BioMicroCenter:Computing - Revision history

Stuart S. Levine at 21:28, 30 April 2013

Stuart S. Levine — Tue, 30 Apr 2013 21:28:10 GMT

Stuart S. Levine at 19:45, 30 April 2013

Stuart S. Levine — Tue, 30 Apr 2013 19:45:12 GMT

←Older revision		Revision as of 19:45, 30 April 2013
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	{{BioMicroCenter}}		{{BioMicroCenter}}
-

	[[Image:BMC10101.png\|right]]		[[Image:BMC10101.png\|right]]

Stuart S. Levine at 18:57, 29 April 2013

Stuart S. Levine — Mon, 29 Apr 2013 18:57:10 GMT

←Older revision		Revision as of 18:57, 29 April 2013
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	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.

-	== HARDWARE ==	+	== [[BioMicroCenter:Servers\|HARDWARE]] ==
	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.

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	* Requests for software changes to Rous should be made to [[BioMicroCenter:People\|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].		* Requests for software changes to Rous should be made to [[BioMicroCenter:People\|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].

-	== SOFTWARE ==	+	== [[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		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

Stuart S. Levine: /* HARDWARE */

Stuart S. Levine — Fri, 22 Jun 2012 01:46:39 GMT

HARDWARE

←Older revision		Revision as of 01:46, 22 June 2012
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	== HARDWARE ==		== HARDWARE ==
-	The BioMicro Center ~~Supports~~ a ~~number of storage~~ and computational ~~services for~~ CORE ~~members~~. 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 ===
		+	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].<BR><BR>
		+
		+	'''We strongly encourage all labs using Illumina sequencing or bioinformatics analysis to have networked data storage. Either Rowley or BMC-PUB storage is required to utilize our computer cluster or our Galaxy server.'''

	=== STORAGE: [[BioMicroCenter:BMCPub\|BMC-PUB servers]] ===		=== STORAGE: [[BioMicroCenter:BMCPub\|BMC-PUB servers]] ===
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	* Currently, users are limited to 24 simultaneous processes on the server.		* Currently, users are limited to 24 simultaneous processes on the server.
	* Requests for software changes to Rous should be made to [[BioMicroCenter:People\|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].		* Requests for software changes to Rous should be made to [[BioMicroCenter:People\|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].
-

	== SOFTWARE ==		== SOFTWARE ==

Stuart S. Levine: /* Server Software Installed on ROUS */

Stuart S. Levine — Wed, 20 Jun 2012 15:29:14 GMT

Server Software Installed on ROUS

←Older revision		Revision as of 15:29, 20 June 2012
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	cufflinks/2.0.1 r/2.14.0(default) wx/2.8.12(default)		cufflinks/2.0.1 r/2.14.0(default) wx/2.8.12(default)
	gatk/1.3-21-gcb284ee r/2.14.2		gatk/1.3-21-gcb284ee r/2.14.2
-	Other ~~packages, such as BLAST and BLAT are~~ installed but have not yet been converted to module packages.	+	Other packagesare installed but have not yet been converted to module packages. These include:

-	* ~~'''~~BLAST~~'''~~	+	* BLAST / BLAT
-	* '''BLAT~~'''~~	+	* GenePattern
-	* ~~'''Bowtie'''~~	+	* IGV
-	* '''GenePattern~~'''~~	+	* MACS
-	* ~~'''Genome Analysis Tool Kit'''~~	+	* MAQ
-	* '''IGV~~'''~~	+	* MEME
-	* ~~'''Illumina Pipeline/CASAVA'''~~	+	* Velvet
-	* '''MACS~~'''~~	+
-	* ~~'''~~MAQ~~'''~~	+
-	* ~~'''~~MEME~~'''~~	+
-	* '''R'''	+
-	* '''SAMTOOLS'''	+
-	* '''Tophat'''	+
-	* ~~'''~~Velvet~~'''~~	+

	== [[BioMicroCenter:BioInformaticsStaff\|BIOINFORMATICS SERVICES]] ==		== [[BioMicroCenter:BioInformaticsStaff\|BIOINFORMATICS SERVICES]] ==

Stuart S. Levine at 15:27, 20 June 2012

Stuart S. Levine — Wed, 20 Jun 2012 15:27:17 GMT

←Older revision		Revision as of 15:27, 20 June 2012
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	* Requests for software changes to Rous should be made to [[BioMicroCenter:People\|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].		* Requests for software changes to Rous should be made to [[BioMicroCenter:People\|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].

