Difference between revisions of "Sandbox"

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{{Template:}}
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__TOC__
Welcome to DeoxyriboNucleicAwesome's BIOMOD Wiki!
 
{{Template:}}
 
  
[[Image:Example.jpg]]
 
  
[[Image:.jpg|thumb|right]]
 
Jon Sack, Ph.D.
 
<pre>
 
[[Image:whatever.png]]
 
</pre>
 
==Research interests==
 
COMPOSITE MATERIALS [PMC] IN BONE GRAFTING SUBSTITUTES.
 
  
 +
----
  
function ddm()
+
== My Test of OpenWetWare Editing ==
{
+
I would like to try the following editing tasks:
  
// Variables, change these in case you need to set other class names (mmhide_ for
+
I
// contribute users for example)
+
want
var parentClass='isParent';      //gets applied when the LI has a nested UL
+
to keep
var activeParentClass='isActive';        //gets applied when the nested UL is visible
+
lines
var preventHoverClass='nohover';        //denotes a navigation that should not get any hover effects
+
separate
var indicateJSClass='dhtml';    //gets applied to the main navigation when Javascript is available
 
var toHideClass='hiddenChild';  //gets applied to hide the nested UL
 
var toShowClass='shownChild';    //gets applied to show the nested UL
 
var currentClass='current';      //denotes the current active sub element and prevents collapsing
 
var d=document.getElementById('nav');  //denotes the navigation element
 
  
// if DOM is not available stop right here.
 
if(!document.getElementById && !document.createTextNode){return;}
 
  
// if the navigation element is available, apply the class denoting DHTML capabilities
+
open micoooooooo
if(d)
+
* Add a [hyperlink](https://uk.yahoo.com/?ilc=400).
{
+
** For example: Link to the paper can be found HERE[http://www.nature.com/nature/journal/v403/n6767/pdf/403339a0.pdf].
d.className+=d.className==''?indicateJSClass:' '+indicateJSClass;
+
* Add a document or Dropbox link:
var lis,i,firstUL,j,apply;
+
** Addition of document: [[Image: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.
  
// loop through all LIs and check which ones have a nested UL
+
[[Image:popcorn.jpg]]
lis=d.getElementsByTagName('li');
 
for(i=0;i<lis.length;i++)
 
{
 
firstUL=lis[i].getElementsByTagName('ul')[0]
 
// if there is a nested UL, deactivate the first nested link and apply the class to show
 
// there is a nested list
 
if(firstUL)
 
{
 
lis[i].childNodes[0].onclick=function(){return false;}
 
lis[i].className+=lis[i].className==''?parentClass:' '+parentClass;
 
// check if there is a "current" element
 
apply=true;
 
if(new RegExp('\\b'+currentClass+'\\b').test(lis[i].className)){apply=false;}
 
if(apply)
 
{
 
for(j=0;j<firstUL.getElementsByTagName('li').lengt h;j++)
 
{
 
if(new RegExp('\\b'+currentClass+'\\b').test(firstUL.getE lementsByTagName('li')[j].className)){apply=false;break}
 
}
 
}
 
// if there is no current element, apply the class to hide the nested list
 
if(apply)
 
{
 
firstUL.className+=firstUL.className==''?toHideCla ss:' '+toHideClass;
 
// check if there is a class to prevent hover effects and only apply the function
 
// onclick if that is the case, otherwise apply it onclick and onhover
 
if(new RegExp('\\b'+preventHoverClass+'\\b').test(d.class Name))
 
{
 
lis[i].onclick=function(){doddm(this);}
 
} else {
 
lis[i].onclick=function(){doddm(this);}
 
lis[i].onmouseover=function(){doddm(this);}
 
lis[i].onmouseout=function(){doddm(null);}
 
}
 
// if there is a current element, define the list as being kept open and apply the
 
// classes to show the nested list and define the parent LI as an active one
 
} else {
 
lis[i].keepopen=1;
 
firstUL.className+=firstUL.className==''?toShowCla ss:' '+toShowClass;
 
lis[i].className=lis[i].className.replace(parentClass,activeParentClass);
 
}
 
}
 
}
 
}
 
// function to show and hide the nested lists and add the classes to the parent LIs
 
function doddm(o)
 
{
 
var childUL,isobj,swap;
 
  
// loop through all LIs of the navigation     
+
== References ==
lis=d.getElementsByTagName('li');
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{{Reflist}}
for(i=0;i<lis.length;i++)
 
{
 
isobj=lis[i]==o;
 
// function to exchange class names in an object
 
swap=function(tmpobj,tmporg,tmprep)
 
{
 
tmpobj.className=tmpobj.className.replace(tmporg,t mprep)     
 
