BioMicroCenter:BIG meeting: Difference between revisions
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{{BioMicroCenter}} | {{BioMicroCenter}} | ||
==2013-2014 academic year== | |||
{| border=1 | |||
!width 150px align="center"|DATE | |||
!width 150px align="center"|TIME | |||
!width 150px align="center"|Presenter | |||
!width 150px align="center"|Location | |||
!width 150px align="center"|Room | |||
!width 150px align="center"|NOTES | |||
|-align="center" | |||
|SEP17 | |||
|noon | |||
|JIE WU (MIT) | |||
|MIT | |||
|68-156 | |||
|Copy Number Variation from single mammalian cells. | |||
|-align="center" | |||
|OCT1 | |||
|noon | |||
| | |||
| | |||
| | |||
| | |||
|-align="center" | |||
|OCT15 | |||
|noon | |||
|BRAD CHAPMAN (HSPH) | |||
| | |||
| | |||
| | |||
|-align="center" | |||
|OCT29 | |||
|noon | |||
|VINCENT BUTTY (MIT) | |||
|MIT | |||
|68-156 | |||
| | |||
|-align="center" | |||
|NOV5 | |||
|noon | |||
|GEORGE BELL (WI) | |||
|WI | |||
|WI-332 | |||
| | |||
|-align="center" | |||
|NOV19 | |||
|noon | |||
| | |||
| | |||
| | |||
| | |||
|-align="center" | |||
|DEC3 | |||
|noon | |||
|CHARLIE WHITTAKER (MIT) | |||
|MIT | |||
|68-156 | |||
| | |||
|-align="center" | |||
|DEC17 | |||
|noon | |||
| | |||
| | |||
| | |||
| | |||
|-align="center" | |||
|JAN7 | |||
|noon | |||
|HD or DM | |||
|MIT | |||
|68-156 | |||
| | |||
|-align="center" | |||
|JAN21 | |||
|noon | |||
|MATTHEW MCCORMACK (MGH) | |||
| | |||
| | |||
| | |||
|-align="center" | |||
|FEB11 | |||
|noon | |||
|PRAT THIRU (WI) | |||
|WI | |||
|WI-332 | |||
| | |||
|-align="center" | |||
|MAR4 | |||
|noon | |||
|STUART LEVINE (MIT) | |||
|MIT | |||
|68-156 | |||
|AGBT Meeting Review | |||
|-align="center" | |||
|MAR18 | |||
|noon | |||
| | |||
| | |||
| | |||
| | |||
|-align="center" | |||
|APR1 | |||
|noon | |||
|INMA BARRASA (WI) | |||
|WI | |||
|WI-332 | |||
| | |||
|-align="center" | |||
|APR15 | |||
|noon | |||
|HD or DM | |||
|MIT | |||
|68-156 | |||
| | |||
|-align="center" | |||
|APR29 | |||
|noon | |||
|BINGBING YUAN (WI) | |||
|WI | |||
|WI-332 | |||
| | |||
|-align="center" | |||
|MAY13 | |||
|noon | |||
|BARRY KESNER (MGH) | |||
| | |||
| | |||
| | |||
|} | |||
==2013-2014 academic year== | ==2013-2014 academic year== | ||
{| border=1 | {| border=1 | ||
Line 13: | Line 142: | ||
| Sept 12 | | Sept 12 | ||
| noon | | noon | ||
| Matthew McCormack | | Matthew McCormack (MolBio) | ||
| MGH | | MGH | ||
| Simches 7.240 | | Simches 7.240 | ||
Line 20: | Line 149: | ||
| Sept 26 | | Sept 26 | ||
| noon | | noon | ||
| Vincent Butty | | Vincent Butty (MIT) | ||
| MIT | | MIT | ||
| 68-156 | | 68-156 | ||
| | | Reference-free sequence variation discovery | ||
|- | |- | ||
| Oct 24 | | Oct 24 | ||
| noon | | noon | ||
| | | Mark Borowski (Novartis) | ||
| MIT | | MIT | ||
| 68-156 | | 68-156 | ||
| | | Life in Pharmaa | ||
|- | |- | ||
| Nov 14 | | Nov 14 | ||
| noon | | noon | ||
| George Marnellos | | George Marnellos (HMS) | ||
| | | MIT | ||
| | | 68-156 | ||
| | | non-reference organism RNA-seq analysis (assembly and differential <BR> expression) using tools like Trinity and edgeR/DESeq | ||
|- | |- | ||
| Dec 5 | | Dec 5 | ||
| noon | | noon | ||
| Charlie Whittaker | | Charlie Whittaker (MIT) | ||
| MIT | | MIT | ||
| 68-156 | | 68-156 | ||
| | | | ||
|- | |- | ||
| Jan 9, 2014 | | Jan 9, 2014 | ||
| noon | | noon | ||
| Jie Wu | | Jie Wu (MIT) | ||
| MIT | | MIT | ||
| 68-156 | | 68-156 | ||
| | | [http://nar.oxfordjournals.org/content/41/10/5149 OLego] and [http://bioinformatics.oxfordjournals.org/content/27/21/3010 SpliceTrap] | ||
|- | |- | ||
| Jan 23 | | Jan 23 | ||
| noon | | noon | ||
