BioMicroCenter:News: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
 
(85 intermediate revisions by 7 users not shown)
Line 1: Line 1:
{{BioMicroCenter}}
{{BioMicroCenter}}


.
== Welcome to the MIT BIOMICRO CENTER ==
{|
|valign=top style="width:60%;padding-right:10px;"|
== BioMicro Center News ==
== BioMicro Center News ==
{|
|rowspan=2 valign=top style="width:60%;padding-right:10px;"|
=== May 24, 2011 ===




Dear users,


We have a number of updates to let you all know about that have happened in the last few months.
|valign="top"|
 
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]].
 
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.
== ABOUT THE BIOMICRO CENTER ==


Thank you all for your support,
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 [http://biology.mit.edu Department of Biology], the [http://ki.mit.edu Koch Institute for Integrative Cancer Research], the [http://be.mit.edu Department of Biological Engineering] and the [http://cehs.mit.edu MIT Center for Environmental Health Sciences.] The BioMicro Center provides MIT faculty members with integrated facilities for high-throughput data-intensive genomics, bioinformatic analysis, as well as large-scale database storage, management, data mining and data modeling required to fully implement systems approaches to investigate a broad spectrum of biological problems.  The BioMicro Center is designed to maximize the likelihood of successfully designing, implementing, and analyzing systems biology data. With an expert staff available for consultation and collaboration, including several full time bioinformatics scientists and experimentalist with significant experience in systems biology, ample resources exist to assist MIT researchers in any aspect of the research project. This unique cross-disciplinary collaboration leverages resources, spreading institutional commitment, and providing an environment that strongly encourages intellectual rapport between scientists that contributes to the success of projects. This collaborative environment creates a unique opportunity for interactions of biologists and biological engineers who study a broad range of problems.  Investigators are able to adopt novel techniques to address their topics of interest as well as develop new collaborations throughout the institute. <BR><BR>


-Stuart Levine
Experimental and analytical work done in the BioMicro Center is funded by the NIH and must be made available through the NIH's open access policy. All Koch Institute and CEHS labs '''must''' acknowledge their core grants for work done in the core with the following language.
* KI ''"This work was funded by the National Cancer Institute of the NIH under award P30-CA14051"''
* [[BioMicroCenter:CEHS13|CEHS]] ''"This work was funded by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109"''


=== Jan 2011 ===
== PUBLICATIONS ==
Dear Users,<BR><BR>
I hope everyone had a great holiday. We have a couple updates as we begin the year.<BR><BR>
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>
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>
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>
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>
Thank you all for your support,<BR><BR>
-Stuart Levine<BR><BR>


 
Publications from [https://www.ncbi.nlm.nih.gov/sites/myncbi/stuart.levine.1/bibliography/47165401/public/?sortby=pubDate&sdirection=descending Stuart Levine]
 
 
|valign="top"|


== PREVIOUS NEWSLETTERS ==
== PREVIOUS NEWSLETTERS ==
 
'''[[BioMicroCenter:News2017+|2017+]]'''<BR>
 
'''[[BioMicroCenter:News2016|2016]]'''<BR>
'''[[BioMicroCenter:News2015|2015]]'''<BR>
'''[[BioMicroCenter:News2014|2014]]'''<BR>
'''[[BioMicroCenter:News2013|2013]]'''<BR>
'''[[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}}


|}
|}

Latest revision as of 05:26, 28 March 2023

HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

.

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

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 for Integrative Cancer Research, the Department of Biological Engineering and the MIT Center for Environmental Health Sciences. The BioMicro Center provides MIT faculty members with integrated facilities for high-throughput data-intensive genomics, bioinformatic analysis, as well as large-scale database storage, management, data mining and data modeling required to fully implement systems approaches to investigate a broad spectrum of biological problems. The BioMicro Center is designed to maximize the likelihood of successfully designing, implementing, and analyzing systems biology data. With an expert staff available for consultation and collaboration, including several full time bioinformatics scientists and experimentalist with significant experience in systems biology, ample resources exist to assist MIT researchers in any aspect of the research project. This unique cross-disciplinary collaboration leverages resources, spreading institutional commitment, and providing an environment that strongly encourages intellectual rapport between scientists that contributes to the success of projects. This collaborative environment creates a unique opportunity for interactions of biologists and biological engineers who study a broad range of problems. Investigators are able to adopt novel techniques to address their topics of interest as well as develop new collaborations throughout the institute.

Experimental and analytical work done in the BioMicro Center is funded by the NIH and must be made available through the NIH's open access policy. All Koch Institute and CEHS labs must acknowledge their core grants for work done in the core with the following language.

