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.


Contents

Data Storage

The BioMicro Center currently provides minimal data storage any lab associated with our core departments (100GB) free of charge on BioNet. Information about this storage can be found HERE. We are currently investigating options for providing larger amounts of data storage for an annual free (See the December Newsletter).

Computational Services

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:

BioInformatics Services

Bioinformatics consulting is available with Stuart Levine by appointment only. Bioinformatic projets are undertaken by the BioMicro Center on a collaborative basis and resources in this are are highly limited. Expanding the Bioinformatics resources is one of our top priorities.


Additional bioinformatics support is available through

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.
  • 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.
  • 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.
  • 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.

Server-Based Software

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

  • MATLAB A mathematical programming language used for mathematical modeling, as well as analyzing and visualizing data.
  • 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.
  • 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.

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.
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