BioMicroCenter:Computing

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===Desktop Software===
===Desktop Software===
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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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* [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.
* [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.

Revision as of 21:29, 23 May 2011

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

  • 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-Supported Software

  • 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.
  • 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.

Server Software Installed on ROUS

A large amount of software is installed on our cluster server including:

  • BLAST
  • BLAT
  • Bowtie
  • GenePattern
  • Genome Analysis Tool Kit
  • IGV
  • Illumina Pipeline/CASAVA
  • MACS
  • MAQ
  • MEME
  • R
  • SAMTOOLS
  • Tophat
  • Velvet

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 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. 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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