-	== ~~GALAXY~~ ==	+
		+	== 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
		+
		+	===Desktop Software===
		+	* [http://biomicro-bioanalyzer.mit.edu/ '''Agilent 2100 Expert'''] This software package is used to control the [[BioMicroCenter:2100BioAnalyzer\|Agilent 2100 Bioanalyzer]] and to perform analysis of the output, including microfluidic and electrophoretic assays for RNA, DNA and proteins, as well as two-color flow cytometry. The software can be installed on your desktop to allow users to do additional analyses.
		+
		+	* [[BioMicroCenter:EVOware\|'''Tecan EvoWare Standard''']] This software is available as part of our robotics service. Identical to the software used on the [[BioMicroCenter:Tecan_Freedom_Evo\|Tecan EVO 150s]], the software contains a simulator that can be used to design your robotics experiments at your bench.
		+
		+	=== Galaxy ===
	[[ Image:BioMicroCenter_GalaxyFront.png \| thumb \| right \| 300px \| Front Page of the MIT Galaxy Site ]]		[[ Image:BioMicroCenter_GalaxyFront.png \| thumb \| right \| 300px \| Front Page of the MIT Galaxy Site ]]
	[http://galaxy.psu.edu/ Galaxy] is an exciting new bioinformatics platform that is designed to bring complicated informatics tools to bench scientists. Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more. For many users, the public Galaxy instance at Penn State can provide a very robust tool.		[http://galaxy.psu.edu/ Galaxy] is an exciting new bioinformatics platform that is designed to bring complicated informatics tools to bench scientists. Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more. For many users, the public Galaxy instance at Penn State can provide a very robust tool.
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	These rules are in place for the ALPHA phase and are subject to change without notice. Please email Stuart Levine or Charlie Whittaker with comments and suggestions.		These rules are in place for the ALPHA phase and are subject to change without notice. Please email Stuart Levine or Charlie Whittaker with comments and suggestions.

-	~~== 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
-
-	~~===Desktop Software===~~
-	* [http://biomicro-bioanalyzer.mit.edu/ '''Agilent 2100 Expert'''] This software package is used to control the [[BioMicroCenter:2100BioAnalyzer\|Agilent 2100 Bioanalyzer]] and to perform analysis of the output, including microfluidic and electrophoretic assays for RNA, DNA and proteins, as well as two-color flow cytometry. The software can be installed on your desktop to allow users to do additional analyses.
-
-	* [[BioMicroCenter:EVOware\|'''Tecan EvoWare Standard''']] This software is available as part of our robotics service. Identical to the software used on the [[BioMicroCenter:Tecan_Freedom_Evo\|Tecan EVO 150s]], the software contains a simulator that can be used to design your robotics experiments at your bench.

