BioMicroCenter:BIG meeting: Difference between revisions
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{{BioMicroCenter}} | {{BioMicroCenter}} | ||
== | ==2016-2017 academic year== | ||
Meetings will be at MIT Biology (room TBA) or at Whitehead (for Whitehead presenters; 7th floor larger classroom). A session leader is welcome to present a project, a published work (like a journal club), share notes from a conference, or present anything else of interest to our group of applied bioinformatics scientists. The format can be a presentation and/or a discussion. Questions? Contact Barry Kesner or George Bell. | |||
{| border=1 | {| border=1 | ||
!width 150px align="center"| | !width 150px align="center"|Date | ||
!width 150px align="center"| | !width 150px align="center"|Time | ||
!width 150px align="center"|Presenter | !width 150px align="center"|Presenter | ||
!width 150px align="center"|Location | !width 150px align="center"|Location | ||
!width 150px align="center"|Room | !width 150px align="center"|Room | ||
!width 150px align="center"| | !width 150px align="center"|Notes | ||
|-align="center" | |||
|Oct 6 | |||
|11 am | |||
| | |||
| | |||
| | |||
| | |||
|-align="center" | |||
|Oct 20 | |||
|11 am | |||
|Prat Thiru (WI) | |||
|Whitehead | |||
|7th floor | |||
| | |||
|-align="center" | |||
|Nov 3 | |||
|11 am | |||
|Brad Chapman (HSPH) | |||
|MIT | |||
| | |||
| | |||
|-align="center" | |||
|Nov 17 | |||
|11 am | |||
|Matthew McCormack (Harvard) | |||
|MIT | |||
| | |||
| | |||
|-align="center" | |-align="center" | ||
| | |Dec 1 | ||
| | |11 am | ||
|( | |George Bell (WI) | ||
| | |Whitehead | ||
| | |7th floor | ||
| | | | ||
|-align="center" | |-align="center" | ||
| | |Dec 15 | ||
| | |11 am | ||
|Lorena Pantano (HSPH) | |||
|MIT | |||
| | |||
| | | | ||
|-align="center" | |||
|Jan 5 | |||
|11 am | |||
|Inma Barrasa (WI) | |||
|Whitehead | |||
|7th floor | |||
| | |||
|-align="center" | |||
|Jan 19 | |||
|11 am | |||
|Charlie Whittaker (MIT) | |||
|MIT | |||
| | |||
| | | | ||
|-align="center" | |||
|Feb 2 | |||
|11 am | |||
|Jie Wu (MIT) | |||
|MIT | |||
| | |||
| | | | ||
|-align="center" | |||
|Feb 16 | |||
|11 am | |||
|Matt Shirley (NIBR) | |||
|MIT | |||
| | |||
| | |||
|-align="center" | |||
|Mar 2 | |||
|11 am | |||
|Stuart Levine (MIT) | |||
|MIT | |||
|68-156 (probably) | |||
|Review of AGBT | |||
|-align="center" | |||
|Mar 16 | |||
|11 am | |||
|Bingbing Yuan (WI) | |||
|Whitehead | |||
|7th floor | |||
| | | | ||
|-align="center" | |-align="center" | ||
| | |Apr 6 | ||
| | |11 am | ||
|Huiming Ding (MIT) | |||
|MIT | |||
| | | | ||
| | | | ||
|-align="center" | |||
|Apr 20 | |||
|11 am | |||
|Duanduan Ma (MIT) | |||
|MIT | |||
| | |||
| | |||
|-align="center" | |||
|May 4 | |||
|11 am | |||
| | | | ||
| | | | ||
| | |||
| | |||
|-align="center" | |||
|May 18 | |||
|11 am | |||
|Yanmei Huang (WI) | |||
|Whitehead | |||
|7th floor | |||
| | |||
|} | |||
==2015-2016 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" | |-align="center" | ||
|OCT22 | |OCT22 | ||
|11a | |11a | ||
|(MIT) | |VINCENT BUTTY (MIT) | ||
|MIT | |MIT | ||
|68-156 | |68-156 | ||
| | |Dimensionality reduction for single cell data | ||
|-align="center" | |-align="center" | ||
|NOV5 | |NOV5 | ||
|11a | |11a | ||
|BRAD CHAPMAN (HSPH) | |BRAD CHAPMAN (HSPH) | ||
| | |MIT | ||
| | |[http://whereis.mit.edu/?go=68 68-156] | ||
