Biomod/2011/TeamJapan/Tokyo/Notebook/Tools

From OpenWetWare
Jump to: navigation, search


<html> <!--<head>--> <!-- We refer to the wiki of team iGEM Heidlberg 2009. -->

      <style type="text/css">

/* ====================

  主に全体に関わるCSS

   ==================== */

      body {behavior: url(http://www.xs4all.nl/~peterned/htc/csshover3-source.htc);}
      .clear {clear:both;}

body.mediawiki {

                       font-size: 14px;

background-color:#707070; background-position: center center; background-attachment: fixed; background-repeat: no-repeat; font-family: Calibri, Verdana, helvetica, sans-serif; }

               h1 {
                       padding: 0px 20px 5px 20px;
                       font-size: 34px;
                       font-weight: bold;
               }
               h2 {
                       padding: 20px 20px 5px 20px;
                       font-size: 25px;
                       color: #0083eb;
                       text-decoration: none;
                       font-weight: bold;}
                       border: none;
               h2 a {
                       color: #eb8300;
               }
               h3 {
                       padding: 20px 20px 5px 20px;
                       font-size: 20px;
                       color: #000;
                       font-decoration: none;
                       font-weight: bold;
               }
               h1.firstHeading {

display: none;

               }

p { text-align: justify; } a:link { color: #00a5ea; text-decoration: none } a:visited { color:#00a5ea; text-decoration: none } a:hover {

                       color: #eb8300;

text-decoration: none } a:active { color:#f29400; text-decoration: none } #bodyContent {

                       width: 970px;
                       margin: 0px 0px 0px;
                       background-color:#ffffff;
                       border-width: 0px 1px 0px 1px;
                       border-color: #000000;
               }
               #content {
                       padding-left: 0px; width: 970px;
               }

table#team_members {

                       text-align: justify;
                       border: 0;
               }

table#team_members h2, table#team_members h3 {

                       clear: both;
               }

#content * a:hover {

                       text-decoration:none;
               }

#main_wrapper {

                       position:absolute;
                       left:0px;
                       top:20px;

margin-top: 0; width: 969px; height: 221px; align: center; border-style: solid;

                       border-color: white;

} /* ====================

  メニューの画像を変更できる部分
  ==================== */

#header {

                       position:relative;
                       left:0px;
                       top:0px;

margin-top: 0; width: 969px; height: 221px; align: left; background-color: #FFFFFF;

                       background-image: url(http://openwetware.org/images/e/e0/NEW_header.jpg); 

} /* ====================

  以下、特殊なclassに適用される
  ==================== */

#navigation { position:absolute;

                       left:18px; top:155px; width:1200px; height:69px;

z-index:100;

                       background-color: transparent;
                       float: left; 

color: #0000FF; } #super_main_wrapper {

                       position:absolute;
                       left:0px;
                       top:227px;

width: 975px; align: center; background-color: #ede8e2;

                       heigth: auto;
               }
               #SubWrapper {
                       width: 645px;
                       padding: 0px;
                       border-left:4px solid #ede8e2;
                       float: left;
                       margin-top: 0px;
                       background-color: #ede8e2;
               }
               #SubWrapper * p, #SubWrapper p  {
                       padding: 0 20px;
                       text-align: justify;
                       font-size: 12px;
               }
               #SubWrapper * h3, #SubWrapper h3 {
                       padding-top: 10px;
                       font-size: 18px;
               }
               #news {
                       width: 322px;
                       margin-top: 0px;
                       float: left;
                       background-color: #d8d5d0;
                       border-right:4px solid #ede8e2;
               }
               #news p {
                       padding: 0 20px 20px 20px;
                       text-align: justify;
                       font-size: 12px;
               }
               #news h3 {
                       padding: 10px 20px;
                       font-size: 18px;
               }
               #mission_box {
                       width:650px;
                       float: left;
               }
               #team_box, #heartbeat_box, #notebook_box, #parts_box, #gallery_box, #sponsors_box, .boxy {
                       width:215px;
                       float: left;
                       padding: 10px 0 0 0;
               }
               div.tleft {
                       border-width: 0px;
                       margin:0;
                       padding:0;
                       border-color:transparent;
               }

/* ====================

  ここからプルダウン周辺のデザイン
  ==================== */
  1. menu * {

margin: 0; padding: 0; }

  1. menu {

behavior: url(http://www.xs4all.nl/~peterned/htc/csshover3-source.htc); <!-- fuer ie6 --> font-family: calibri, verdana, sans-serif;

       font-color: #ffffff;

font-size: 19px; background-color: transparent; float:left; padding: 12px 0 0 0; }

  1. menu ul {

float: left; list-style: none; }

  1. menu ul li {

background-color:transparent;

       position:relative;

float:left; list-style: none; padding: 10px 20px 0 0;

       font-weight: bold;
       width: auto;