	===Server-Supported Software===		===Server-Supported Software===
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	=== Server Software Installed on ROUS ===		=== Server Software Installed on ROUS ===
-	A large amount of software is installed on our cluster server ~~including~~:	+	A large amount of software is installed on our cluster server. The modules available as of June 2012 include:
		+	-------------------------------------- /home/software/modulefiles ---------------------------------------
		+	bedtools/2.15.0(default) gatk/1.4-30-gf2ef8d1 r/2.15.0
		+	bedtools/2.16.1 hdf5/1.8.8(default) samtools/0.1.18(default)
		+	bowtie/2.0.0b3(default) jre/1.6.0-29(default) snpeff/2.0.5d
		+	bowtie2/2.0.0-beta5 ki-bmc/20120516 snpsnift/1.3.4b
		+	bowtie2/2.0.0-beta6(default) ki-bmc/pipeline_0.9(default) sra/2.1.10
		+	bwa/0.4.6 matlab/2011b(default) tabix/0.2.5(default)
		+	bwa/0.6.1(default) muscle/3.8.31(default) tophat/1.4.1(default)
		+	casava/1.8.2 olb/1.9.0 tophat/2.0.0
		+	cufflinks/1.2.1(default) olb/1.9.4(default) tophat/2.0.3
		+	cufflinks/1.3.0 polysh/0.4(default) ucsc-tools/20120530(default)
		+	cufflinks/2.0.0 python/2.7.2(default) vcftools/0.1.8a
		+	cufflinks/2.0.1 r/2.14.0(default) wx/2.8.12(default)
		+	gatk/1.3-21-gcb284ee r/2.14.2
		+	Other packages, such as BLAST and BLAT are installed but have not yet been converted to module packages.
		+
	* '''BLAST'''		* '''BLAST'''
	* '''BLAT'''		* '''BLAT'''

Stuart S. Levine at 15:21, 20 June 2012

Stuart S. Levine — Wed, 20 Jun 2012 15:21:03 GMT

←Older revision		Revision as of 15:21, 20 June 2012
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	* '''Velvet'''		* '''Velvet'''

-	== BIOINFORMATICS SERVICES ==	+	== [[BioMicroCenter:BioInformaticsStaff\|BIOINFORMATICS SERVICES]] ==
		+	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.]]

-	~~Bioinformatic Services in the BioMicro center~~ are ~~focused primarily on automatic and expanding analyses given~~ to ~~users~~ with ~~their result data~~. ~~Limitted bioinformatics consulting~~ is ~~also available through [[BioMicroCenter:People\|Stuart Levine and Fugen Li]] by appointment~~ for CORE lab members. ~~Bioinformatic projects are undertaken by the BioMicro Center~~ on ~~a '''collaborative''' basis. Expanding~~ the ~~Bioinformatics resources~~ is ~~one of our top priorities~~. ~~[[BioMicroCenter:Pricing\|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.
-		+
-	* [[BioMicroCenter:MicroArrayAnalysis\|Microarray Analysis]]	+
-	* [[BioMicroCenter:IlluminaAnalysis\|General Illumina Analysis]]	+
-	* [[BioMicroCenter:ChIPSeqAnalysis\|ChIP-seq Analysis]]	+

		+	More information about bioinformatics support through the BioMicro Center is available [[BioMicroCenter:BioInformaticsStaff\|HERE''']].