| George Bell | | George Bell (WI) | ||
| Whitehead | | Whitehead | ||
| 4th floor Conference Room | |||
| Resource Sharing (code, data, web tools, methods, etc.) <BR> within our group, across Whitehead, and to the public. | |||
|- | |- | ||
| Feb 6 | | Feb 6 | ||
| noon | | noon | ||
| | | Lax Iyer (Tufts) | ||
| MIT | | MIT | ||
| 68-156 | | 68-156 | ||
| | | RNASeq study on Astroglia Development | ||
|- | |- | ||
| Feb 27 | | Feb 27 | ||
| noon | | noon | ||
| Rory Kirchner | | Rory Kirchner | ||
| | | MIT | ||
| | | 68-156 | ||
| bcbio.rnaseq, an automated way to compare different RNA-seq differential expression callers | | bcbio.rnaseq, an automated way to compare different RNA-seq differential expression callers | ||
|- | |- | ||
Line 93: | Line 208: | ||
| MIT | | MIT | ||
| 68-156 | | 68-156 | ||
| | | Transposition and cancer | ||
|- | |- | ||
| Mar 27 | | Mar 27 | ||
Line 118: | Line 233: | ||
| May 15 | | May 15 | ||
| noon | | noon | ||
| | | Duan Ma | ||
| | | MIT | ||
| | | 68-156 | ||
| | | | ||
|- | |- |
Revision as of 07:40, 22 August 2014
HOME -- | SEQUENCING -- | LIBRARY PREP -- | HIGH-THROUGHPUT -- | COMPUTING -- | OTHER TECHNOLOGY |
2013-2014 academic year
DATE | TIME | Presenter | Location | Room | NOTES |
---|---|---|---|---|---|
SEP17 | noon | JIE WU (MIT) | MIT | 68-156 | Copy Number Variation from single mammalian cells. |
OCT1 | noon | ||||
OCT15 | noon | BRAD CHAPMAN (HSPH) | |||
OCT29 | noon | VINCENT BUTTY (MIT) | MIT | 68-156 | |
NOV5 | noon | GEORGE BELL (WI) | WI | WI-332 | |
NOV19 | noon | ||||
DEC3 | noon | CHARLIE WHITTAKER (MIT) | MIT | 68-156 | |
DEC17 | noon | ||||
JAN7 | noon | HD or DM | MIT | 68-156 | |
JAN21 | noon | MATTHEW MCCORMACK (MGH) | |||
FEB11 | noon | PRAT THIRU (WI) | WI | WI-332 | |
MAR4 | noon | STUART LEVINE (MIT) | MIT | 68-156 | AGBT Meeting Review |
MAR18 | noon | ||||
APR1 | noon | INMA BARRASA (WI) | WI | WI-332 | |
APR15 | noon | HD or DM | MIT | 68-156 | |
APR29 | noon | BINGBING YUAN (WI) | WI | WI-332 | |
MAY13 | noon | BARRY KESNER (MGH) |
2013-2014 academic year
DATE | TIME | Presenter | Location | Room | NOTES |
---|---|---|---|---|---|
Sept 12 | noon | Matthew McCormack (MolBio) | MGH | Simches 7.240 | call 617-726-5944 to get upstairs |
Sept 26 | noon | Vincent Butty (MIT) | MIT | 68-156 | Reference-free sequence variation discovery |
Oct 24 | noon | Mark Borowski (Novartis) | MIT | 68-156 | Life in Pharmaa |
Nov 14 | noon | George Marnellos (HMS) | MIT | 68-156 | non-reference organism RNA-seq analysis (assembly and differential expression) using tools like Trinity and edgeR/DESeq |
Dec 5 | noon | Charlie Whittaker (MIT) | MIT | 68-156 | |
Jan 9, 2014 | noon | Jie Wu (MIT) | MIT | 68-156 | OLego and SpliceTrap |
Jan 23 | noon | George Bell (WI) | Whitehead | 4th floor Conference Room | Resource Sharing (code, data, web tools, methods, etc.) within our group, across Whitehead, and to the public. |
Feb 6 | noon | Lax Iyer (Tufts) | MIT | 68-156 | RNASeq study on Astroglia Development |
Feb 27 | noon | Rory Kirchner | MIT | 68-156 | bcbio.rnaseq, an automated way to compare different RNA-seq differential expression callers |
Mar 13 | noon | Huiming Ding | MIT | 68-156 | Transposition and cancer |
Mar 27 | noon | Yanqun Wang | Novartis | ||
Apr 10 | noon | Jingzhi Zhu | MIT | 68-156 | |
May 1 | noon | Penny Wang | MGH | ||
May 15 | noon | Duan Ma | MIT | 68-156 | |
May 29 | noon | OPEN |
2013
DATE | TIME | Presenter | Location | Room | NOTES |
---|---|---|---|---|---|
1/10 (Thursday) | 12p | Vincent Butty | MIT | 68-156 | Proteomics application of Next-Gen sequencing technologies |
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 |