}
 
// if the current LI does not have an indicator to be kept visible
 
if(!lis[i].keepopen)
 
{
 
childUL=lis[i].getElementsByTagName('ul')[0];
 
// check if there is a nested UL and if the current LI is not the one clicked on
 
// and exchange the classes accordingly (ie. hide all other nested lists and
 
// make the LIs parent rather than active.
 
if(childUL)   
 
{     
 
if(new RegExp('\\b'+preventHoverClass+'\\b').test(d.class Name))
 
{
 
if(new RegExp('\\b'+activeParentClass+'\\b').test(lis[i].className))
 
{
 
swap(childUL,isobj?toShowClass:toHideClass,isobj?t oHideClass:toShowClass);   
 
swap(lis[i],isobj?activeParentClass:parentClass,isobj?parentC lass:activeParentClass); 
 
} else {
 
  
swap(childUL,isobj?toHideClass:toShowClass,isobj?t oShowClass:toHideClass);   
+
----
swap(lis[i],isobj?parentClass:activeParentClass,isobj?activeP arentClass:parentClass); 
 
}
 
} else {
 
swap(childUL,isobj?toHideClass:toShowClass,isobj?t oShowClass:toHideClass);   
 
swap(lis[i],isobj?parentClass:activeParentClass,isobj?activeP arentClass:parentClass); 
 
}
 
}
 
}
 
}
 
}
 
}
 
window.onload=function()
 
{
 
ddm();
 
// add other functions to be called onload below
 
}
 
  
 +
'''EmbryoName HK023- chicken embryo- Stage 19.5 - 8.12.14'''
  
In this researdfasdfch, natural fibers like Sisal (Agave sisalana), Banana (Musa sepientum) & Roselle (Hibiscus sabdariffa), Sisal and banana (hybrid), Roselle and banana (hybrid) and Roselle and sisal (hybrid) are fabricated with bio epoxy resin using molding method. In this work, impact strength of Sisal and banana (hybrid), Roselle and banana (hybrid and Roselle and sisal (hybrid) composite at dry and wet conditions were studied. Impact test were conducted izod impact testing machine. In this work micro structure of the specimens are scanned by the Scanning Electron Microscope.
 
  
I also invested heavily in Myspace, and lost most of my life savings.
+
==Experiment==
  
 +
'''Objective'''
 +
To transform HB101s with a plasmid encoding GFP (called pGFP) and express this protein by inducing with arabinose. Testing out openwetware
 +
'''Procedure'''
  
{{scroll box|width=75%|text=
+
* 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)
  
<dpl>
+
'''Notes'''
category=SL-Coding
+
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.
mode = unordered
 
order = descending
 
</dpl>
 
}}
 
  
==Education==
+
==Files==
<!--Include info about your educational background-->
 
* Ph.D., Stanford University, Department of Biological Sciences
 
* B.A., Reed College, Biochemistry
 
  
==Institutional Affiliation==
+
*
 +
*
 +
*
 +
*
  
Assistant Professor
+
*
 +
** abd dfg
 +
**
  
Department of Physiology & Membrane Biology
+
==Results==
  
School of Medicine
+
===Facial===
 +
(Green)
  
University of California
+
* '''''Afferents'''''
 +
 
  
4126 Tupper Hall
+
* '''''Efferents'''''
  
One Shields Avenue
 
  
Davis, California 95616
 
  
530.752.4131 tel
 
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>
+
===VIII ===
 +
(green)
  
{{math|''x''<sup>2</sup>+''y''<sup>2</sup>{{=}}''z''<sup>2</sup>}}
+
* '''''Afferents'''''
  
<math>x^2+y^2=z^2</math>
 
  
&sum;i=∞
 
  
<math>e^{\pi i} + 1 = 0</math>
+
* '''''Efferents'''''
  
<math>\frac{\sqrt{2\alpha_1+e^2}}{\log \alpha_2}</math>
 
  
==Google Docs==
+
* '''''Other'''''
{{#widget:Google Document
 
|id=19hEjXbw_pwVjY5vwu-hQGfqpLTuwWQemRzEsCvJw640
 
}}
 
  
<html>
+
 
<div id="car" style="width:100%; color:#SAFRDA;">
+
 
hai
+
===Basal plate ===
</div>
+
(red)
</html>
+
 
 +
 
 +
==Summary==
 +
 
 +
'''Questions'''
 +
 
 +
'''Future'''
 +
 
 +
 
 +
<META HTTP-EQUIV="refresh" CONTENT="10;URL=http://my.newplace.com/">
 +
 
 +
 
 +
Mary {pad|4em} had a little lamb.
 +
 
 +
'''Badrul Arefin'''
 +
 
 +
 
 +
# 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.