| | |[https://github.com/chapmanb/bcbio-nextgen bcbio development work] supporting [http://bcb.io/2015/09/17/hg38-validation/ human build 38], [https://github.com/bcbio/bcbio.github.io/blob/master/_posts/2015-10-05-vardict-filtering.md low frequency variant calling] and support for Docker and the Common Workflow Language: [https://github.com/chapmanb/bcbb/blob/master/talks/big2015_bcbio/big2015_bcbio.pdf validation slides], [https://github.com/chapmanb/bcbb/blob/master/talks/bioindocker2015_bcbio/chapman_bioindocker.pdf Docker/CWL slides] | ||
|-align="center" | |-align="center" | ||
|NOV19 | |NOV19 | ||
|11a | |11a | ||
| | |Jie Wu (MIT) | ||
| | |MIT | ||
| | |68-156 | ||
| | |Finding methods for reliable detection of megabase-scale CNV in single cell sequencing data. | ||
|-align="center" | |-align="center" | ||
|DEC3 | |DEC3 | ||
|11a | |11a | ||
|( | |Lorena Pantano (HSPH) | ||
| | | | ||
| | | | ||
| | | | ||
|-align="center" | |-align="center" | ||
Line 62: | Line 164: | ||
|Inma Barrasa (WI) | |Inma Barrasa (WI) | ||
|WI | |WI | ||
| | |7th floor classroom | ||
| | | | ||
|-align="center" | |-align="center" | ||
|JAN7 | |JAN7 | ||
|11a | |11a | ||
|(MIT) | |Duanduan Ma (MIT) | ||
|MIT | |MIT | ||
|68-156 | |68-156 | ||
| | |An easy and convenient TCGA gold miner for biologists | ||
|-align="center" | |-align="center" | ||
|JAN21 | |JAN21 | ||
Line 76: | Line 178: | ||
|George Bell (WI) | |George Bell (WI) | ||
|WI | |WI | ||
| | |7th floor classroom | ||
| | |Genome and gene representations: Options for expression analysis | ||
|-align="center" | |-align="center" | ||
|FEB4 | |FEB4 | ||
|11a | |11a | ||
| | |George Marnellos (Harvard) | ||
| | | | ||
| | | | ||
Line 97: | Line 199: | ||
|Prat Thiru (WI) | |Prat Thiru (WI) | ||
|WI | |WI | ||
| | |7th floor classroom | ||
| | | | ||
|-align="center" | |-align="center" | ||
|MAR24 | |MAR24 | ||
|11a | |11a | ||
|Matt McCormack (MGH) | |||
| | | | ||
| | | | ||
| | | | ||
|-align="center" | |-align="center" | ||
| | |APR14 | ||
|11a | |11a | ||
|Huiming Ding(MIT) | |Huiming Ding (MIT) | ||
|MIT | |MIT | ||
|68-156 | |68-156 | ||
Line 116: | Line 218: | ||
|APR28 | |APR28 | ||
|11a | |11a | ||
| | |Laurent Gautier (Novartis) | ||
| | | | ||
| | | | ||
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|MAY12 | |MAY12 | ||
|11a | |11a | ||
| | |BARRY KESNER (MGH) | ||
| | | | ||
| | | | ||
Line 132: | Line 234: | ||
|Yanmei Huang (WI) | |Yanmei Huang (WI) | ||
|WI | |WI | ||
| | |7th floor classroom | ||
| | | | ||
|} | |} | ||
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|68-156 | |68-156 | ||
|Copy Number Variation from single mammalian cells. | |Copy Number Variation from single mammalian cells. | ||
|-align="center" | |-align="center" | ||
|OCT15 | |OCT15 |
Revision as of 11:05, 29 September 2016
HOME -- | SEQUENCING -- | LIBRARY PREP -- | HIGH-THROUGHPUT -- | COMPUTING -- | OTHER TECHNOLOGY |
2016-2017 academic year
Meetings will be at MIT Biology (room TBA) or at Whitehead (for Whitehead presenters; 7th floor larger classroom). A session leader is welcome to present a project, a published work (like a journal club), share notes from a conference, or present anything else of interest to our group of applied bioinformatics scientists. The format can be a presentation and/or a discussion. Questions? Contact Barry Kesner or George Bell.