	Additional bioinformatics support is available through		Additional bioinformatics support is available through
	* [http://luria.mit.edu/CCR_BCC/ The Bioinformatics and Computing Core Facility] at the [http://web.mit.edu/ki/index.html Koch Institute for Integrated Cancer Research]		* [http://luria.mit.edu/CCR_BCC/ The Bioinformatics and Computing Core Facility] at the [http://web.mit.edu/ki/index.html Koch Institute for Integrated Cancer Research]
	* [http://jura.wi.mit.edu/bio/ Bioinformatics and Research Computing] at the [http://www.whitehead.mit.edu/ Whitehead Institute]		* [http://jura.wi.mit.edu/bio/ Bioinformatics and Research Computing] at the [http://www.whitehead.mit.edu/ Whitehead Institute]
-
-	~~== OTHER SERIVCES ==~~
-
-	~~===Computing Facilities===~~
-	The BioMicro Center Inforrmation Technology group consists of a full time System Administrator, with subcontracted capabilities in operating and server administration and network implementation. Solutions are tailored to the individual as well as labs needs. System training and documentation is provided and created as needed.
-	* '''Security and Network Administration''' The BioMicro Center facility supports a private subnet for improved security and performance. The BioMicro Center employs a Cisco 2641 firewall separating it from the general MIT network. A Cisco 4006 Chassis based switch provides gigabit interfaces from satellite lab switches as well out NET APP fliers and fiber connection to the NE 47 machines room and Beowulf cluster. A local consulting firm assists with security, monitoring and system hardening procedures. These include installing intrusion detection system as well as centrally monitored system “syslog” server which delivers system status every 24 hours by email. The BioMicro Center leverages MIT’s Win Athena network environment which provided tested security patches and well as security based “group policy settings”. All Linux based servers are connected to MIT’s RHEL Satellite update service.
-	* '''Data Integrity''' Data generated by the BioMicro Center is stored initially on one of two Net App 880 fiber channel based filers, and are snapped mirrored on a remote tier NETAPP filer over a private network. These three file servers are RAID 10 based and are additionally backed up utilizing MIT’s enterprise level TSM service and are archived in Building W91 on the MIT campus. MIT’s TSM service is also utilized to provide backups for the remaining file servers administered by the BioMicro Center.
-
-	~~=== OLD INFO ===~~
-	~~'''Data Storage & Research Network Administration Services'''~~
-	The Department of Biology and Biological Engineering maintain primary network storage of associated labs to facilitate data sharing in the environment surrounding the Biomicro Center. This service is the planned to be phased out due to high support costs.
-
-
-	Research network support is provided by System Administrator [[BioMicroCenter:People\|Stephen]]. Stephen's role is to assist labs by providing network related training, access to the data storage environment, configuring network peripherals, laptops, desktops and independent servers. Information about this storage can be found [[BioMicroCenter:NetworkInformation\|HERE]].

Stuart S. Levine: /* HARDWARE */

Stuart S. Levine — Wed, 20 Jun 2012 15:08:59 GMT

HARDWARE

←Older revision		Revision as of 15:08, 20 June 2012
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	The BioMicro Center Supports a number of storage and computational services for CORE members. 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 Supports a number of storage and computational services for CORE members. 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 ===	+	=== STORAGE: [[BioMicroCenter:BMCPub\|BMC-PUB servers]] ===
	[[ Image:BioMicroCenter_BMCpub1.png \| thumb \| right \| 150px \| BMC-pub server]]		[[ Image:BioMicroCenter_BMCpub1.png \| thumb \| right \| 150px \| BMC-pub server]]
-	* BioMicro Center Public Storage: [[BioMicroCenter:BMCPub\|BMC-PUB servers]]
	The BioMicroCenter Public Server (BMC Pub) is a data storage service offered by the Center. The server is designed to provided low cost server based storage for labs and facilities at MIT accessible easily from Linux, Windows and Macintosh operating systems. Space is available in 1TB increments. The servers use a RAID6 architecture to accommodate drive failures and are backed up routinely by MIT's [http://ist.mit.edu/backup/tsm TSM] service. Currently the BioMicro Center supports 128TB storage within the BMC-Pub system. More details on how to use the BMC-pub1 system are [[BioMicroCenter:BMCPub\|'''found HERE''']]. Pricing for the servers is [[BioMicroCenter:Pricing\|on the pricing page.]] Users who would like data storage on the BMC-pub systems should contact [[BioMicroCenter:People\|Stephen Goldman]].		The BioMicroCenter Public Server (BMC Pub) is a data storage service offered by the Center. The server is designed to provided low cost server based storage for labs and facilities at MIT accessible easily from Linux, Windows and Macintosh operating systems. Space is available in 1TB increments. The servers use a RAID6 architecture to accommodate drive failures and are backed up routinely by MIT's [http://ist.mit.edu/backup/tsm TSM] service. Currently the BioMicro Center supports 128TB storage within the BMC-Pub system. More details on how to use the BMC-pub1 system are [[BioMicroCenter:BMCPub\|'''found HERE''']]. Pricing for the servers is [[BioMicroCenter:Pricing\|on the pricing page.]] Users who would like data storage on the BMC-pub systems should contact [[BioMicroCenter:People\|Stephen Goldman]].

