BioMicroCenter:Computing

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== HARDWARE ==
== HARDWARE ==
-
The BioMicro Center Supports a number of storage and computational services for CORE members. 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.
 +
 
 +
=== STORAGE ===
 +
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>
 +
 
 +
'''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.'''
=== STORAGE: [[BioMicroCenter:BMCPub|BMC-PUB servers]] ===
=== STORAGE: [[BioMicroCenter:BMCPub|BMC-PUB servers]] ===
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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].
* 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].
-
== GALAXY ==
+
== SOFTWARE ==
 +
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
 +
 
 +
===Desktop Software===
 +
* [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.
 +
 
 +
* [[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.
 +
 
 +
=== Galaxy ===
[[ Image:BioMicroCenter_GalaxyFront.png | thumb | right | 300px | Front Page of the MIT Galaxy Site ]]
[[ Image:BioMicroCenter_GalaxyFront.png | thumb | right | 300px | Front Page of the MIT Galaxy Site ]]
[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.  
[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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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.
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.
-
== SOFTWARE ==
 
-
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
 
-
 
-
===Desktop Software===
 
-
* [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.
 
-
 
-
* [[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-Supported Software===
===Server-Supported Software===
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=== Server Software Installed on ROUS ===
=== Server Software Installed on ROUS ===
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A large amount of software is installed on our cluster server including:
+
A large amount of software is installed on our cluster server. The modules available as of June 2012 include:
-
* '''BLAST'''
+
-------------------------------------- /home/software/modulefiles ---------------------------------------
-
* '''BLAT'''
+
bedtools/2.15.0(default)    gatk/1.4-30-gf2ef8d1        r/2.15.0
-
* '''Bowtie'''
+
bedtools/2.16.1              hdf5/1.8.8(default)          samtools/0.1.18(default)
-
* '''GenePattern'''
+
bowtie/2.0.0b3(default)      jre/1.6.0-29(default)        snpeff/2.0.5d
-
* '''Genome Analysis Tool Kit'''
+
bowtie2/2.0.0-beta5          ki-bmc/20120516              snpsnift/1.3.4b
-
* '''IGV'''
+
bowtie2/2.0.0-beta6(default) ki-bmc/pipeline_0.9(default) sra/2.1.10
-
* '''Illumina Pipeline/CASAVA'''
+
bwa/0.4.6                    matlab/2011b(default)        tabix/0.2.5(default)
-
* '''MACS'''
+
bwa/0.6.1(default)          muscle/3.8.31(default)      tophat/1.4.1(default)
-
* '''MAQ'''
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casava/1.8.2                olb/1.9.0                    tophat/2.0.0
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* '''MEME'''
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cufflinks/1.2.1(default)    olb/1.9.4(default)          tophat/2.0.3
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* '''R'''
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cufflinks/1.3.0              polysh/0.4(default)          ucsc-tools/20120530(default)
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* '''SAMTOOLS'''
+
cufflinks/2.0.0              python/2.7.2(default)        vcftools/0.1.8a
-
* '''Tophat'''
+
cufflinks/2.0.1              r/2.14.0(default)            wx/2.8.12(default)
-
* '''Velvet'''
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gatk/1.3-21-gcb284ee        r/2.14.2
 +
Other packagesare installed but have not yet been converted to module packages. These include:
 +
 
 +
* BLAST / BLAT
 +
* GenePattern
 +
* IGV
 +
* MACS
 +
* MAQ
 +
* MEME
 +
* Velvet
== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==
== [[BioMicroCenter:BioInformaticsStaff|BIOINFORMATICS SERVICES]] ==

Revision as of 21:46, 21 June 2012

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 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.

STORAGE

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 TSM service.

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.

STORAGE: BMC-PUB servers

BMC-pub server
BMC-pub server

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 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 found HERE. Pricing for the servers is on the pricing page. Users who would like data storage on the BMC-pub systems should contact Stephen Goldman.

STORAGE: Koch Institute Isilon Cluster

For users with appointments in the 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 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 Illumina Sequencing and data delivery. Users who would like data storage on Rowley should contact Charlie Whittaker.

COMPUTATION: BMC/BCC Computation Cluster (ROUS)

ROUS
ROUS

Rous is a Linux cluster, initially purchase in September 2009. Rous, named after the Nobel prize winning cancer researcher Peyton Rous (and not 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.

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.

Some additional useful facts about Rous:

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.

Galaxy

Front Page of the MIT Galaxy Site
Front Page of the MIT Galaxy Site

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.

To make things even easier, in collaboration with the Bioinformatics and Computing Core Facility at the Koch Institutewe have created a 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:

  • GALAXY is for MIT researchers ONLY. Anyone else on the server may have their data deleted at any time -- Just don't do it.
  • File paths, etc, are likely to change.
  • GALAXY use will eventually require purchase of storage as part of the BMC-PUB or ROWLEY networks.
  • GALAXY runs on the same rous nodes as our Illumina sequencers. Jobs may be deleted if they are abusing the resource.

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.


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 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.
  • 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. The modules available as of June 2012 include:

-------------------------------------- /home/software/modulefiles ---------------------------------------
bedtools/2.15.0(default)     gatk/1.4-30-gf2ef8d1         r/2.15.0
bedtools/2.16.1              hdf5/1.8.8(default)          samtools/0.1.18(default)
bowtie/2.0.0b3(default)      jre/1.6.0-29(default)        snpeff/2.0.5d
bowtie2/2.0.0-beta5          ki-bmc/20120516              snpsnift/1.3.4b
bowtie2/2.0.0-beta6(default) ki-bmc/pipeline_0.9(default) sra/2.1.10
bwa/0.4.6                    matlab/2011b(default)        tabix/0.2.5(default)
bwa/0.6.1(default)           muscle/3.8.31(default)       tophat/1.4.1(default)
casava/1.8.2                 olb/1.9.0                    tophat/2.0.0
cufflinks/1.2.1(default)     olb/1.9.4(default)           tophat/2.0.3
cufflinks/1.3.0              polysh/0.4(default)          ucsc-tools/20120530(default)
cufflinks/2.0.0              python/2.7.2(default)        vcftools/0.1.8a
cufflinks/2.0.1              r/2.14.0(default)            wx/2.8.12(default)
gatk/1.3-21-gcb284ee         r/2.14.2

Other packagesare installed but have not yet been converted to module packages. These include:

  • BLAST / BLAT
  • GenePattern
  • IGV
  • MACS
  • MAQ
  • MEME
  • Velvet

BIOINFORMATICS SERVICES

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.

Additional bioinformatics support is available through

Personal tools