Date | Time | Presenter | Location | Room | Notes |
---|---|---|---|---|---|
Oct 6 | 11 am | ||||
Oct 20 | 11 am | Prat Thiru (WI) | Whitehead | 7th floor | |
Nov 3 | 11 am | Brad Chapman (HSPH) | MIT | ||
Nov 17 | 11 am | Matthew McCormack (Harvard) | MIT | ||
Dec 1 | 11 am | George Bell (WI) | Whitehead | 7th floor | |
Dec 15 | 11 am | Lorena Pantano (HSPH) | MIT | ||
Jan 5 | 11 am | Inma Barrasa (WI) | Whitehead | 7th floor | |
Jan 19 | 11 am | Charlie Whittaker (MIT) | MIT | ||
Feb 2 | 11 am | Jie Wu (MIT) | MIT | ||
Feb 16 | 11 am | Matt Shirley (NIBR) | MIT | ||
Mar 2 | 11 am | Stuart Levine (MIT) | MIT | 68-156 (probably) | Review of AGBT |
Mar 16 | 11 am | Bingbing Yuan (WI) | Whitehead | 7th floor | |
Apr 6 | 11 am | Huiming Ding (MIT) | MIT | ||
Apr 20 | 11 am | Duanduan Ma (MIT) | MIT | ||
May 4 | 11 am | ||||
May 18 | 11 am | Yanmei Huang (WI) | Whitehead | 7th floor |
2015-2016 academic year
DATE | TIME | Presenter | Location | Room | NOTES |
---|---|---|---|---|---|
OCT22 | 11a | VINCENT BUTTY (MIT) | MIT | 68-156 | Dimensionality reduction for single cell data |
NOV5 | 11a | BRAD CHAPMAN (HSPH) | MIT | 68-156 | bcbio development work supporting human build 38, low frequency variant calling and support for Docker and the Common Workflow Language: validation slides, Docker/CWL slides |
NOV19 | 11a | Jie Wu (MIT) | MIT | 68-156 | Finding methods for reliable detection of megabase-scale CNV in single cell sequencing data. |
DEC3 | 11a | Lorena Pantano (HSPH) | |||
DEC17 | 11a | Inma Barrasa (WI) | WI | 7th floor classroom | |
JAN7 | 11a | Duanduan Ma (MIT) | MIT | 68-156 | An easy and convenient TCGA gold miner for biologists |
JAN21 | 11a | George Bell (WI) | WI | 7th floor classroom | Genome and gene representations: Options for expression analysis |
FEB4 | 11a | George Marnellos (Harvard) | |||
Feb 25 | 11a | STUART LEVINE (MIT) | MIT | 68-156 | AGBT/ABRF Meeting Review |
MAR10 | 11a | Prat Thiru (WI) | WI | 7th floor classroom | |
MAR24 | 11a | Matt McCormack (MGH) | |||
APR14 | 11a | Huiming Ding (MIT) | MIT | 68-156 | |
APR28 | 11a | Laurent Gautier (Novartis) | |||
MAY12 | 11a | BARRY KESNER (MGH) | |||
MAY26 | 11a | Yanmei Huang (WI) | WI | 7th floor classroom |
2014-2015 academic year
DATE | TIME | Presenter | Location | Room | NOTES |
---|---|---|---|---|---|
SEP17 | noon | JIE WU (MIT) | MIT | 68-156 | Copy Number Variation from single mammalian cells. |
OCT15 | noon | BRAD CHAPMAN (HSPH) | MIT | 68-156 | Validation with bcbio-nextgen on structural variation, joint calling and cancer tumor/normal. slides |
OCT29 | noon | VINCENT BUTTY (MIT) | MIT | 68-156 | Single-molecule barcoding: applications and analytic challenges |
NOV5 | noon | GEORGE BELL (WI) | WI | WI-332 | Happy yeast and fast fish |
NOV19 | noon | RUSLAN SADREYEV (MGH) | |||
DEC3 | noon | CHARLIE WHITTAKER (MIT) | MIT | 68-156 | |
DEC17 | noon | GEORGIOS MARNELLOS (HMS) | |||
JAN7 | noon | 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 | YANQUN WANG (MGH) | |||
APR1 | noon | INMA BARRASA (WI) | WI | WI-332 | |
APR15 | noon | HUIMING DING | 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 |