BioMicroCenter:BIG meeting: Difference between revisions
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{{BioMicroCenter}} | {{BioMicroCenter}} | ||
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== | ||
Line 74: | Line 239: | ||
| BioPython | | BioPython | ||
|- | |- | ||
| 6/ | | 6/28 | ||
| 12p | | 12p | ||
| Ruslan Sadreyev | | 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 | | TBA | ||
| | | | ||
| | |- | ||
| 8/23 | |||
| 12p | |||
| Lakshmanan Iyer | |||
| Tufts Medical | |||
| | |||
| RNAseq Analysis | |||
|- | |||
| 9/15 (Thursday) | |||
| 12p | |||
| Brad Chapman | |||
| MIT | |||
| 76-558 | |||
| [http://bcbio.wordpress.com/2011/08/19/distributed-exome-analysis-pipeline-with-cloudbiolinux-and-cloudman/ distributed exome analysis pipeline] [http://www.slideshare.net/chapmanb/developing-distributed-analysis-pipelines-with-shared-community-resources-using-cloudbiolinux-and-cloudman slides] | |||
|- | |||
| 10/6 (Thursday) | |||
| 12p | |||
| Stuart Levine | |||
| MIT | |||
| 68-274 | |||
| 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. |
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 |