-	* Koch Institute Storage: [http://rous.mit.edu/index.php/BCC_Computing_Resources Isilon ~~server~~]	+	=== STORAGE: [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. This Isilon cluster was purchased in September 2010. The server is named after [http://en.wikipedia.org/wiki/Janet_Rowley Janet Rowley], a pioneer in the field of chromosome translocations in cancer and winner of the 2009 national medal of science and 2009 presidential medal of freedom. The cluster currently consists of seven 36NL nodes and three 108NL nodes with a total capacity of over 500TB and is accessible from any networked computer. Rowley serves as the primary storage device used by the BioMicro Center for [[BioMicroCenter:Sequencing\|Illumina Sequencing]] and data delivery. Users who would like data storage on Rowley should contact [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].		For users with appointments in the [http://ki.mit.edu Koch Institute], storage is also available on the KI's Isilon server, Rowley. This Isilon cluster was purchased in September 2010. The server is named after [http://en.wikipedia.org/wiki/Janet_Rowley Janet Rowley], a pioneer in the field of chromosome translocations in cancer and winner of the 2009 national medal of science and 2009 presidential medal of freedom. The cluster currently consists of seven 36NL nodes and three 108NL nodes with a total capacity of over 500TB and is accessible from any networked computer. Rowley serves as the primary storage device used by the BioMicro Center for [[BioMicroCenter:Sequencing\|Illumina Sequencing]] and data delivery. Users who would like data storage on Rowley should contact [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].

-	=== COMPUTATION ===	+	=== COMPUTATION: [http://rous.mit.edu/index.php/Rous.mit.edu_accounts BMC/BCC Computation Cluster (ROUS)] ===
	[[ Image:BioMicroCenter_ROUSimage.jpg \| thumb \| right \| 150px \| 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>

-	* [http://rous.mit.edu/index.php/Rous.~~mit.edu_accounts BioMicro Center / Koch Institute Computational Cluster (ROUS)]~~	+	Currently, we are reworking the way the queues on Rous work. In addition to a general queue, similar to what is on Rous now, the new system will have lab specific queue where jobs from that lab will have priority on a specific node (or nodes) of the server. Similar to the data storage model, access to these nodes will be on a charge back basis to recover the cost of the instrumentation. We are currently in the testing phase of this project. <BR><BR>
-	~~Rous is~~ a ~~Linux cluster~~, ~~initial purchase in September 2009. It uses x86 architecture with 96 processing cores and 304 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>~~	+
-	<BR>	+
-	<BR>	+

		+	Some additional useful facts about Rous:
		+	* Rous uses Sun Grid Engine (SGE) to manage jobs. <BR>[http://rous.mit.edu/index.php/SGE_Instructions_and_Tips HOW TO SUBMIT JOBS WITH SGE] <BR>
		+	* Rous uses Modules to handle software packages. <BR> [http://rous.mit.edu/index.php/Managment_of_Software_Packages_with_module HOW TO USE MODULES] <BR>
		+	* Currently, users are limited to 24 simultaneous processes on the server.
		+	* Requests for software changes to Rous should be made to [[BioMicroCenter:People\|Stuart Levine]] and [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].

