BioMicroCenter:Computing

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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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==[[BioMicroCenter:BMCPub|Biomicro Center Public Storage Server]]==
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== HARDWARE ==
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This new pilot project will offer inexpensive server based storage in one terabyte increments and above to labs and centers. Terabytes are available at $500 per year. This service included MIT's TSM backup as well as network administration services. Detailed information about this service [[BioMicroCenter:BMCPub | can be found '''HERE''']]. Contact [[BioMicroCenter:People|Stuart Levine or Stephen Goldman]] for more details.
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The BioMicro Center Supports a number of storage and computational services
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==Data Storage & Research Network Administration Services==
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=== STORAGE ===
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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.
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* BioMicro Center Public Storage: [[BioMicroCenter:BMCPub|BMC-PUB servers]]
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--Storage available to all CORE labs at [[BioMicroCenter:Prices|$500/TB/yr]]
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* Koch Institute Storage: Isilon server
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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]].
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=== COMPUTATION ===
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* [http://rous.mit.edu/index.php/Rous.mit.edu_accounts BioMicro Center / Koch Institute Computational Cluster (ROUS)]
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==BioInformatics Services==
 
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Bioinformatics consulting is available with [[BioMicroCenter:People|Stuart Levine]] by appointment only. Bioinformatic projects are undertaken by the BioMicro Center on a collaborative basis. Expanding the Bioinformatics resources is one of our top priorities.
 
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== 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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Additional bioinformatics support is available through
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===Desktop 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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* [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==
 
* '''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.
* '''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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* '''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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* '''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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* [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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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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* [[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-Based Software===
 +
 
* '''MATLAB''' A mathematical programming language used for mathematical modeling, as well as analyzing and visualizing data.
* '''MATLAB''' A mathematical programming language used for mathematical modeling, as well as analyzing and visualizing data.
 +
 +
* [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'''] IPA is 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.
 +
* '''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.
* '''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.
 +
* '''Lasergene v8.0''' A software package that provides sequence assembly including next-generation sequence analysis; simplified primer design, and expanded SNP reporting and management.
* '''Lasergene v8.0''' A software package that provides sequence assembly including next-generation sequence analysis; simplified primer design, and expanded SNP reporting and management.
 +
* '''COMSOL Multiphysics''' This software package creates a simulation environment that facilitates all steps in the modeling process.
* '''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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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.
 +
 
 +
== BioInformatics Services ==
 +
 
 +
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. Bioinformatic projects are undertaken by the BioMicro Center on a '''collaborative''' basis. Expanding the Bioinformatics resources is one of our top priorities. [[BioMicroCenter:Prices|Prices for Bioinformatics support are available.]]
 +
 
 +
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://jura.wi.mit.edu/bio/ Bioinformatics and Research Computing] at the [http://www.whitehead.mit.edu/ Whitehead Institute]
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== 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.  
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.  
* '''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.
* '''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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==Computational Services==
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=== OLD INFO ===
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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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'''Data Storage & Research Network Administration Services'''
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* No longer available: [[BioMicroCenter:Computing/Clusters|Computing/Clusters]]
+
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]].

Revision as of 15:23, 11 November 2010

Image:BioMicroCenter-header6.jpg


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

Contents

HARDWARE

The BioMicro Center Supports a number of storage and computational services

STORAGE

--Storage available to all CORE labs at $500/TB/yr

  • Koch Institute Storage: Isilon server

COMPUTATION


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

Desktop Software

  • 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.
  • 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. The software can be installed on your desktop to allow users to do additional analyses.
  • Tecan EvoWare Standard This software is available as part of our robotics service. Identical to the software used on the Tecan EVO 150s, the software contains a simulator that can be used to design your robotics experiments at your bench.

Server-Based Software

  • MATLAB A mathematical programming language used for mathematical modeling, as well as analyzing and visualizing data.
  • 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.
  • 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.
  • INGENUITY PATHWAY ANALYSIS IPA is 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.
  • 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.
  • Lasergene v8.0 A software package that provides sequence assembly including next-generation sequence analysis; simplified primer design, and expanded SNP reporting and management.
  • COMSOL Multiphysics This software package creates a simulation environment that facilitates all steps in the modeling process.

The BioMicro Center staff supports four license servers for desktop use. Please contact Stephen Goldman for more information about using these software packages.

BioInformatics Services

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 Stuart Levine and Fugen Li by appointment. Bioinformatic projects are undertaken by the BioMicro Center on a collaborative basis. Expanding the Bioinformatics resources is one of our top priorities. Prices for Bioinformatics support are available.

Additional bioinformatics support is available through

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 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 HERE.

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