Difference between revisions of "BioMicroCenter:News"

From OpenWetWare
Jump to: navigation, search
(RECENT & UPCOMING CHANGES)
(PUBLICATIONS)
(41 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 
{{BioMicroCenter}}
 
{{BioMicroCenter}}
  
 
+
== BioMicro Center News ==
 
{|
 
{|
|rowspan=2 style="width:55%;padding-right:10px"|
+
|rowspan=2 valign=top style="width:60%;padding-right:10px;"|  
===JANUARY/FEBRUARY NEWSLETTER===
 
  
January/February 2009 - HIGHLIGHTS
+
== JANUARY 9, 2013 ==
* New BioMicro Website at http://web.mit.edu/biomicro
+
Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of. <BR><BR>
* New plate reader available for use in 68-252d.
+
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>
* Tecan EVO robotic training Feb 14th
+
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>
* BioMicro Center Renovation in February
+
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.
  
It has been a very busy month in the BioMicro Center and we have a number of improvements to share with everyone. First, this month we have activated our new website (http://web.mit.edu/biomicro). This page has information about all of the resources available at the BioMicro Center as well as forms for download, calendars to schedule time on our machines and prices. The website is also set up as a wiki on the OpenWetWare platform to create a repository for information to help optimize experiments and to help shape the site to make it more useful to you. We are continuing to improve the site so check back often. You can [[Join|sign up for a wiki account.]]
 
  
This month we also introduced the Varioskan plate reader. This plate reader can handle plates from 6 to 384 wells and can do fluorometrics, lumisetrics and photometrics at most wavelengths between 200 and 1000nm (there is some variability depending on the application). The Varioskan is also capable of doing real time kinetic experiments and has the ability to add up to three reagents to the plate. The Varioskan is currently located in 68-252d. More information, including data validation and a calendar to schedule time on the Varioskan can be found on [[BioMicroCenter:Varioskan|our website]].
 
  
We are also proceeding apace with our activation of the Tecan EVO robotic liquid handler. The EVO is able to automate most routine molecular biology protocols for high-throughput. We have scheduled a training session for the EVO on February 14th with the staff from Tecan. If you are interested in learning about the EVO or the types of reactions that can be run on the machine, or in attending the training session, please contact me.
 
  
Lastly, we are beginning the process of remodeling the BioMicro Center lab space to create more room. We are planning on doing this stepwise so as to have as minimal an impact on our services as possible, though access to portions of the lab may be restricted at times. The final layout is also [[BioMicroCenter:RenoPlans|on our website]] along with all of our monthly updates.
+
|valign="top"|
  
-Stuart Levine
+
== 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>
|valign="top" width="45%"|
+
'''[[BioMicroCenter:News2011|2011]]'''<BR>
 +
'''[[BioMicroCenter:News2010|2010]]'''
 +
<br>
  
===RECENT & UPCOMING CHANGES===
+
== RECENT CHANGES TO THE WEBSITE ==
 
 
{{BioMicroCenter:News/Changes/Content}}
 
 
 
 
 
<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
 
 
 
{|
 
|-
 
|'''[[BioMicroCenter:News/2008|2008]]'''
 
|-
 
|{{BioMicroCenter:News/2008/Content}}
 
<!-- Remove Comments when Jan 2009 Newsletter is ready
 
|-
 
|'''[[BioMicroCenter:News/2009|2009]]'''
 
|-
 
|{{BioMicroCenter:News/2009/Content}}
 
Remove Comments when Jan 2009 Newsletter is ready -->
 
|}
 
 
 
<br>
 
<B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
 
 
{{BioMicroChanges}}
 
{{BioMicroChanges}}
  
 
|}
 
|}

Revision as of 20:16, 11 January 2013

BioMicroCenter-header6.jpg

<html> <style type="text/css">

  1. menuh-container{

position: absolute; top: 1em; left: 1em; }

  1. menuh{

font-family: arial, helvetica, sans-serif; width:100%; float:left; margin:2em; margin-top: 1em; }

  1. menuh top_parent{

/* border-style: none; */ }

  1. menuh a{

text-align: center; display:block; white-space:nowrap; margin:0; padding: 0.3em; }

  1. menuh a:link, #menuh a:visited, #menuh a:active{ /* menu at rest */

color: black; background-color: white; text-decoration:none; }

  1. menuh a:hover{ /* menu at mouse-over */

color: black; background-color: #f0f0d1; text-decoration:none; }

  1. menuh a.top_parent, #menuh a.top_parent:hover{ /* attaches down-arrow to all top-parents */

font-size: 10pt; background-image: url(navdown_white.gif); background-position: right center; background-repeat: no-repeat; }

