BioMicroCenter:Computing

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{{BioMicroCenter}}
{{BioMicroCenter}}
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[[Image:BMC10101.png|right]]
[[Image:BMC10101.png|right]]
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The BioMicro Center’s computing mission is to support a core set of bioinformatics applications and also to provide advanced computational, data storage, data security and data backup services.
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The BioMicro Center supports a broad set of computational services for CORE members including hardware, software and informatic support.  
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==Data Storage & Research Network Administration Services==
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The Department of Biology and Biological Engineering maintain primary network storage of (100GB) free of charge for associated labs to facilitate data sharing in the environment surrounding the Biomicro Center.
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Research network support is provided this community by System Administrator Stephen Goldman sgoldman<AT>mit.edu. Stephen role is to assist these labs by providing network related training, access to the data storage environment,configuring network peripherals,laptops, desktops and independent servers.
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Information about this storage can be found [[BioMicroCenter:NetworkInformation|HERE]]. We are currently investigating options for providing larger amounts of data storage for an annual free (See the [[BioMicroCenter:News/2008/December|December Newsletter]]).
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==Computational Services==
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== [[BioMicroCenter:Servers|SERVERS]] ==
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At this time, the BioMicro Center is no longer able to provide servers on which to preform data analysis. This is an area we are looking to reintroduce in the future, depending on funding. Information about our previous services is linked below:
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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.
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* No longer available: [[BioMicroCenter:Computing/Clusters|Computing/Clusters]]
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==BioInformatics Services==
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[[Image:BMC_servers.png|center|600px]]
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Bioinformatics consulting is available with [[BioMicroCenter:People|Stuart Levine]] by appointment only. Bioinformatic projets are undertaken by the BioMicro Center on a collaborative basis. Expanding the Bioinformatics resources is one of our top priorities.
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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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!width=300px| [[BioMicroCenter:BMCPub|bmc-pubN.mit.edu]]
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!width=300px| [http://rous.mit.edu/index.php/BCC_Computing_Resources rowley.mit.edu]
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|- align="center"
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|Linux Cluster
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|High Density Storage <BR> Available to CORE labs
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|Isilon Cluster <BR> Available to KI labs only
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|-
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|
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*SGE queueing system
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*Free account has limited queue
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*Requires purchase of storage
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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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* Available on Mac/PC/UNIX
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* Available any place at MIT or VPN
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* Data available for analysis on ROUS
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* Can create public spaces (web access)
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|-
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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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|}
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Additional bioinformatics support is available through
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== [[BioMicroCenter:Software|SOFTWARE]] ==
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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]
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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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* [http://jura.wi.mit.edu/bio/| Bioinformatics and Research Computing] at the [http://www.whitehead.mit.edu/| Whitehead Institute]
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==Desktop Software==
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== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==
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* '''Spotfire Decision Site with Array Explorer for PC'''  This highly intuitive database mining software can be used for expression profiling with microarrays and also for a wide range of data analysis .In addition to the basic Spotfire package, we have licensed the array explorer module.
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[[Image:BMC_informatics_team.png|thumb|right|400xp|Informatics Team]]
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* '''Affymetrix GeneChip Operating Software, GCOS''' A software package that performs fundamental data analysis for Affymetrix Gene Chips and calculates the fold change (log average ratio), as well as performing to chip comparisons. The program also includes data mining tools including clustering and self organizing maps.
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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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* '''Agilent Feature Extractor''' This software package performs all high throughput analysis of Agilent microarrays up to 244,000 probes per slide. The software automatically locates and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, performs array normalization and calculates statistical confidences.
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* '''Agilent 2100 Expert''' This software package is used to control the 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.
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==Server-Based Software==
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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.
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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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* '''MATLAB''' A mathematical programming language used for mathematical modeling, as well as analyzing and visualizing data.
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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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* '''Genome Analyzer Pipeline (Illumina)''' This software package is a highly customizable workflow engine designed to work with the Illumina Genome analyzer. Softeare in this package is used to convert image data generated by the Genome Analyzer to quality scored base calls as well as rapid alignment of sequences to reference genomes. This software was developed as a result of extensive collaborations with many of the world’s leading sequencing centers.
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==Computing Facilities==
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More information about bioinformatics support through the BioMicro Center is available [[BioMicroCenter:BioInformaticsStaff|HERE''']].
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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.
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* '''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.
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* '''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.
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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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