	== GALAXY ==		== GALAXY ==

Stuart S. Levine at 14:30, 20 June 2012

Stuart S. Levine — Wed, 20 Jun 2012 14:30:39 GMT

←Older revision		Revision as of 14:30, 20 June 2012
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	== HARDWARE ==		== HARDWARE ==
-	The BioMicro Center Supports a number of storage and computational services	+	The BioMicro Center Supports a number of storage and computational services for CORE members. 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 ===		=== STORAGE ===
	[[ Image:BioMicroCenter_BMCpub1.png \| thumb \| right \| 150px \| BMC-pub server]]		[[ Image:BioMicroCenter_BMCpub1.png \| thumb \| right \| 150px \| BMC-pub server]]
	* BioMicro Center Public Storage: [[BioMicroCenter:BMCPub\|BMC-PUB servers]]		* BioMicro Center Public Storage: [[BioMicroCenter:BMCPub\|BMC-PUB servers]]
-	The BioMicroCenter Public Server (BMC ~~Pub1~~) is a service offered by the Center. The server is designed to provided low cost server based storage for labs and facilities at MIT accessible from Linux, Windows and Macintosh operating systems. ~~This server~~ is ~~operated~~ on ~~annual fee basis of~~ [[BioMicroCenter:~~Pricing~~\|~~$500/TB/yr~~]]. ~~BMC public~~ servers (BMC-pub~~) are available all CORE labs~~.	+	The BioMicroCenter Public Server (BMC Pub) is a data storage service offered by the Center. The server is designed to provided low cost server based storage for labs and facilities at MIT accessible easily from Linux, Windows and Macintosh operating systems. Space is available in 1TB increments. The servers use a RAID6 architecture to accommodate drive failures and are backed up routinely by MIT's [http://ist.mit.edu/backup/tsm TSM] service. Currently the BioMicro Center supports 128TB storage within the BMC-Pub system. More details on how to use the BMC-pub1 system are [[BioMicroCenter:BMCPub\|'''found HERE''']]. Pricing for the servers is [[BioMicroCenter:Pricing\|on the pricing page.]] Users who would like data storage on the BMC-pub systems should contact [[BioMicroCenter:People\|Stephen Goldman]].

-	* Koch Institute Storage: Isilon server	+	* Koch Institute Storage: [http://rous.mit.edu/index.php/BCC_Computing_Resources Isilon server]
		+	For users with appointments in the [http://ki.mit.edu Koch Institute], storage is also available on the KI's Isilon server, Rowley. This Isilon cluster was purchased in September 2010. The server is named after [http://en.wikipedia.org/wiki/Janet_Rowley Janet Rowley], a pioneer in the field of chromosome translocations in cancer and winner of the 2009 national medal of science and 2009 presidential medal of freedom. The cluster currently consists of seven 36NL nodes and three 108NL nodes with a total capacity of over 500TB and is accessible from any networked computer. Rowley serves as the primary storage device used by the BioMicro Center for [[BioMicroCenter:Sequencing\|Illumina Sequencing]] and data delivery. Users who would like data storage on Rowley should contact [http://rous.mit.edu/index.php/Charlie_Whittaker Charlie Whittaker].

	=== COMPUTATION ===		=== COMPUTATION ===

Stuart S. Levine at 15:51, 21 June 2011

Stuart S. Levine — Tue, 21 Jun 2011 15:51:26 GMT

←Older revision		Revision as of 15:51, 21 June 2011
Line 19:		Line 19:

	* [http://rous.mit.edu/index.php/Rous.mit.edu_accounts BioMicro Center / Koch Institute Computational Cluster (ROUS)]		* [http://rous.mit.edu/index.php/Rous.mit.edu_accounts BioMicro Center / Koch Institute Computational Cluster (ROUS)]
-	Rous is a Linux cluster, initial purchase in September 2009. It uses x86 architecture with 96 processing cores and 304 GB RAM. Rous is the primary server for handling data analysis from Illumina sequencing and for the GALAXY instance at MIT.	+	Rous is a Linux cluster, initial purchase in September 2009. It uses x86 architecture with 96 processing cores and 304 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>
		+	<BR>
		+	<BR>

-	~~== GALAXY ==~~

		+	== GALAXY ==
		+	[[ Image:BioMicroCenter_GalaxyFront.png \| thumb \| right \| 300px \| Front Page of the MIT Galaxy Site ]]
	[http://galaxy.psu.edu/ Galaxy] is an exciting new bioinformatics platform that is designed to bring complicated informatics tools to bench scientists. Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more. For many users, the public Galaxy instance at Penn State can provide a very robust tool.		[http://galaxy.psu.edu/ Galaxy] is an exciting new bioinformatics platform that is designed to bring complicated informatics tools to bench scientists. Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more. For many users, the public Galaxy instance at Penn State can provide a very robust tool.