BioMicroCenter:News

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== BioMicro Center News ==
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== Welcome to the MIT BIOMICRO CENTER ==
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=== Nov 9, 2010 ===
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== BioMicro Center News ==
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Dear Users,<BR><BR>
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=== MARCH 11, 2013 ===
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This month, though the generous contributions of Penny Chisholm and Chris Burge, we are pleased to announce the addition of an Illumina HiSeq2000 to our sequencing capacity. We have been testing the HiSeq for a couple months and have been able to obtain over 100,000 usable reads per lane. This service is now available to all CORE lab members. For those labs that do not require a full lane for each sample, we also can provide multiplexing of samples as part of our sample preparation service. More information about the HiSeq and multiplexing can be found on our website.<BR><BR>
+
Quick update from BioMicro: <BR><BR>
 +
The [[BioMicroCenter:Wafergen|Wafergen qPCR system]] is now operational. We have done a couple pilot experiments so far and it does seem to work, if there are a few more limitations than we anticipated. We are working with Wafergen to see how many of these can be alleviated but you are more than welcome to try it out and see if it would be useful to you. They have given us quite competitive pricing that is a lot lower than the cost for the [[BioMicroCenter:Fluidigm|Fluidigm BioMark]] . Please email us if you are interested in training.
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The Technology Seminar Series is also continuing on. The seminar series is designed to showcase a different technology in the facility each week and to bring you up to date on the latest advances and future directions of the technology. The seminar is at noon in 68-180 on Mondays and lunch will be provided.  We have asked the companies we have invited to bring their scientists to speak (not the sales team) so you have a chance to interact with them directly. The current list of speakers can be found [[BioMicroCenter:Technology_Seminar_Series|on our website]]<BR><BR>
 
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Finally, we have been able to negotiate a lower rate for the reagents for Illumina sample preparation. This price reduction went in to effect on Nov 1st and is listed on our website. We are always looking for ways we can reduce the cost of our services without compromising quality.
 
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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>
 
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Thank you all for your support,<BR>
+
=== 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.
 +
 
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-Stuart Levine
 
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=== Sep 12, 2010 ===
 
-
Dear Users,<BR><BR>
 
-
Today marks the beginning of our Technology Seminar Series. This seminar series is designed to showcase a different technology in the facility each week and to bring you up to date on the latest advances and future directions of the technology. This week’s speaker is from Nanostring which makes the nCounter, an imaging system that allows direct visualization of hybridization reactions. The seminar is at noon in 68-180 and lunch will be provided.  We have asked the companies we have invited to bring their scientists to speak (not the sales team) so you have a chance to interact with them directly. Following Nanostring will be Beckman-Coulter Genomics and then NuGEN. The current list of speakers can be found on [[BioMicroCenter:Technology_Seminar_Series|our website]]<BR><BR>
 
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This past month, though the generous contributions of Chris Burge, Ernest Fraenkel and The Koch Institute we were able to add a new robot for Illumina sample preparation. The Beckman-Coulter SPRI-TE handles many of the routine steps in preparing Illumina libraries, including size selection. The SPRI-TE is available either as part of our DNA sample preparation services or as an a la carte service. You can learn more on our website and next week at the seminar.<BR><BR>
 
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Finally, this month we will be saying goodbye to Allison Perrotta who has been a technician in the BioMicro Center for the past two years. Allison was instrumental in setting up our Illumina sequencers and has been involved in setting up our sample preparation service. We are currently conducting a search for her replacement (please send any good candidates our way) but we will miss her very much.<BR><BR>
 
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Thank you all for your support,<BR>
 
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-Stuart Levine
 
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|valign="top"|
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== PREVIOUS NEWSLETTERS ==
+
== ABOUT THE BIOMICRO CENTER ==
 +
The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the [Department of Biology], the [Koch Institute], the [Department of Biological Engineering] and the [Center for Environmental Health Sciences.] The BioMicro Center offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina Genome Analyzer (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms continues to be a significant portion of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the Koch Instistute as the MicroArray Technologies Core and as part of the Bioinformatics and Computing Core and the MIT Center for Environmental Health Sciences as part of the Genomics and Imaging Core<BR><BR>
-
'''[[BioMicroCenter:News2010|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>
 +
== PREVIOUS NEWSLETTERS ==
 +
 +
'''[[BioMicroCenter:News2012|2012]]'''<BR>
 +
'''[[BioMicroCenter:News2011|2011]]'''<BR>
 +
'''[[BioMicroCenter:News2010|2010]]'''
<br>
<br>
 +
== RECENT CHANGES TO THE WEBSITE ==
== RECENT CHANGES TO THE WEBSITE ==
{{BioMicroChanges}}
{{BioMicroChanges}}
|}
|}

Revision as of 17:29, 11 March 2013

Image:BioMicroCenter-header6.jpg

.

Contents

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

MARCH 11, 2013

Quick update from BioMicro:

The Wafergen qPCR system is now operational. We have done a couple pilot experiments so far and it does seem to work, if there are a few more limitations than we anticipated. We are working with Wafergen to see how many of these can be alleviated but you are more than welcome to try it out and see if it would be useful to you. They have given us quite competitive pricing that is a lot lower than the cost for the Fluidigm BioMark . Please email us if you are interested in training.


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.



ABOUT THE BIOMICRO CENTER

The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the [Department of Biology], the [Koch Institute], the [Department of Biological Engineering] and the [Center for Environmental Health Sciences.] The BioMicro Center offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina Genome Analyzer (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms continues to be a significant portion of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the Koch Instistute as the MicroArray Technologies Core and as part of the Bioinformatics and Computing Core and the MIT Center for Environmental Health Sciences as part of the Genomics and Imaging Core

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. . pmid:22981692. PubMed HubMed [Paper1]
  2. Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. . pmid:22847430. PubMed HubMed [Paper2]
  3. Kelly L, Huang KH, Ding H, and Chisholm SW. . pmid:22102570. PubMed 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. . pmid:21892155. PubMed 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. . pmid:20720539. PubMed HubMed [Paper1]
  2. Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. . pmid:20581084. PubMed HubMed [Paper2]
All Medline abstracts: PubMed HubMed

2009

  1. Boselli M, Rock J, Unal E, Levine SS, and Amon A. . pmid:19531355. PubMed HubMed [Paper1]

PREVIOUS NEWSLETTERS

2012
2011
2010

RECENT CHANGES TO THE WEBSITE

17 October 2014

       10:21 BioMicroCenter:BIG meeting (diff; hist) . .  (+95) . . Brad Chapman (Talk | contribs) (2013-2014 academic year: )
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