BioMicroCenter:Computing

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{{BioMicroCenter}}
{{BioMicroCenter}}
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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.  
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== [[BioMicroCenter:Servers|HARDWARE]] ==
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== [[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.
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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=== STORAGE ===
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[[Image:BMC_servers.png|center|600px]]
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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>
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'''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.'''
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{| border=1 align="center"
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!width=300px| [http://rous.mit.edu/index.php/Rous.mit.edu_accounts rous.mit.edu]
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=== STORAGE: [[BioMicroCenter:BMCPub|BMC-PUB servers]] ===
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!width=300px| [[BioMicroCenter:BMCPub|bmc-pubN.mit.edu]]
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[[ Image:BioMicroCenter_BMCpub1.png | thumb | right | 150px | BMC-pub server]]
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!width=300px| [http://rous.mit.edu/index.php/BCC_Computing_Resources rowley.mit.edu]
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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]].
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|- align="center"
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|Linux Cluster
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=== STORAGE: [http://rous.mit.edu/index.php/BCC_Computing_Resources Koch Institute Isilon Cluster]===
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|High Density Storage <BR> Available to CORE labs
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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].
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|Isilon Cluster <BR> Available to KI labs only
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|-
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=== COMPUTATION: [http://rous.mit.edu/index.php/Rous.mit.edu_accounts BMC/BCC Computation Cluster (ROUS)] ===
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[[ Image:BioMicroCenter_ROUSimage.jpg | thumb | right | 150px | ROUS ]]
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*SGE queueing system
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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>
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*Free account has limited queue
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*Requires purchase of storage
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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>
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|colspan="2"|
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*[http://ist.mit.edu/backup/tsm TSM backup of all data].
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Some additional useful facts about Rous:
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* Available on Mac/PC/UNIX
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* 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>
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* Available any place at MIT or VPN
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* 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>
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* Data available for analysis on ROUS
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* Currently, users are limited to 24 simultaneous processes on the server.
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* Can create public spaces (web access)
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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].
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|-
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*24 Nodes
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*184 cores
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*688 GB RAM
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*200+TB
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*99% uptime (est)
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*9TB Volumes
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*RAID6 architecture
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*500+TB
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*99.9% uptime (est)
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*No volume limit
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*KI users only
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|}
== [[BioMicroCenter:Software|SOFTWARE]] ==
== [[BioMicroCenter:Software|SOFTWARE]] ==
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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
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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
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===Desktop Software===
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* [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.
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* [[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.
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=== Galaxy ===
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[[ Image:BioMicroCenter_GalaxyFront.png | thumb | right | 300px | Front Page of the MIT Galaxy Site ]]
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[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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To make things even easier, in collaboration with the [http://luria.mit.edu/CCR_BCC/ Bioinformatics and Computing Core Facility] at the [http://web.mit.edu/ki/index.html Koch Institute]we have created a '''[http://bmc-analyze.mit.edu:8080/ GALAXY INSTANCE]''' here at MIT. This version is still in ALPHA but is available for MIT researchers and it works. Feel free to explore and to begin using it. Some rules:
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* '''[http://bmc-analyze.mit.edu:8080/ GALAXY]''' is for MIT researchers ONLY. Anyone else on the server may have their data deleted at any time -- Just don't do it.
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* File paths, etc, are likely to change.
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* '''[http://bmc-analyze.mit.edu:8080/ GALAXY]''' use will eventually require purchase of storage as part of the BMC-PUB or ROWLEY networks.
