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== BioMicro Center News ==
 
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=== May 13, 2010 ===
+
== JANUARY 9, 2013 ==
In order to increase the space available for equipment in the BioMicro Center, we are doing a little more remodeling. Please note the following changes:
+
Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of. <BR><BR>
* The freezers have been relocated to the 304 hallway
+
First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.  <BR><BR>
* The RT-PCR machines will be moving to the 316 entry.
+
During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.  <BR><BR>
We hope this change will make accessing the [[BioMicroCenter:RTPCR|RT-PCR]] machines easier and will also create room for the [[BioMicroCenter:Tecan_Freedom_Evo|new Tecan EVO 150]], scheduled to arrive in early June. Keep an eye on this page for future updates!
+
Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting  how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week.
 +
If you have any concerns, please do not hesitate to contact me.
  
=== April 19, 2010 ===
 
  
Starting next month, the [http://mit.edu/ki/index.html Koch Institute] and the MIT BioMicro Center will be hosting a [http://www.nanostring.com/ Nanostring] nCounter system on a trial basis. The [http://www.nanostring.com/products/ncounter/ nCounter system] is a [http://www.nanostring.com/applications/technology/ single molecule visualizer] that quantitatively detects RNA and other nucleic acids using a hybridization system in a highly multiplex manner. The system uses color-coded molecular barcodes to digitally count nucleic acid molecules in solution. The system does not use enzymes for detecting the nucleic acids, allowing direct measurements of mRNA from a variety of input materials including degraded RNA or crude cell lysates.
 
  
The instruments will be located in the BioMicro Center and will be available to all members of the MIT community. We will be using this time to gauge the level of interest in the nCounter and whether it would be a viable system to purchase.
 
  
If you are interested in learning more, we will be hosting a seminar with [http://www.nanostring.com/ Nanostring] representatives on April 30th. The seminar will be at 11am in 68-181. Nanostring representatives will be available after the talk to discuss the instruments and specific applications. More information is in the [[Media:Nanostring_abstract.pdf‎|ABSTRACT]] for the talk.
+
|valign="top"|
  
=== April 1, 2010 ===
+
== PUBLICATIONS ==
 +
'''2013'''<BR><BR>
 +
'''2012'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=22981692 <!-SL Boyer: Heart->
 +
#Paper2 pmid=22847430 <!-SL Saeij->
 +
#Paper3 pmid=22102570 <!-HD Chisholm->
 +
</biblio>
 +
'''2011'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=21892155 <!-SL Sur->
 +
</biblio>
 +
'''2010'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=20720539 <!-SL Young->
 +
#Paper2 pmid=20581084 <!-SL Zwaka->
 +
</biblio>
 +
'''2009'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=19531355 <!-SL Amon->
 +
</biblio>
  
Thanks to the generosity of a grant from the [http://www.moore.org/ Moore Foundation] to Dr. Penny Chisholm and ARRA funding to Dr. Chris Burge the BioMicro Center will be significantly expanding our sequencing capacity over the next 4-6 months. The first step of this expansion begins today with the addition of a new [http://www.illumina.com/systems/genome_analyzer_iix.ilmn GAIIx] and [http://www.illumina.com/systems/genome_analyzer/cbot.ilmn cBot] from Illumina. We are working hard to get ''"Ryland"'' and ''"Agustus Gloop"'' up and running and we hope to be able to shorten our queue times very soon!
+
== PREVIOUS NEWSLETTERS ==
  
=== March 2010 ===
+
'''[[BioMicroCenter:News2012|2012]]'''<BR>
Due to an increase in the cost of Illumina reagents, increase in data file size, and the complexity of sample preps, we have had to increase, slightly, the cost of Illumina sequencing. These new rates will be effective on samples submitted after April 1, 2010. Samples already in the queue will use the current rates.
+
'''[[BioMicroCenter:News2011|2011]]'''<BR>
 
+
'''[[BioMicroCenter:News2010|2010]]'''
{| border=1 align="right"
+
<br>
! ILLUMINA SEQUENCING
 
!width=100| MIT - current
 
!width=100| MIT - April 1, 2010
 
!width=100| unit
 
! Notes
 
|-
 
| Single End (36nt)
 
|align="right"| $805
 
|align="right"| $860
 
|align="center"| per lane
 
| inlcudes quality control (RT-PCR or BioAnalyzer), sequencing, genome alignment and data storage of Firecrest files for 2 yrs.
 
|-
 
| Paired End (36+36nt)
 
|align="right"| $1,385
 
|align="right"| $1,450
 
|align="center"| per lane
 
|
 
|-
 
| Add'l 36nt
 
|align="right"| $295
 
|align="right"| $300
 
|align="center"| per lane
 
 
|-
 
| Sample Multiplexing
 
|align="right"| $0
 
|align="right"| $50
 
|align="center"| per 10 samples combined
 
| Combined over the whole order. Only applies to samples combined by BCM technicians.
 
|-
 
| Repriming
 
|align="right"| $200
 
|align="right"| $300
 
|align="center"| per flow cell
 
| Uses 6nt. Cost is divided by number of lanes requiring repriming. Repriming is required for standard Illumina multiplexing.
 
|-
 
|}
 
<BR>
 
Non-MIT rates are 30% higher for academic institutions and 50% highers for non-academic institutions. Priority is given to samples from CORE facilities.
 
