BioMicroCenter:BIG meeting: Difference between revisions

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{{BioMicroCenter}}


Please fill out the [http://www.doodle.com/8aetbhdxx4p68byx survey] to help us schedule the next academic year.
Full Speaker Rotation is '''[[BioMicroCenter:BIG_Rotation||HERE]]'''.
==2013==
{| border=1
! width 100 align="center"|DATE
! width 100 align="center"|TIME
! width 100 align="center"|Presenter
! width 100 align="center"|Location
! width 100 align="center"|Room
! width 100 align="center"|NOTES
|-
| 1/10 (Thursday)
| 12p
| Vincent Butty
| MIT
| 68-156
| TBA
|-
| 2/14
| 12p
| Huiming Ding
| MIT
| 68-156
| Evaluation of Cuffdiff2 for RNA-seq Differential Analysis and CaBlast for Compressive Genomics
|-
| 3/14
| 12p
| Lakshmanan Iyer
| MIT
| 68-156
| Communicating ENCODE data and using it to analyze rare diseases
|-
| 3/28
| 12p
| Stuart Levine / George Bell / Mark Borowski
| MIT
| 68-156
| AGBT & ABRF Meeting Reviews
|-
|}
 
==2012==
{| border=1
! width 100 align="center"|DATE
! width 100 align="center"|TIME
! width 100 align="center"|Presenter
! width 100 align="center"|Location
! width 100 align="center"|Room
! width 100 align="center"|NOTES
|-
| 1/26 (Thursday)
| 12p
| Brian Haas (Broad Institute)
| MIT
| [http://whereis.mit.edu/?go=76 76-558]
| [http://www.ncbi.nlm.nih.gov/pubmed/21572440 Trinity]
|-
| 2/23 (Thursday)
| 12p
| Brad Chapman
| MIT
| [http://whereis.mit.edu/?go=68 68-180]
| Extending the GATK for variant comparisons; [http://chapmanb.github.com/bcbio.variation/presentations/gatk_clojure.pdf slides] [https://github.com/chapmanb/bcbio.variation code]
|-
| 3/22 (Thursday)
| 12p
| Vincent Butty
| MIT
| [http://whereis.mit.edu/?go=68 68-181]
| RNA-Seq quality control and quantitation of alternative RNA processing
|-
| 4/12 (Thursday)
| 12p
| Kip Bodi
| Tufts Medical
|
| Journal Club
|-
| 5/3
| 12p
| Huiming Ding
| MIT
| [http://whereis.mit.edu/?go=68 68-180]
| "High-throughput generation, optimization and analysis of genome-scale metabolic models." by Henry, C. S. et al.
|-
| 5/24
| 12p
| Joshua Ainsley (Tufts) - Hosted by Lakshmanan Iyer
| Tufts
| [http://campusmaps.tufts.edu/boston/?fid=B011 Sackler 851]
| Characterizing dendritic translation with RNA-Seq
|-
| 6/7
| 12p
| Toshi Ohsumi
| MGH
| Sinches 5 - Darwin Room
| MolBioLib: a C++11 Bioinformatics Framework
|-
| 6/21
| 12p
| Juli Klemm (NIH/NCI)
| MIT
| [http://whereis.mit.edu/?go=68 68-156]
| [[BioMicroCenter:BIG_meeting:KlemmTalk|Informatics at NCI]]
|-
| 7/12
| 12p
| Ryan Abo
| MIT
| [http://whereis.mit.edu/?go=68 68-274]
| discovery of active enhancers using GRO-seq data. <BR>
Core, LJ, Waterfall, JJ, Lis, JT (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 5909:1845-8. <BR>
Melgar, MF, Collins, FS, Sethupathy, P (2011). Discovery of active enhancers through bidirectional expression of short transcripts. Genome Biol., 12, 11:R113.
|-
| 7/26
| 12p
| Yanqun Wang
| MGH
| TBA
| TBA
|-
| 9/13
| 12p
| Stuart Levine
| MIT
| [http://whereis.mit.edu/?go=68 68-156]
| Replicates in Informatics: http://genome.cshlp.org/content/22/9/1813.full.pdf+html
|-
| 9/27
| 12p
| Charlie Whittaker
| KI
| [http://whereis.mit.edu/?go=68 68-156]
| Teaching Bioinformatics
|-
| 10/18
| 12p
| Brad Chapman
| MIT
| [http://whereis.mit.edu/?go=68 68-156]
| Biological resources for Amazon: CloudBioLinux, CloudMan, BioCloudCentral [http://www.slideshare.net/chapmanb/big-cloud-2012 slides]
|-
| 11/8
| 12p
| Ruslan Sadreyev
| MGH
| Darwin Room
| Methods for analyzing allelic expression of RNA.
|-
| 11/29
| 12p
| George Bell
| WI
| 4th floor conference room
| TargetScan
|-
| 12/13
| 12p
| Rory Kirchner
| MIT
| 68-156
| iPython and iPython Notebook
|-
|}
 
==2011==
==2011==
Schedule for 2011.  
Schedule for 2011.  
Line 116: Line 280:
  | 68-274
  | 68-274
  | Comparison of ChIP-seq algorithms
  | Comparison of ChIP-seq algorithms
|-
| 10/27 (Thursday)
| 12p
| [http://about.me/pablopareja Pablo Pareja]
| MIT
| [http://whereis.mit.edu/?go=76 76-258]
| [http://www.bio4j.com/ Bio4j Graph based analysis and visualization] [http://www.slideshare.net/pablo_pareja/bio4j slides]
|-
| 11/?? (Thursday)
| 12p
| Paola Favaretto
| MIT
|
| RNAseq - part I
|-
| 12/15
| 12p
| Charlie Whittaker
| MIT
|
| RNAseq - part II
  |-
  |-
|}
|}
<BR>
<BR>

Revision as of 08:09, 18 March 2013

HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

Full Speaker Rotation is |HERE.