  1. menuh a.parent, #menuh a.parent:hover{ /* attaches side-arrow to all parents */

font-size: 10pt; background-image: url(nav_white.gif); background-position: right center; background-repeat: no-repeat; }

  1. menuh ul{

font-size: 8pt; font-family: arial, helvetica, sans-serif; list-style:none; margin:0; padding:0; float:left; width:13em; /* width of all menu boxes */ }

  1. menuh li{

position:relative; min-height: 1px; /* Sophie Dennis contribution for IE7 vertical-align: bottom; /* Sophie Dennis contribution for IE7 */ }

  1. menuh ul ul{

position:absolute; z-index:500; top:auto; display:none; padding: 1em; margin:-1em 0 0 -1em; }

  1. menuh ul ul ul{

top:0; left:100%; } div#menuh li:hover{ cursor:pointer; z-index:100; } div#menuh li:hover ul ul, div#menuh li li:hover ul ul, div#menuh li li li:hover ul ul, div#menuh li li li li:hover ul ul {display:none;}

div#menuh li:hover ul, div#menuh li li:hover ul, div#menuh li li li:hover ul, div#menuh li li li li:hover ul {display:block;}

/* End CSS Drop Down Menu */ </style> <style type="text/css" media="screen">

  1. menuh-container{

font-size: 1em; position: relative; top:0; left: 5%; width: 90%; margin: 0px; border: 1px solid white; } </style>

</html>

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

25 September 2017

     16:32 

PrivateWikis‎‎ (2 changes | history) . . (-8). . [Yardena Cohen‎ (2×)]

     

16:32

(cur | prev) . . (+3). . Yardena Cohen (talk | contribs) (23)

     

16:31

(cur | prev) . . (-11). . Yardena Cohen (talk | contribs) (new contact page)

     16:32 

New server‎‎ (5 changes | history) . . (+718). . [Yardena Cohen‎ (5×)]

     

16:32

(cur | prev) . . (+26). . Yardena Cohen (talk | contribs) (private wikis link)

     

16:23

(cur | prev) . . (+157). . Yardena Cohen (talk | contribs) (check spam folder)

     

14:35

(cur | prev) . . (-17). . Yardena Cohen (talk | contribs) (idk when searches will work)

     

14:34

(cur | prev) . . (+267). . Yardena Cohen (talk | contribs) (rearrange, more info on passwords & emails)

     

14:27

(cur | prev) . . (+285). . Yardena Cohen (talk | contribs) (confirm emails)

     14:28  Main Page‎ (diff | hist) . . (+75). . Yardena Cohen (talk | contribs) (confirm email)

     14:09 

(User creation log). .

[Yardena Cohen‎ (2×)]

     

14:09

. . User account Abhilash (talk | contribs) was created by Yardena Cohen (talk | contribs) and password was sent by email ‎

     

14:09

. . User account Jrajbhandary (talk | contribs) was created by Yardena Cohen (talk | contribs) and password was sent by email ‎

     12:14 

(Upload log). .

[Trevor S. Heaton‎; Anshul Krishnan‎ (2×); Vinh T. Le‎ (3×)]

     

12:14

. . Vinh T. Le (talk | contribs) uploaded File:ZOLA9252017 3.PNG

     

12:14

. . Vinh T. Le (talk | contribs) uploaded File:ZOLA9252017 2.PNG

     

12:13

. . Vinh T. Le (talk | contribs) uploaded File:ZOLA9252017 1.PNG

     

09:18

. . Trevor S. Heaton (talk | contribs) uploaded a new version of File:Graph 1.PNG

     

06:18

. . Anshul Krishnan (talk | contribs) uploaded File:BME100TempVTrials.png

     

06:10

. . Anshul Krishnan (talk | contribs) uploaded File:BME100L3Temp.png

24 September 2017

N    22:33  MediaWiki:Tagline‎ (diff | hist) . . (+16). . Yardena Cohen (talk | contribs) (less parsing)
N    22:32  MediaWiki:Pagetitle-view-mainpage‎ (diff | hist) . . (+11). . Yardena Cohen (talk | contribs) (less parsing)
N    22:32  MediaWiki:Opensearch-desc‎ (diff | hist) . . (+16). . Yardena Cohen (talk | contribs) (english-only?)
N    21:21  MediaWiki:Pagetitle‎ (diff | hist) . . (+16). . Yardena Cohen (talk | contribs) (idk if this will help or hurt)
N    21:18  MediaWiki:Aboutsite‎ (diff | hist) . . (+17). . Yardena Cohen (talk | contribs) (one less thing to parse)

     20:08 

(Upload log). .

