Difference between revisions of "Sandbox"

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<html>
+
__TOC__
<head>
 
<style>
 
<!-- HIDE WIKI STUFF -->
 
  
#column-one { display:none; width:0px;}
 
.container{background-color: #ffffff; margin-top:0px}
 
.OWWNBcpCurrentDateFilled {display: none;}
 
#content {  width: 0px; margin: 0 auto auto 0;  padding: 0em 0em 0em 0em; align: center;}
 
#column-content {width: 0px; float: left; margin: 0 0 0 0;padding: 0;}
 
.firstHeading {display:none; width:0px;}
 
#globalWrapper{width:984px; background-color: #ffffff; margin-left: auto; margin-right: auto}
 
#column-one {display:none; width:0px;background-color: #ffffff;}
 
#content{ margin: 0 0 0 0; align: center; padding: 12px; width: 960px;background-color: #ffff; border: 0;}
 
#bodyContent{ width: 960px; align: center; background-color: #ffffff;}
 
#column-content{width: 984px;background-color: #ffff;}
 
#footer{display: none; position: center; width: 960px}
 
@media screen {
 
    body { background: #ffffff url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat; }
 
}
 
  
</style>
 
  
<style>
+
----
  
* {
+
== My Test of OpenWetWare Editing ==
text-shadow: 0px 1px 2px #aaa;
+
I would like to try the following editing tasks:
}
 
  
#bodyContent, #column-content, #content {
+
I
background: #ffffff url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat;
+
want
}
+
to keep
 +
lines
 +
separate
  
#column-content {
 
border-left: 1px solid #888;
 
border-right: 1px solid #888;
 
}
 
  
#header {
+
open micoooooooo
  width: 960px;
+
* Add a [hyperlink](https://uk.yahoo.com/?ilc=400).
  height: 304px;
+
** For example: Link to the paper can be found HERE[http://www.nature.com/nature/journal/v403/n6767/pdf/403339a0.pdf].
  background: url(http://openwetware.org/images/3/3b/Biomod-2012-UTokyo-UT-Hongo_header_test2.png) no-repeat;
+
* Add a document or Dropbox link:
  background-size: 100% auto;
+
** Addition of document: [[Image:Alex_Members.jpg]]
  margin-bottom: 0px;
+
** Addition of Dropbox link: The file can be downloaded from Dropbox via this [LINK]
  padding: 0px 0px 0px 0px;
+
* Cite a paper.
/* border-bottom: 1px solid #DEDEDE; */
+
** Hopefully see the list of references at the bottom of the page.
}
+
** This is a really interesting study <ref>Reference goes here</ref>
 +
* Add a picture.
  
#menu {
+
[[Image:popcorn.jpg]]
  display: block;
 
  width: 956px;
 
  padding: 0px;
 
  background-color: black;
 
  border: 2px solid #888;
 
  margin-bottom: 15px;
 
}
 
  
ul.menu li a {
+
== References ==
  display: block;
+
{{Reflist}}
/*  border: 1px solid #474655; */
 
  padding: 8px 10px;
 
  text-decoration: none;
 
/*  color: #333; */
 
  color: #fff;
 
/*  width: 121px;  */
 
  margin: 0px;
 
  text-align: center;
 
  font-size: large;
 
}
 
  
ul.menu li a:hover{
+
----
  color: cyan;
 
}
 
  
ul.menu {
+
'''EmbryoName HK023- chicken embryo- Stage 19.5 - 8.12.14'''
/*  display: none;
 
  position: absolute; */
 
  height: 40px;
 
  margin:0;
 
  padding:0;
 
  list-style:none;
 
  float: center;
 
}
 
  
ul.menu li {
 
/*  display:inline;*/
 
  margin:0;
 
  padding:6px;
 
  float: left;
 
  position: relative;
 
}
 
  
ul.menu li:hover ul {
+
==Experiment==
  display: block;
 
  position: absolute;
 
  z-index: 100;
 
}
 
  
ul.submenu {
+
'''Objective'''
  display: none;
+
To transform HB101s with a plasmid encoding GFP (called pGFP) and express this protein by inducing with arabinose. Testing out openwetware
  list-style: none;
+
'''Procedure'''
  background-color: #f0f0f0;
 
  border: 1px solid #ccc;
 
}
 
  
ul.submenu li {
+
* Trigeminal nerve bilaterally DiO crystals
  float: none;
+
* 7th/8th nerve bilaterally DiI crystals (Big chunk on 7th nerve on L side and big chunk on 8th on R side)
  margin: 0px;
 