  • KI "This work was funded by the National Cancer Institute of the NIH under award P30-CA14051"
  • CEHS "This work was funded by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109"

PUBLICATIONS

Publications from Stuart Levine

PREVIOUS NEWSLETTERS

2017+
2016
2015
2014
2013
2012
2011
2010

RECENT CHANGES TO THE WEBSITE

List of abbreviations:
N
This edit created a new page (also see list of new pages)
m
This is a minor edit
b
This edit was performed by a bot
(±123)
The page size changed by this number of bytes

25 April 2024

     23:55  Flow and Pattern Asymmetries‎‎ 50 changes history −656 [Courtneychau‎ (50×)]
     
23:55 (cur | prev) −14 Courtneychau talk contribs (→‎Mixing on the Microfluidic Scale)
     
23:55 (cur | prev) −43 Courtneychau talk contribs (→‎Reynolds Number (Re))
     
23:55 (cur | prev) −46 Courtneychau talk contribs (→‎Péclet Number (Pe))
     
23:55 (cur | prev) −31 Courtneychau talk contribs (→‎Stokes Flow)
     
23:54 (cur | prev) −151 Courtneychau talk contribs (→‎Stokes Flow)
     
23:50 (cur | prev) +184 Courtneychau talk contribs (→‎References)
     
23:46 (cur | prev) 0 Courtneychau talk contribs (→‎Active Mixing Methods)
     
23:46 (cur | prev) +1 Courtneychau talk contribs (→‎Passive Mixing Methods)
     
23:45 (cur | prev) 0 Courtneychau talk contribs (→‎Chaotic Advection)
     
23:44 (cur | prev) 0 Courtneychau talk contribs (→‎Mixing on the Microfluidic Scale)
     
23:43 (cur | prev) +28 Courtneychau talk contribs (→‎Stokes Flow)
     
23:39 (cur | prev) +1 Courtneychau talk contribs (→‎Stokes Flow) Tag: Manual revert
     
23:38 (cur | prev) −1 Courtneychau talk contribs (→‎Stokes Flow)
     
23:37 (cur | prev) +11 Courtneychau talk contribs
     
23:36 (cur | prev) +15 Courtneychau talk contribs
     
23:33 (cur | prev) 0 Courtneychau talk contribs (→‎References)
     
23:30 (cur | prev) +3 Courtneychau talk contribs (→‎Passive Mixing Methods)
     
23:28 (cur | prev) −426 Courtneychau talk contribs
     
23:16 (cur | prev) +1,656 Courtneychau talk contribs (→‎References)
     
23:14 (cur | prev) 0 Courtneychau talk contribs (→‎Applications of Asymmetric Flow)
     
23:13 (cur | prev) 0 Courtneychau talk contribs (→‎Active Mixing Methods)
     
23:12 (cur | prev) −1 Courtneychau talk contribs (→‎Passive Mixing Methods)
     
23:11 (cur | prev) 0 Courtneychau talk contribs (→‎Microfluidic Mixers)
     
23:10 (cur | prev) 0 Courtneychau talk contribs (→‎Chaotic Advection)
     
23:08 (cur | prev) 0 Courtneychau talk contribs (→‎Mixing on the Microfluidic Scale)
     
23:06 (cur | prev) +6 Courtneychau talk contribs (→‎References)
     
23:04 (cur | prev) −179 Courtneychau talk contribs (→‎Applications of Asymmetric Flow)
     
23:03 (cur | prev) +16 Courtneychau talk contribs (→‎Pneumatic Valves and Mixers)
     
23:02 (cur | prev) +16 Courtneychau talk contribs (→‎Active Mixing Methods)
     
23:02 (cur | prev) −334 Courtneychau talk contribs (→‎Active Mixing Methods)
     
22:56 (cur | prev) −415 Courtneychau talk contribs (→‎Passive Mixing Methods)
     
22:52 (cur | prev) −115 Courtneychau talk contribs (→‎Herringbone Mixer)
     
22:52 (cur | prev) −457 Courtneychau talk contribs (→‎Passive Mixing Methods)
     
22:38 (cur | prev) 0 Courtneychau talk contribs (→‎Microfluidic Mixers)
     
22:35 (cur | prev) −315 Courtneychau talk contribs (→‎Mixing on the Microfluidic Scale)
     
22:14 (cur | prev) 0 Courtneychau talk contribs (→‎Stokes Flow)
     
22:12 (cur | prev) 0 Courtneychau talk contribs (→‎Péclet Number (Pe))
     
22:11 (cur | prev) +6 Courtneychau talk contribs (→‎Reynolds Number (Re))
     
22:10 (cur | prev) +2 Courtneychau talk contribs (→‎Diffusion and Advection)
     
22:07 (cur | prev) +2 Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
22:05 (cur | prev) +2 Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
22:04 (cur | prev) +4 Courtneychau talk contribs (→‎Fundamentals of Mixing)
     
22:02 (cur | prev) +471 Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
21:52 (cur | prev) +78 Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
21:50 (cur | prev) +6 Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
21:44 (cur | prev) −1 Courtneychau talk contribs (→‎Twists and Bends)
     
21:39 (cur | prev) 0 Courtneychau talk contribs (→‎Stokes Flow)
     
21:38 (cur | prev) +450 Courtneychau talk contribs
     
20:54 (cur | prev) −1,079 Courtneychau talk contribs
     
20:38 (cur | prev) −6 Courtneychau talk contribs (→‎Herringbone Mixer)