[Anna Hoge‎ (2×)]

     

20:08

. . Anna Hoge (talk | contribs) uploaded File:AHgraph4.png

     

18:52

. . Anna Hoge (talk | contribs) uploaded File:AHgraph3.png

23 September 2017

     17:17  MediaWiki:Contactpage-pagetext‎ (diff | hist) . . (+36). . Yardena Cohen (talk | contribs) (don't ask me science questions plz)

     17:05 

(Deletion log). .

[Yardena Cohen‎ (6×)]

     

17:05

. . Yardena Cohen (talk | contribs) deleted page User talk:Deepak P Patil(Automatically deleted when merging users)

     

17:05

. . Yardena Cohen (talk | contribs) deleted page User:Deepak P Patil(Automatically deleted when merging users)

     

16:39

. . Yardena Cohen (talk | contribs) deleted page User talk:Chun H Hsieh(Automatically deleted when merging users)

     

16:39

. . Yardena Cohen (talk | contribs) deleted page User:Chun H Hsieh(Automatically deleted when merging users)

     

15:39

. . Yardena Cohen (talk | contribs) deleted page User talk:Satu Strandman(Automatically deleted when merging users)

     

15:39

. . Yardena Cohen (talk | contribs) deleted page User:Satu Strandman(Automatically deleted when merging users)

     17:05 

(User merge log). .

[Yardena Cohen‎ (6×)]

     

17:05

. . Yardena Cohen (talk | contribs) Deleted user: Deepak P Patil (8544) ‎

     

17:05

. . Yardena Cohen (talk | contribs) User Deepak P Patil (8544) merged to Anonymous (0) ‎

     

16:39

. . Yardena Cohen (talk | contribs) Deleted user: Chun H Hsieh (13046) ‎

     

16:39

. . Yardena Cohen (talk | contribs) User Chun H Hsieh (13046) merged to Anonymous (0) ‎

     

15:39

. . Yardena Cohen (talk | contribs) Deleted user: Satu Strandman (13640) ‎

     

15:39

. . Yardena Cohen (talk | contribs) User Satu Strandman (13640) merged to Anonymous (0) ‎

N    14:04 

MediaWiki:Contactpage-label‎‎ (2 changes | history) . . (+7). . [Yardena Cohen‎ (2×)]

     

14:04

(cur | prev) . . (-4). . Yardena Cohen (talk | contribs) (one word so it doesn't get wrapped)

N    

13:59

(cur | prev) . . (+11). . Yardena Cohen (talk | contribs) (label text for footer?)

     14:02 

New server‎‎ (2 changes | history) . . (-137). . [Yardena Cohen‎ (2×)]

     

14:02

(cur | prev) . . (+10). . Yardena Cohen (talk | contribs) (contact form)

     

11:34

(cur | prev) . . (-147). . Yardena Cohen (talk | contribs) (it happened)

N    14:01 

MediaWiki:Contactpage-url‎‎ (4 changes | history) . . (+21). . [Yardena Cohen‎ (4×)]

     

14:01

(cur | prev) . . (-23). . Yardena Cohen (talk | contribs) (relative again)

     

14:01

(cur | prev) . . (-10). . Yardena Cohen (talk | contribs) (actual url)

     

13:59

(cur | prev) . . (+23). . Yardena Cohen (talk | contribs) (full url?)

N    

13:57

(cur | prev) . . (+31). . Yardena Cohen (talk | contribs) (relative link)

     13:52 

(User rights log). .

[Yardena Cohen‎ (2×)]

     

13:52

. . Yardena Cohen (talk | contribs) changed group membership for Oww Op from bureaucrat and administrator to staff ‎

     

13:52

. . Yardena Cohen (talk | contribs) changed group membership for Oww Op from (none) to administrator and bureaucrat ‎

     13:47 (User creation log) . . User account Oww Op (talk | contribs) was created by Yardena Cohen (talk | contribs) and password was sent by email ‎
     11:34 (Patrol log) . . Yardena Cohen (talk | contribs) automatically marked revision 996201 of page New server patrolled ‎
     11:33  BIOL398-04/S15:Class Assignments by Week‎ (diff | hist) . . (-3). . Redirect fixer (talk | contribs) (Automatically fixing double redirect from Tessa A. Morris Class Assignments by Week to Tessa Morris Class Assignments by Week in a maintenance job.)