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=== May 24, 2011 ===
 
  
 +
== JANUARY 9, 2013 ==
 +
Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of. <BR><BR>
 +
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>
 +
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>
 +
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.
  
Dear users,
 
  
We have a number of updates to let you all know about that have happened in the last few months.
 
  
First, we have continued to expand our [[BioMicroCenter:Illumina Library Preparation|DNA sample preparation services]]  . Over the past few months, we have been experimenting with the Nextera sample prep kit to complement our SPRIworks service. Where the SPRIworks system uses sonicated DNA, the Nextera kit is built to handle intact genomic DNA, using a transposase to fragment the DNA and is particularly suitable for applications that use entire genomic DNA, including copy number variation and de novo and resequencing projects. In addition, we have taken advantage of recent work from the Broad to improve our library representation by modifying our amplification protocol. The Nextera service is now available through BioMicro for the same price as the SPRIworks system and includes molecular [[BioMicroCenter:Multiplex|barcoding]] of the library. For more information about the Nextera system, please email  [[BioMicroCenter:People|Ryan Sinapius]].
 
  
In the [[BioMicroCenter:Microarrays|microarray]] area, we have made significant improvements to our Agilent microarray service. First, we have upgraded our scanner to 2um resolution, which will allow scanning of Agilent’s newest 1 million feature arrays. This has been coupled with an upgrade of the scanning and analysis software that can now handle additional quality controls. In addition, we have been working with Agilent to bring down the prices of their microarrays and we will be able to offer them at a significant discount beginning in July that will bring the [[BioMicroCenter:Pricing|price]] of microarray analysis down significantly. For more information about changes in the Agilent platform, please talk with [[BioMicroCenter:People|Manlin Luo]].
+
|valign="top"|
 
 
Finally, in response to user demand we have purchased a number of licenses for TIBCO Spotfire Analytics. Spotfire is a widely used data analysis and visualization tool. It can handle a number of clustering functions and statistical tests and has very robust graphical capabilities. If you are interested in trying out Spotfire, please contact [[BioMicroCenter:People|Stephen Goldman]].
 
 
 
As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.
 
  
Thank you all for your support,
+
== PUBLICATIONS ==
 
+
'''2013'''<BR><BR>
-Stuart Levine
+
'''2012'''<BR><BR>
 
+
<biblio>
=== Jan 2011 ===
+
#Paper1 pmid=22981692 <!-SL Boyer: Heart->
Dear Users,<BR><BR>
+
#Paper2 pmid=22847430 <!-SL Saeij->
I hope everyone had a great holiday. We have a couple updates as we begin the year.<BR><BR>
+
#Paper3 pmid=22102570 <!-HD Chisholm->
One of our goals for this year is to reduce our turnaround time as much as we can. We’ve taken a couple steps in this direction (though we have a long way to go!). First, we have brought a number of additional technicians on board. Michael Gravina joins us from Alnylam and will be working on the Illumina platform. Barbara Karampalas is joining us part time to work on automation. In addition we added two new coop students, Katie Sullivan and Justin Elliott, who will be taking Eris’ place as he returns to Northeastern, and we are looking to make an additional hire in the bioinformatics area (in collaboration with the Koch Institute Bioinformatics and Computing Core). Make sure you say hello the next time you stop by.<BR><BR>
+
</biblio>
In addition to new staff, we have also upgraded some of our equipment. This week we are adding a new Caliper LabChip system. The LabChip is a high throughput version of the Agilent BioAnalyzer (which uses Caliper technology) and can process hundreds of samples in a batch. Our on-site testing with the LabChip had a significant effect on the speed at which we were able to handle quality control. In order to automate the process, we will have to increase the minimum volume of sample we accept (to 5ul). For most applications, simply diluting your samples 2 fold prior to submission will be sufficient. We will be using the LabChip to handle high sensitivity DNA and standard RNA samples while small RNA, pico RNA and protein samples will continue to be run on the BioAnalyzer.  Prices for the LabChip and the BioAnalyzer will be the same but we will be able to offer discounts on large sample submissions that are run on the Caliper. <BR><BR>
+
'''2011'''<BR><BR>
Finally, we are in the finishing stages of beta testing our new RNA-seq sample prep service.  An addition to our existing DNA sample prep, we will be able to accept submissions of total RNA for sequencing just as we do for microarrays. Our current protocol is derived from Chris Burge’s lab but we are also testing kits from NuGEN for digital gene expression (DGE) which we hope will offer microarray quality results for considerably lower costs. If you are interested in helping out and have samples you are willing to contribute, please contact Ryan Sinapius who is coordinating the effort. <BR><BR>
+
<biblio>
As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.<BR><BR>
+
#Paper1 pmid=21892155 <!-SL Sur->
Thank you all for your support,<BR><BR>
+
</biblio>
-Stuart Levine<BR><BR>
+
'''2010'''<BR><BR>
 
+
<biblio>
 
+
#Paper1 pmid=20720539 <!-SL Young->
 
+
#Paper2 pmid=20581084 <!-SL Zwaka->
 
+
</biblio>
|valign="top"|
+
'''2009'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=19531355 <!-SL Amon->
 +
</biblio>
  
 
== PREVIOUS NEWSLETTERS ==
 
== PREVIOUS NEWSLETTERS ==
  
 
+
'''[[BioMicroCenter:News2012|2012]]'''<BR>
 +
'''[[BioMicroCenter:News2011|2011]]'''<BR>
 
'''[[BioMicroCenter:News2010|2010]]'''
 
'''[[BioMicroCenter:News2010|2010]]'''
 +
<br>
  
<br>
 
 
== RECENT CHANGES TO THE WEBSITE ==
 
== RECENT CHANGES TO THE WEBSITE ==
 
{{BioMicroChanges}}
 
{{BioMicroChanges}}
  
 
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Revision as of 20:16, 11 January 2013

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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
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