BioMicroCenter:Computing: Difference between revisions

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[[Image:BMC10101.png|right]]
[[Image:BMC10101.png|right]]
The BioMicro Center supports a broad set of computational services for CORE members including hardware, software and informatic support.  
The BioMicro Center supports a broad set of computational services for CORE members including hardware, software and informatic support.  
== [[BioMicroCenter:Servers|SERVERS]] ==
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 ===
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>
{|
|
''' [[BioMicroCenter:BMCPub|BMC-PUB servers]] '''
[[ Image:BioMicroCenter_BMCpub1.png | thumb | right | 150px | BMC-pub server]]
||
||
'''[http://rous.mit.edu/index.php/BCC_Computing_Resources Koch Institute Isilon Cluster]'''
For users with appointments in the [http://ki.mit.edu Koch Institute], storage is also available on the KI's Isilon server, Rowley.
|}
=== 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]] ==
The BioMicro Center collaborates with the [http://luria.mit.edu/CCR_BCC/ Koch Institute Bioinformatics Computing Core] and the [http://libguides.mit.edu/bioinfo 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


== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==
== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==
[[Image:BMC_informatics_team|thumb|right|400xp|Informatics Team]]
[[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.]]  


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More information about bioinformatics support through the BioMicro Center is available [[BioMicroCenter:BioInformaticsStaff|HERE''']].
More information about bioinformatics support through the BioMicro Center is available [[BioMicroCenter:BioInformaticsStaff|HERE''']].
== [[BioMicroCenter:Software|BIOINFORMATICS TOOLS]] ==
The BioMicro Center collaborates with the [http://luria.mit.edu/CCR_BCC/ Koch Institute Bioinformatics Computing Core] and the [http://libguides.mit.edu/bioinfo MIT Libraries] to support a number of bioinformatics tools that are available for members of the MIT community. Generally these break down into software packages from companies, either for secondary analysis of assays or for tertiary annotation, or informatics tools installed on our computing environment. Please check out the [[BioMicroCenter:Software|Software page]] for more informaiton
== [[BioMicroCenter:Servers|BIOIT / SERVERS / DATA STORAGE]] ==
The BioMicro Center supports a computing environment tailored to support the research needs of the life sciences community at MIT, focused on supporting genomics and related mutliomic analyses. This environment provides the necessary computing infrastructure for the systems biology technologies in the core as well as for laboratories in the life sciences. <BR><BR>
Key features tailoring the system to life sciences researchers:<BR>
- data allocations by lab, not by user, ensuring persistence<BR>
- data redundancy through multiple backups<BR>
- data access through mountable drives on windows, mac, and linux.<BR>
- separate computing environment with genomics and related analytical software pre-installed<BR>
- backend connections available direct to high-data output utilization minimizing network impact<BR>
- high-RAM nodes required for complex mutliomic analysis.<BR>
The BioMicroCenter system is currently used by over 40 laboratories with over 600 users.<BR>
Charges for the equipment are billed on an annual basis.<BR>

Latest revision as of 17:53, 22 January 2024

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.

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.

BIOINFORMATICS TOOLS

The BioMicro Center collaborates with the Koch Institute Bioinformatics Computing Core and the MIT Libraries to support a number of bioinformatics tools that are available for members of the MIT community. Generally these break down into software packages from companies, either for secondary analysis of assays or for tertiary annotation, or informatics tools installed on our computing environment. Please check out the Software page for more informaiton

BIOIT / SERVERS / DATA STORAGE

The BioMicro Center supports a computing environment tailored to support the research needs of the life sciences community at MIT, focused on supporting genomics and related mutliomic analyses. This environment provides the necessary computing infrastructure for the systems biology technologies in the core as well as for laboratories in the life sciences.

Key features tailoring the system to life sciences researchers:
- data allocations by lab, not by user, ensuring persistence
- data redundancy through multiple backups
- data access through mountable drives on windows, mac, and linux.
- separate computing environment with genomics and related analytical software pre-installed
- backend connections available direct to high-data output utilization minimizing network impact
- high-RAM nodes required for complex mutliomic analysis.
The BioMicroCenter system is currently used by over 40 laboratories with over 600 users.

Charges for the equipment are billed on an annual basis.
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