}
 
  
ul.submenu li a {
+
'''Notes'''
  text-align: left;
+
No obvious contamination, purposelly put a greater chunk of dye on the 7th nerve on the L side and the 8th nerve on the R side so will see if there is any visible difference between the amount of neurons labelled in different positions within the rhombomere.  
  margin: 0px;
 
  width: 340px;
 
  padding: 0 0 0 12px;
 
  color: black;
 
  text-decoration: none;
 
  font-size: large
 
}
 
  
ul.submenu li a:hover {
+
==Files==
  color: black;
 
  text-decoration: underline;
 
}
 
  
.thumb {
+
*
  border-image: url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat;
+
*
}
+
*
 +
*
  
.mytable {
+
*
  border-image: url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat;
+
** abd dfg
}
+
**
  
</style>
+
==Results==
</head>
 
<body>
 
  
  <div style="text-align: right">
+
===Facial===
    <p><a href="http://openwetware.org/index.php?title=Template:Biomod/2012/UTokyo/UT-Hongo&action=edit">edit this header</a></p>
+
(Green)
  </div>
 
  
  <div style="height: 60px; margin-bottom: 18px;">
+
* '''''Afferents'''''
    <div style="float: left; width: 250px; padding: 3px; background-color: white;">
+
    
      <a href="http://biomod.net/"><img src="http://openwetware.org/images/8/82/Biomod2012-logo.png" width="250px" height="50px"></img></a>
 
    </div>
 
    <div style="float: right; width: 240px; padding: 3px; background-color: white;">
 
      <a href="http://www.u-tokyo.ac.jp/en/" target="_blank"><img src="http://www.u-tokyo.ac.jp/en/images/banner/UT-logo.gif" width="234" height="60" border="0" alt="The University of Tokyo"></img></a>
 
    </div>
 
   </div>
 
  
    <div id="header">
+
* '''''Efferents'''''
    </div>
 
  
    <div id="menu">
 
      <ul class="menu">
 
<li class="toppage"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo">Top</a></li>
 
<li class="motives"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro">Motives</a></li>
 
<!-- <li class="design"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Function">Design</a></li> -->
 
<li class="result"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly">Design & Results</a>
 
  <ul class="submenu">
 
    <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Assembly_of_the_DNA_Shell">Assembly of the DNA Shell</a></li>
 
    <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Capturing_ability">Capturing Ability</a></li>
 
    <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Immobilizing_on_microfluidic_device">Immobilizing on microfluidic device</a></li>
 
    <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Supporting_Enzyme">Supporting Enzyme</a></li>
 
  </ul>
 
</li>
 
<li class="method"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Method">Method</a></li>
 
<li class="futurework"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork">Progress & Beyond</a></li>
 
<li class="team"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Team">Team</a></li>
 
<li class="acknowledgement"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement">Acknowledgement</a></li>
 
      </ul>
 
    </div>
 
  
</body>
 
</html>
 
  
  
==Institutional Affiliation==
 
  
Assistant Professor
 
  
Department of Physiology & Membrane Biology
+
===VIII ===
 +
(green)
  
School of Medicine
+
* '''''Afferents'''''
  
University of California
 
  
4126 Tupper Hall
 
  
One Shields Avenue
+
* '''''Efferents'''''
  
Davis, California 95616
 
  
530.752.4131 tel
+
* '''''Other'''''
530.752.5314 lab tel
 
530.752.5423 fax
 
  
jsack@ucdavis.edu
 
  
==Math Practice==
 
  
''x''<sup>2</sup>+''y''<sup>2</sup>=''z''<sup>2</sup>
+
===Basal plate ===
 +
(red)
  
{{math|''x''<sup>2</sup>+''y''<sup>2</sup>{{=}}''z''<sup>2</sup>}}
 
  
<math>x^2+y^2=z^2</math>
+
==Summary==
  
&sum;i=∞
+
'''Questions'''
  
<math>e^{\pi i} + 1 = 0</math>
+
'''Future'''
  
<math>\frac{\sqrt{2\alpha_1+e^2}}{\log \alpha_2}</math>
 
  
==Google Docs==
+
<META HTTP-EQUIV="refresh" CONTENT="10;URL=http://my.newplace.com/">
{{#widget:Google Document
 
|id=19hEjXbw_pwVjY5vwu-hQGfqpLTuwWQemRzEsCvJw640
 
}}
 
  
<html>
+
 
<div id="car" style="width:100%; color:#SAFRDA;">
+
Mary {pad|4em} had a little lamb.
hai
+
 