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* '''[http://bmc-analyze.mit.edu:8080/ GALAXY]''' runs on the same rous nodes as our Illumina sequencers. Jobs may be deleted if they are abusing the resource.
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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.
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===Server-Supported Software===
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* [http://spotfire.tibco.com/ '''Spotfire'''] is a widely used data analysis and visualization tool. It can handle a number of clustering functions and statistical tests and has very robust graphical capabilities. The BioMicro Center operates a Spotfire server that is available to anyone at MIT. Licenses for Spotfire are available through the BioMicro Center on a yearly basis.
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* '''MATLAB''' A mathematical programming language used for mathematical modeling, as well as analyzing and visualizing data.
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* [http://libguides.mit.edu/content.php?pid=14149&sid=171340 '''BioBASE'''] The BIOBASE Knowledge Library (BKL) contains comprehensive sets of protein databases such as HumanPSD, WormPD, GPGR-PD, PombePD,  and MycopathPD in addition to analysis tools such as TRANSFAC, TRANSPATH, and ExPlain. BKL brings together curated data, analysis tools, and gene-centered information. BKL is one of the best ways to quickly assess a vast set of protein properties for a given protein or set of proteins.
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* [http://libguides.mit.edu/content.php?pid=14149&sid=223198 '''GeneGO Metacore'''] GeneGo is a leading provider of data mining & analysis solutions in systems biology. MetaCore, GeneGo's flapship product, is an integrated software suite for functional analysis of experimental data. MetaCore is based on a curated database of human protein-protein, protein-DNA interactions, transcription factors, signaling and metabolic pathways, disease and toxicity, and the effects of bioactive molecules.
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* [http://libguides.mit.edu/content.php?pid=14149&sid=843471 '''INGENUITY PATHWAY ANALYSIS'''] software that helps researchers model, analyze, and understand complex biological and chemical systems relevant to their experimental data. Researchers can search the scientific literature and find insights most relevant to their experimental data; analyze and build pathway models related to thier experimental data;and share and collaborate with colleagues. IPA is currently licensed through June 2012.
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* '''MacVector''' a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions.
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* '''Lasergene v8.0''' A software package that provides sequence assembly including next-generation sequence analysis; simplified primer design, and expanded SNP reporting and management.
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* '''COMSOL Multiphysics''' This software package creates a simulation environment that facilitates all steps in the modeling process.
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The BioMicro Center staff supports four license servers for desktop use. Please contact [[BioMicroCenter:People|Stephen Goldman]] for more information about using these software packages.
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=== Server Software Installed on ROUS ===
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A large amount of software is installed on our cluster server. The modules available as of June 2012 include:
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-------------------------------------- /home/software/modulefiles ---------------------------------------
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bedtools/2.15.0(default)    gatk/1.4-30-gf2ef8d1        r/2.15.0
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bedtools/2.16.1              hdf5/1.8.8(default)          samtools/0.1.18(default)
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bowtie/2.0.0b3(default)      jre/1.6.0-29(default)        snpeff/2.0.5d
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bowtie2/2.0.0-beta5          ki-bmc/20120516              snpsnift/1.3.4b
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bowtie2/2.0.0-beta6(default) ki-bmc/pipeline_0.9(default) sra/2.1.10
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bwa/0.4.6                    matlab/2011b(default)        tabix/0.2.5(default)
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bwa/0.6.1(default)          muscle/3.8.31(default)      tophat/1.4.1(default)
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casava/1.8.2                olb/1.9.0                    tophat/2.0.0
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cufflinks/1.2.1(default)    olb/1.9.4(default)          tophat/2.0.3
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cufflinks/1.3.0              polysh/0.4(default)          ucsc-tools/20120530(default)
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cufflinks/2.0.0              python/2.7.2(default)        vcftools/0.1.8a
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cufflinks/2.0.1              r/2.14.0(default)            wx/2.8.12(default)
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gatk/1.3-21-gcb284ee        r/2.14.2
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Other packagesare installed but have not yet been converted to module packages. These include:
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* BLAST / BLAT
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* GenePattern
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* IGV
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* MACS
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* MAQ
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* MEME
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* Velvet
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== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==
== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==
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[[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''']].
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Additional bioinformatics support is available through
 
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* [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]
 
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* [http://jura.wi.mit.edu/bio/ Bioinformatics and Research Computing] at the [http://www.whitehead.mit.edu/ Whitehead Institute]
 

Current revision

Image:BioMicroCenter-header6.jpg

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
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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