 
 
 
 
|-
 
|valign="top" width="45%"|
 
 
 
===RECENT & UPCOMING CHANGES===
 
 
 
{{BioMicroCenter:News/Changes/Content}}
 
 
 
 
 
<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
 
 
 
{|
 
|'''[[BioMicroCenter:News/2009|2009]]'''
 
|-
 
|{{BioMicroCenter:News/2009/Content}}
 
|-
 
|'''[[BioMicroCenter:News/2008|2008]]'''
 
|-
 
|{{BioMicroCenter:News/2008/Content}}
 
|}
 
  
<br>
+
== RECENT CHANGES TO THE WEBSITE ==
<B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
 
 
{{BioMicroChanges}}
 
{{BioMicroChanges}}
  
 
|}
 
|}

Revision as of 20:16, 11 January 2013

BioMicroCenter-header6.jpg

BIOMICRO GENOMICS HIGH-THROUGHPUT COMPUTING TOOLS QUICK LINKS

BioMicro Center News

JANUARY 9, 2013

Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of.

First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.

During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.

Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week. If you have any concerns, please do not hesitate to contact me.



PUBLICATIONS

2013

2012

  1. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, and Bruneau BG. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28;151(1):206-20. DOI:10.1016/j.cell.2012.07.035 | PubMed ID:22981692 | HubMed [Paper1]
  2. Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity. Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13458-63. DOI:10.1073/pnas.1117047109 | PubMed ID:22847430 | HubMed [Paper2]
  3. Kelly L, Huang KH, Ding H, and Chisholm SW. ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40. DOI:10.1093/nar/gkr1022 | PubMed ID:22102570 | HubMed [Paper3]
All Medline abstracts: PubMed | HubMed

2011

  1. Mellios N, Sugihara H, Castro J, Banerjee A, Le C, Kumar A, Crawford B, Strathmann J, Tropea D, Levine SS, Edbauer D, and Sur M. miR-132, an experience-dependent microRNA, is essential for visual cortex plasticity. Nat Neurosci. 2011 Sep 4;14(10):1240-2. DOI:10.1038/nn.2909 | PubMed ID:21892155 | HubMed [Paper1]

2010

  1. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, and Young RA. Mediator and cohesin connect gene expression and chromatin architecture. Nature. 2010 Sep 23;467(7314):430-5. DOI:10.1038/nature09380 | PubMed ID:20720539 | HubMed [Paper1]
  2. Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev. 2010 Jul 15;24(14):1479-84. DOI:10.1101/gad.1935210 | PubMed ID:20581084 | HubMed [Paper2]
All Medline abstracts: PubMed | HubMed

2009

  1. Boselli M, Rock J, Unal E, Levine SS, and Amon A. Effects of age on meiosis in budding yeast. Dev Cell. 2009 Jun;16(6):844-55. DOI:10.1016/j.devcel.2009.05.013 | PubMed ID:19531355 | HubMed [Paper1]

PREVIOUS NEWSLETTERS

2012
2011
2010

RECENT CHANGES TO THE WEBSITE

19 October 2017

     04:10 

BioMicroCenter:BioinfoClasses‎‎ (3 changes | history) . . (+132). . [Charlie Whittaker‎ (3×)]

     

04:10

(cur | prev) . . (+9). . Charlie Whittaker (talk | contribs) (Teaching Schedule)

     

04:09

(cur | prev) . . (0). . Charlie Whittaker (talk | contribs) (Teaching Schedule)

     

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     03:36  User:Timothee Flutre‎ (diff | hist) . . (+146). . Timothee Flutre (talk | contribs) (add contrib breedR and SO)

 m   02:27 

How to write a research paper‎‎ (2 changes | history) . . (+91). . [Formand‎ (2×)]

 m   

02:27

(cur | prev) . . (-1). . Formand (talk | contribs) (External links)

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18 October 2017

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BME100 f2017:Group8 W1030 L4‎‎ (2 changes | history) . . (+426). . [Jennifer L. Brodsky‎; Jacob Tomas Harrison Haye‎]

     

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     15:20  BME100 f2017:Group7 W0800 L4‎ (diff | hist) . . (-4). . Miguel R. Almanza Lopez (talk | contribs) (OUR TEAM)

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(Upload log). .

[Miguel R. Almanza Lopez‎; Kaifu Chen‎ (2×); Jacob Tomas Harrison Haye‎ (4×); Alivia Ankrum‎ (8×)]

     

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     14:40 

BME100 f2017:Group1 W1030 L4‎‎ (14 changes | history) . . (+1,316). . [Emily A. Hanzlick‎ (7×); Abby E. Krell‎ (7×)]

     

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