}

  1. menu a {

color: #FFFFFF; display: inline; text-decoration: none; }

  1. menu a:visited {

color:#FFFFFF; text-decoration: none }

  1. menu a:hover {

color: #00a5ea; }

  1. menu ul li ul {

display: none; position: absolute; left: 0px;

       width: 155px;
       heigth: 1%;

font-size: 19px; opacity: 0.8; list-style: none;

       top: 30px;
       padding-top: 20px;
       z-index:500;

}

  1. menu ul li:hover ul {

display: inline;

       background-position: bottom;

}

  1. menu ul li ul li {

width: 100%; list-style: none;

       background-color: #000;
       margin: -1px;
       padding: 0px 0 0 5px;
       display: inline;

}

</style> <!-- </head> -->


<!-- ############################# BODY!!!!! #################################### -->

<!-- <body> --> <!--[if IE]> <style type="text/css">

  1. SubWrapper {width: 645px;}
  2. news {width: 317px;}
  3. super_main_wrapper {position:static;}
  4. navigation {left: 15px;}
  5. menu ul li ul {left: -2px; top: 22px;}

</style> <![endif]--> <div id="main_wrapper">

 <div id="header">

<div id="navigation"> <div id="menu" style="position:static"> <ul> <li><a class="aMain" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo">Home</a></li> <li><a class="aTeam" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Team/Students">Team</a></li> <li><a class="aProject" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Project</a> <!-- <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Overview</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/introduction">Introduction</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Model">Model</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Devices">Devices</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Modes">Modes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Results</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> </ul> --> <li><font color="#ffffff">Results</font> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Experiments</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Design</a></li> </ul></li> <!-- <li><a class="Simulation" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a class="DNA design" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Designs</a></li> --> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Protocols">Protocols</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Lab.notebook">Notes</a></li> <li><a class="aNotebook" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sponsors/">Sponsors</a></li> <li><a class="aSitemap" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sitemap">Sitemap</a></li>

</ul> </div><!-- end drop menu --> </div> <!-- end navigation --> </div> </div> <!-- For IE 6 --> <script type="text/javascript">

/***********************************************

  • CSS Vertical List Menu- by JavaScript Kit (www.javascriptkit.com)
  • Menu interface credits: http://www.dynamicdrive.com/style/csslibrary/item/glossy-vertical-menu/
  • This notice must stay intact for usage
  • Visit JavaScript Kit at http://www.javascriptkit.com/ for this script and 100s more
                                                                                              • /

var menuids=new Array("verticalmenu") //Enter id(s) of UL menus, separated by commas var submenuoffset=-2 //Offset of submenus from main menu. Default is -2 pixels.

function createcssmenu(){ for (var i=0; i<menuids.length; i++){

 var ultags=document.getElementById(menuids[i]).getElementsByTagName("ul")
   for (var t=0; t<ultags.length; t++){
   var spanref=document.createElement("span")

spanref.className="arrowdiv" spanref.innerHTML="&nbsp;&nbsp;" ultags[t].parentNode.getElementsByTagName("a")[0].appendChild(spanref)

   ultags[t].parentNode.onmouseover=function(){
   this.getElementsByTagName("ul")[0].style.left=this.parentNode.offsetWidth+submenuoffset+"px"
   this.getElementsByTagName("ul")[0].style.display="block"
   }
   ultags[t].parentNode.onmouseout=function(){
   this.getElementsByTagName("ul")[0].style.display="none"
   }
   }
 }

} if (window.addEventListener) window.addEventListener("load", createcssmenu, false) else if (window.attachEvent) window.attachEvent("onload", createcssmenu) </script> <!-- </body> --> </html>






Tools

Software

<Sequence Design>

  • NUPACK: Software to design DNA arraignment.
→Direct Link:http://www.nupack.org/partition/browser
  • The DINAMelt Web Server: We used to know K_m of DNA strand.
→Direct Link:http://mfold.rna.albany.edu/?q=DINAMelt

<Software of editing>

  • Paint.net: Image processing software. We used it to control light and shade.
→Direct Link:http://www.paint.net/
  • Image J: Image analysis software. We used it to process photo of electrophoresis.
→Direct Link:http://rsbweb.nih.gov/ij/
  • Inkscape: We used it to draw figures.
→Direct Link:http://inkscape.org/index.php?lang=en
  • Chem Bio Draw: We used it mainly to draw chemical formula.
→Direct Link:http://www.cambridgesoft.com/software/details/?fid=15&pid=226
  • aviutl: We used it mainly to edit YouTube videos.
→Direct Link:http://www.gigafree.net/media/me/aviutl.html
  • trakAxPC: We used it mainly to edit YouTube videos.
→Direct Link:http://www.trakax.com/software/pc/download/
  • CyberLink power director: We used it mainly to edit YouTube videos.
→Direct Link:http://www.cyberlink.com/products/powerdirector/overview_en_US.html