2013

DATE TIME Presenter Location Room NOTES
1/10 (Thursday) 12p Vincent Butty MIT 68-156 TBA
2/14 12p Huiming Ding MIT 68-156 Evaluation of Cuffdiff2 for RNA-seq Differential Analysis and CaBlast for Compressive Genomics
3/14 12p Lakshmanan Iyer MIT 68-156 Communicating ENCODE data and using it to analyze rare diseases
3/28 12p Stuart Levine / George Bell / Mark Borowski MIT 68-156 AGBT & ABRF Meeting Reviews

2012

DATE TIME Presenter Location Room NOTES
1/26 (Thursday) 12p Brian Haas (Broad Institute) MIT 76-558 Trinity
2/23 (Thursday) 12p Brad Chapman MIT 68-180 Extending the GATK for variant comparisons; slides code
3/22 (Thursday) 12p Vincent Butty MIT 68-181 RNA-Seq quality control and quantitation of alternative RNA processing
4/12 (Thursday) 12p Kip Bodi Tufts Medical Journal Club
5/3 12p Huiming Ding MIT 68-180 "High-throughput generation, optimization and analysis of genome-scale metabolic models." by Henry, C. S. et al.
5/24 12p Joshua Ainsley (Tufts) - Hosted by Lakshmanan Iyer Tufts Sackler 851 Characterizing dendritic translation with RNA-Seq
6/7 12p Toshi Ohsumi MGH Sinches 5 - Darwin Room MolBioLib: a C++11 Bioinformatics Framework
6/21 12p Juli Klemm (NIH/NCI) MIT 68-156 Informatics at NCI
7/12 12p Ryan Abo MIT 68-274 discovery of active enhancers using GRO-seq data.

Core, LJ, Waterfall, JJ, Lis, JT (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 5909:1845-8.
Melgar, MF, Collins, FS, Sethupathy, P (2011). Discovery of active enhancers through bidirectional expression of short transcripts. Genome Biol., 12, 11:R113.

7/26 12p Yanqun Wang MGH TBA TBA
9/13 12p Stuart Levine MIT 68-156 Replicates in Informatics: http://genome.cshlp.org/content/22/9/1813.full.pdf+html
9/27 12p Charlie Whittaker KI 68-156 Teaching Bioinformatics
10/18 12p Brad Chapman MIT 68-156 Biological resources for Amazon: CloudBioLinux, CloudMan, BioCloudCentral slides
11/8 12p Ruslan Sadreyev MGH Darwin Room Methods for analyzing allelic expression of RNA.
11/29 12p George Bell WI 4th floor conference room TargetScan
12/13 12p Rory Kirchner MIT 68-156 iPython and iPython Notebook

2011

Schedule for 2011.

DATE TIME Presenter Location Room NOTES
1/18 12p Toshiro Ohsumi MGH Simches 5290
2/1 12p Stuart Levine MIT 68-329 Illumina Quality Control Modules
2/15 12p Paola Favaretto MIT 76-358 Matlab
3/8 12p Fugen Li MIT 68-329 Enhancer Analysis
3/22 12p Charlie Whittaker MIT 76-247 Commercial versus public GO tools
4/12 12p Laurent Gautier
Center for Biological Sequence Analysis, Denmark 		MIT 76-259 R-Python Interface
http://www.cbs.dtu.dk/index.shtml
4/26 12p Michael Reich
Broad Institute 		MIT 68-151 GenePattern Enhancements
5/17 12p Mark Borowsky MGH Simches 5 / Darwin Schneeberger et al., 2009 NatureMethods
6/7 12p Brad Chapman MIT 68-151 BioPython
6/28 12p Ruslan Sadreyev MIT 76-659 Teaching Statistics
7/12 12p Kip Bodi MIT 68-121 Data analysis for DSRG / ABRF
7/26 12p Toshiro Ohsumi MGH TBA
8/23 12p Lakshmanan Iyer Tufts Medical RNAseq Analysis
9/15 (Thursday) 12p Brad Chapman MIT 76-558 distributed exome analysis pipeline slides
10/6 (Thursday) 12p Stuart Levine MIT 68-274 Comparison of ChIP-seq algorithms
10/27 (Thursday) 12p Pablo Pareja MIT 76-258 Bio4j Graph based analysis and visualization slides
11/?? (Thursday) 12p Paola Favaretto MIT RNAseq - part I
12/15 12p Charlie Whittaker MIT RNAseq - part II


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