servers to create a new collaborative computational environment at MIT. These public servers are designed to offer CORE labs access to inexpensive analysis and storage systems that piggy-back on the existing infrastructure. These services are built on a full cost recovery model where the total cost of the servers and services is expected to be recovered over three years. Charges for the equipment are billed on an annual basis.


=== STORAGE ===
[[Image:BMC_servers.png|center|600px]]
Large scale data storage is available through the BioMicro Center. Space is available in 1TB increments on an annual basis. The storage is accessible from Window, Macintosh and Linux operating systems and is backed up by MIT's [http://ist.mit.edu/backup/tsm TSM service]. Two options are available through the BMC<BR><BR>


{|
{| border=1 align="center"
!width=300px| [http://rous.mit.edu/index.php/Rous.mit.edu_accounts rous.mit.edu]
!width=300px| [[BioMicroCenter:BMCPub|bmc-pubN.mit.edu]]
!width=300px| [http://rous.mit.edu/index.php/BCC_Computing_Resources rowley.mit.edu]
|- align="center"
|Linux Cluster
|High Density Storage <BR> Available to CORE labs
|Isilon Cluster <BR> Available to KI labs only
|-
  |
  |
''' [[BioMicroCenter:BMCPub|BMC-PUB servers]] '''
*SGE queueing system
[[ Image:BioMicroCenter_BMCpub1.png | thumb | right | 150px | BMC-pub server]]
*Free account has limited queue
||
*Requires purchase of storage
  ||
  |colspan="2"|  
'''[http://rous.mit.edu/index.php/BCC_Computing_Resources Koch Institute Isilon Cluster]'''
*[http://ist.mit.edu/backup/tsm TSM backup of all data].
For users with appointments in the [http://ki.mit.edu Koch Institute], storage is also available on the KI's Isilon server, Rowley.
* Available on Mac/PC/UNIX
* Available any place at MIT or VPN
* Data available for analysis on ROUS
* Can create public spaces (web access)
|-
|
*24 Nodes
*184 cores
*688 GB RAM
|
*200+TB
*99% uptime (est)
*9TB Volumes
*RAID6 architecture
|
*500+TB
*99.9% uptime (est)
*No volume limit
*KI users only
|}
|}
=== COMPUTATION: [http://rous.mit.edu/index.php/Rous.mit.edu_accounts BMC/BCC Computation Cluster (ROUS)] ===
[[ Image:BioMicroCenter_ROUSimage.jpg | thumb | right | 150px | ROUS ]]
Rous is a Linux cluster, initially purchase in September 2009. Rous, named after the Nobel prize winning cancer researcher [http://www.nobelprize.org/nobel_prizes/medicine/laureates/1966/rous-bio.html Peyton Rous] (and not [http://www.urbandictionary.com/define.php?term=R.O.U.S. Rodents Of Unusual Size]) is equipped with a wide range of bioinformatics software. It uses x86 architecture with 160 processing cores and over 500 GB RAM. Rous is the primary server for handling data analysis from Illumina sequencing and for the GALAXY instance at MIT. Users of Rous '''must''' have an account on either BMC-PUB or on Rowley. <BR><BR>


== [[BioMicroCenter:Software|SOFTWARE]] ==
== [[BioMicroCenter:Software|SOFTWARE]] ==
Line 28: Line 49:


== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==
== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==
[[Image:BMC_informatics_team.png|thumb|right|400xp|Informatics Team]]
A critical aspect of providing our users with genomic data is providing our users with the bioinformatics support to interpret their data readily and to assist them in analyzing data for publications and grants. To accomplish this, the BioMicro Center has a team of informatics scientists on staff able to assist labs with experience in a broad number of methodologies. Bioinformatics consultations are available by appointment for MIT scientists affiliated with MIT CEHS or the departments of Biology and Biological Engineering. Bioinformatic projects are undertaken by the BioMicro Center on a ''collaborative'' basis. [[BioMicroCenter:Pricing|Prices for Bioinformatics support are available.]]  
A critical aspect of providing our users with genomic data is providing our users with the bioinformatics support to interpret their data readily and to assist them in analyzing data for publications and grants. To accomplish this, the BioMicro Center has a team of informatics scientists on staff able to assist labs with experience in a broad number of methodologies. Bioinformatics consultations are available by appointment for MIT scientists affiliated with MIT CEHS or the departments of Biology and Biological Engineering. Bioinformatic projects are undertaken by the BioMicro Center on a ''collaborative'' basis. [[BioMicroCenter:Pricing|Prices for Bioinformatics support are available.]]  


Revision as of 07:08, 29 May 2013

HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

The BioMicro Center supports a broad set of computational services for CORE members including hardware, software and informatic support.

SERVERS

The BioMicro Center has developed and manages a computational infrastructure to support our genomics experimentation and bioinformatics analysis. In response to requests from our users, we have expanded these servers to create a new collaborative computational environment at MIT. These public servers are designed to offer CORE labs access to inexpensive analysis and storage systems that piggy-back on the existing infrastructure. These services are built on a full cost recovery model where the total cost of the servers and services is expected to be recovered over three years. Charges for the equipment are billed on an annual basis.

rous.mit.edu bmc-pubN.mit.edu rowley.mit.edu
Linux Cluster High Density Storage
Available to CORE labs 		Isilon Cluster
Available to KI labs only
  • SGE queueing system
  • Free account has limited queue
  • Requires purchase of storage
  • TSM backup of all data.
  • Available on Mac/PC/UNIX
  • Available any place at MIT or VPN
  • Data available for analysis on ROUS
  • Can create public spaces (web access)
  • 24 Nodes
  • 184 cores
  • 688 GB RAM
  • 200+TB
  • 99% uptime (est)
  • 9TB Volumes
  • RAID6 architecture
  • 500+TB
  • 99.9% uptime (est)
  • No volume limit
  • KI users only

SOFTWARE

The BioMicro Center collaborates with the Koch Institute Bioinformatics Computing Core and the MIT Libraries to support a number of software packages that are available for members of the MIT community. Please check out the Software page for more informaiton

BIOINFORMATICS SERVICES

Informatics Team

A critical aspect of providing our users with genomic data is providing our users with the bioinformatics support to interpret their data readily and to assist them in analyzing data for publications and grants. To accomplish this, the BioMicro Center has a team of informatics scientists on staff able to assist labs with experience in a broad number of methodologies. Bioinformatics consultations are available by appointment for MIT scientists affiliated with MIT CEHS or the departments of Biology and Biological Engineering. Bioinformatic projects are undertaken by the BioMicro Center on a collaborative basis. Prices for Bioinformatics support are available.

If you are looking for informatics support, the easiest way to begin is with an email to biomicro@mit.edu with a brief description of your experiment. One of the members of our informatics staff will reach out to you to schedule a one on one meeting. This meeting is free for CORE lab members. Once an experimental plan is approved we will begin work on your project, checking in with you at regular intervals to be sure the project is on track. The project can be paused at any time by the researcher.

More information about bioinformatics support through the BioMicro Center is available HERE.

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