Difference between revisions of "Bioinformatics and Research Computing (BaRC), Whitehead Institute"

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Whitehead Institute for Biomedical Research, Cambridge, MA
 
Whitehead Institute for Biomedical Research, Cambridge, MA
−
     [http://jura.wi.mit.edu/bio Bioinformatics & Research Computing] (BaRC) Department  
+
     [http://barc.wi.mit.edu/ Bioinformatics & Research Computing] (BaRC) Department  
  
 
Name/Title:  
 
Name/Title:  
−
     Fran Lewitter, Ph.D., Director of BaRC, (lastname AT wi.mit.edu)  
+
     George W. Bell, Ph.D., Director of BaRC, (gbell AT wi.mit.edu)  
  
 
Group size:  
 
Group size:  
−
     - total staff is 6
+
     - Total staff is 5:
−
    - 1 Ph.D. director, 1 Ph.D. Senior Bioinformatics Scientist, 2 Bioinformatics Scientists,
+
      - 1 Ph.D. director  
−
      1 M.S. Bioinformatics Analysts, and 1 Senior Graphics specialist.
+
      - 3 Ph.D. Bioinformatics Scientists  
−
     - We have a full IT department that manages our systems and network.  
+
      - 1 M.S. Senior Bioinformatics Analyst
 +
    - We have a team of consultants for
 +
      - scientific illustration
 +
      - high-throughput image analysis
 +
      - biostatistics (for advanced topics)
 +
     - We have a full IT department that manages our hardware, Linux software, storage, and network.  
 +
 
  
 
Environment:  
 
Environment:  
−
     The Whitehead Institute is a private research institute affiliated with MIT. All PIs at  
+
     The Whitehead Institute is a private research institute affiliated with MIT. All faculty at  
−
     Whitehead hold faculty appointments at MIT. There are 18 labs - 16 Faculty and 2
+
     Whitehead are also Biology professors at MIT. There are about 20 labs - 16 faculty and several
−
     Whitehead Fellows - with undergrads, graduate students, postdocs and technicians.  
+
     Whitehead Fellows - with undergraduates, graduate students, postdocs and technicians.  
 
     Labs range in size from 6 to low 40s.  
 
     Labs range in size from 6 to low 40s.  
  
 
Tools:  
 
Tools:  
−
   We support software on Macs, PCs and Unix. For desktop software we currently  
+
   We support software on Mac, Windows and Linux. For desktop software we currently support LaserGene, MacVector, Sequencher, Gene Construction Kit, the Adobe Creative Suite, PyMOL, and web tools like GeneGo and Oncomine Premium.
−
  support LaserGene, MacVector, Sequencher, Gene Construction Kit. Vector NTI,
+
   We have a huge selection of Linux software.
−
  DNAStrider, lots of graphics software. On the Unix side we have EMBOSS,
 
−
   University of Washington Genome Center Software, NCBI-Blast,
 
−
  Matlab, R, BioConductor, Patscan, Primer3, HMMER, clustalX, etc.  
 
  
 
Pertinent hardware info:  
 
Pertinent hardware info:  
Line 29: Line 32:
  
 
Training:  
 
Training:  
−
   - Hands on mini-courses. See [http://jura.wi.mit.edu/bio/education BaRC Education Pages].
+
   - Hands on mini-courses. See [http://barc.wi.mit.edu/education BaRC Education Pages].
−
   - Our "Hot Topics" series is held monthly and includes less than an hour talk about some  
+
   - Our "Hot Topics" series is held monthly and includes an hour talk plus hands-on session
−
      specific tool or topic. 
+
    about some specific computational or bioinformatics topic.   
−
  - REACH (Roundtable Exchange: Advancing Computational Horizons) is a series for more
 
−
      in-depth presentations of computational biology applications and is primarily for scientists
 
−
      engaged in heavily computational projects.   
 
 
   - We also do lots of one-on-one training.  
 
   - We also do lots of one-on-one training.  
  
 
Bioinformatics support model:  
 
Bioinformatics support model:  
−
   basic model is training, education, consultation and collaboration in the areas  
+
   basic model is consultation, collaboration, training and education
−
  of bioinformatics and graphics.  
+
  in the areas of bioinformatics and graphics.  
  
 
Funding model:  
 
Funding model:  
−
   Institutional funds and grants.
+
   Institutional funds.

Latest revision as of 08:18, 16 July 2019

Whitehead Institute for Biomedical Research, Cambridge, MA 

    Bioinformatics & Research Computing (BaRC) Department

Name/Title: 

   George W. Bell, Ph.D., Director of BaRC, (gbell AT wi.mit.edu)

Group size: 

   - Total staff is 5:
     - 1 Ph.D. director 
     - 3 Ph.D. Bioinformatics Scientists 
     - 1 M.S. Senior Bioinformatics Analyst 
   - We have a team of consultants for
     - scientific illustration
     - high-throughput image analysis
     - biostatistics (for advanced topics)
   - We have a full IT department that manages our hardware, Linux software, storage, and network.


Environment: 

   The Whitehead Institute is a private research institute affiliated with MIT. All faculty at 
   Whitehead are also Biology professors at MIT. There are about 20 labs - 16 faculty and several 
   Whitehead Fellows - with undergraduates, graduate students, postdocs and technicians. 
   Labs range in size from 6 to low 40s.

Tools: 

  We support software on Mac, Windows and Linux. For desktop software we currently support LaserGene, MacVector, Sequencher, Gene Construction Kit, the Adobe Creative Suite, PyMOL, and web tools like GeneGo and Oncomine Premium.
  We have a huge selection of Linux software.

Pertinent hardware info: 

  The IT department supports a large cluster of machines and provides ample storage 
  to support the scientific work at the Institute.

Training: 

  - Hands on mini-courses. See BaRC Education Pages.
  - Our "Hot Topics" series is held monthly and includes an hour talk plus hands-on session 
    about some specific computational or bioinformatics topic.  
  - We also do lots of one-on-one training.

Bioinformatics support model: 

  basic model is consultation, collaboration, training and education 
  in the areas of bioinformatics and graphics.

Funding model: 

  Institutional funds.
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