</div>
+
'''Badrul Arefin'''
</html>
+
 
 +
 
 +
# Jeong M^, {{spaces|7}} <u>Sun D^</u>, Luo M^, Huang Y, Challen GA, <u>Rodriguez B</u>, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, <u>Li W*</u>, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a. <br/> '''''          Nature Genetics''''' . Accepted.
 +
# <u>Akdemir KC</u>, Jain AK, Alton K, Arronow B, J. CA, ..., <u>Li W*</u>, Barton MC*: Genome Wide Profiling Reveals Stimulus-specific Functions of p53 During Differentiation and DNA Damage of Human Embryonic Stem Cells. <br/>'''''Nucleic Acids Res.''''' Accepted
 +
# Klein JB, Piao L, …, <u>Li W</u>, Shi X, Kutateladze TG: KDM5B demethylase binds to its histone target and the product through distinct modules.<br/>''Cell Reports''. Accepted. <br/><br/>'''2013''' <br/><br/>
 +
# <u>Chen K</u>, <u>Xi Y</u>, Pan X, Dent S, He X, <u>Li W*</u>: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing. <br/>'''''Genome Res.''''' 23 (2013) 341-351. [http://www.bcm.edu/news/item.cfm?newsID=6723 BCM News]; [http://epigenie.com/danpos-reveals-dynamic-nucleosomes Epigenie Headline]  <br/><br/>
 +
# <u>Wang L</u>, <u>Park JH</u>, Wang S, Kocher JP, <u>Li W*</u>: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model. <br/>'''''Nucleic Acids Res.''''' 41 (2013) e74.<br/><br/>
 +
# <u>Lin X</u>, <u>Sun D</u>, <u>Rodriguez B</u>, Zhao Q, Sun H, Zhang Y, <u>Li W*</u>: BseQC: Quality Control of bisulfite sequencing experiments. <br/>'''''Bioinformatics''''' 29 (2013) 3227-3229. PMCID: PMC3842756 .<br/><br/>
 +
# <u>Chen K^</u>, Wilson MA^, Hirsch C, Watson A, Liang S, Lu Y, <u>Li W*</u>, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor. <br/>'''''Genome Res.''''' 23 (2013) 312-322. <br/><br/>

Latest revision as of 19:24, 20 October 2017



My Test of OpenWetWare Editing

I would like to try the following editing tasks:

I want to keep lines separate


open micoooooooo

  • Add a [hyperlink](https://uk.yahoo.com/?ilc=400).
    • For example: Link to the paper can be found HERE[1].
  • Add a document or Dropbox link:
    • Addition of document: Alex Members.jpg
    • Addition of Dropbox link: The file can be downloaded from Dropbox via this [LINK]
  • Cite a paper.
    • Hopefully see the list of references at the bottom of the page.
    • This is a really interesting study <ref>Reference goes here</ref>
  • Add a picture.

Popcorn.jpg

References

<references group=""></references>

EmbryoName HK023- chicken embryo- Stage 19.5 - 8.12.14


Experiment

Objective To transform HB101s with a plasmid encoding GFP (called pGFP) and express this protein by inducing with arabinose. Testing out openwetware Procedure

  • Trigeminal nerve bilaterally DiO crystals
  • 7th/8th nerve bilaterally DiI crystals (Big chunk on 7th nerve on L side and big chunk on 8th on R side)

Notes No obvious contamination, purposelly put a greater chunk of dye on the 7th nerve on the L side and the 8th nerve on the R side so will see if there is any visible difference between the amount of neurons labelled in different positions within the rhombomere.

Files

    • abd dfg

Results

Facial

(Green)

  • Afferents


  • Efferents




VIII

(green)

  • Afferents


  • Efferents


  • Other


Basal plate

(red)


Summary

Questions

Future


<META HTTP-EQUIV="refresh" CONTENT="10;URL=http://my.newplace.com/">


Mary {pad|4em} had a little lamb.

Badrul Arefin


  1. Jeong M^, Template:Spaces Sun D^, Luo M^, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W*, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a.
    Nature Genetics . Accepted.
  2. Akdemir KC, Jain AK, Alton K, Arronow B, J. CA, ..., Li W*, Barton MC*: Genome Wide Profiling Reveals Stimulus-specific Functions of p53 During Differentiation and DNA Damage of Human Embryonic Stem Cells.
    Nucleic Acids Res. Accepted
  3. Klein JB, Piao L, …, Li W, Shi X, Kutateladze TG: KDM5B demethylase binds to its histone target and the product through distinct modules.
    Cell Reports. Accepted.

    2013

  4. Chen K, Xi Y, Pan X, Dent S, He X, Li W*: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.
    Genome Res. 23 (2013) 341-351. BCM News; Epigenie Headline

  5. Wang L, Park JH, Wang S, Kocher JP, Li W*: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model.
    Nucleic Acids Res. 41 (2013) e74.

  6. Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W*: BseQC: Quality Control of bisulfite sequencing experiments.
    Bioinformatics 29 (2013) 3227-3229. PMCID: PMC3842756 .

  7. Chen K^, Wilson MA^, Hirsch C, Watson A, Liang S, Lu Y, Li W*, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor.
    Genome Res. 23 (2013) 312-322.