Laboratory instrument

  • Micro fine machining center
Roland MODELA MDX-40A
http://www.rolanddg.com/product/3d/3d/mdx-40a/index.html
  • End mill
TECNOS Co, Ltd.
-RSE230-0.5X2.5---Diameter is 0.5mm
-RSE230-1X5---Diameter is 1mm
-RSE230-3X15---Diameter is 3mm
  • Mili-Q water
http://www.millipore.com/catalogue/item/zrqsvp0ww
  • Tabletop Centrifuge
[1](Only Japanese)
  • Ultracentrifuge
HITACHI himac CT 15RE
http://www.hitachi-koki.com/himac/centrifuges/ct15e/ct15e.html
  • Fluorescence Phase contrast microscope
OLYMPUS CKX41
http://www.microscopy.olympus.eu/microscopes/Life_Science_Microscopes_Routine_microscope_CKX41.html
  • Shaker
LMS SHM2001
http://www.lms.co.jp/commodity/cat1/cat0101/post_43.html
  • Rotator of micro tube
As One MTR-103
http://www.justis.as-1.co.jp/jus-tis/web/DetailEnglish.aspx?sid=justis&catalog=GJ&group=G025401&no=&op_from=jus-tis
  • Band Saw
Hozan K-100
http://www.hozan.co.jp/E/catalog/Metal_working/K100.html
  • DESICCATOR VACUUM
AS ONE 1-068-01
http://www.justis.as-1.co.jp/jus-tis/web/DetailEnglish.aspx?sid=justis&catalog=GJ&group=G007103&no=&op_from=jus-tis
  • Vacuum pumps
TGK LV-435A
http://www.tgk.co.jp/info/0904645105s.html
  • Camera
CASIO EX-F1
http://www.casio-intl.com/dc/ex_f1/
  • Heating Block
THERMO BLOCK ND-M01
http://www.tech-jam.com/scientific_research_equipment/incubator/kn3316700.phtml (Only Japanese)

Material Lists and Kits


Name
grade Supplier
Product code
Cat No Lot No
Sodium Hydroxide Wako 1st Grade Wako 198-13765 1310-73-2 LAN1989
SILPOT 184 ***
DOW CORNING TORAY 03255981 *** 0006410158
Acetone Wako 1st Grade
Wako 012-00343 67-64-1 DCN6798
2-Propanol
Wako 1st Grade
Wako 166-04831 67-63-0 DCM6848
Ethnol(99.5)
Wako 1st Grade
Wako 057-00451 64-17-5 DBM6540
Albumin, from Bovine Serum, Cohn Fraction V, pH7.0
Biochmistry
Wako 013-23291 *** STF3372
Di(N-succinimidyl) Suberate
***
TCI D3895 68528-80-3 CU3BM
Ultra PureTM 1M Tris-HCL pH 8.0 *** invitrogenTM 15568-025 *** 9949164
40(w/v)%-Acrylamide/Bis Mixed Solution (29:1) SP nacalai tesque *** *** L1F7876
Dimethyl Sulfoxide  Wako 1st Grade Wako 043-07216 67-68-5 LAL4398
Sodium Dodecyl Sulfate(SDS) Wako 1st Grade Wako 196-08675 151-4-3 LAN1411
SSC Buffer 20x Concentrate *** SIGMA *** S6639-1L 021M8403
1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide Hydrochloride SU TCI D1601 25952-53-8 FJXDI
N-Hydroxysuccinimide *** TCI H0623 6066-82-6 EOC3E
Suberic acid bis(3-sulfo-N-hydroxysuccinimide ester) sodium salt *** SIGMA S5799-25MG *** 051M4067V
SYBR Gold nucleic acid gel stain *** life technologiesTM S11494 *** 927072
Dimethyl Sulfoxide for Molecular Biology Wako 041-29351 67-68-5 DCN0023
Zinc Sulfate Practical Grade Wako 268-00422 7733-02-0 LAQ6174
Urea for Molecular Biology Wako 211-01213 57-13-6 LAQ5967
Magnesium Chloride *** Wako 136-03995 7786-30-3 LAR4676
Tris-Borate-EDTA Buffer (10X), Nuclease an Protease tested [TBE Buffer] *** nacalai tesque 35440-31 *** L1A6455
Ammonium Peroxodisulfate Wako 1st Grade Wako 018-03282 7727-54-0 HLH7635
N,N,N',N'-TETRAMETHYL- ETHYLENEDIAMINE Wako 1st Grade Wako 202-04003 110-18-9 EPF1167
0.5N EDTA (pH8.0) *** Wako 311-90075 *** 01481B
Glycerol Wako 1st Grade Wako 075-00616 56-81-5 LAQ5416
Disodium Hydrogenphosphate 12-Water Wako 1st Grade Wako 196-02835 10039-32-4 LAQ5931
Sodium Dihydrogenphosphate Dihydrate Wako 1st Grade Wako 192-02815 13472-35-0 LAR4091
Hydrochloride Acid Wako 1st Grade Wako 080-01066 7647-01-0 LAN1065
PolyLink - Protein Coupling Kit for COOH Microparticles For Microparticles 1.0 Micron or Larger *** Polysciences, Inc. 24350 *** 631643
PolyLink EDAC ***
Polysciences, Inc. 2435C *** 631321