Biomod/2011/TeamJapan/Tokyo/Notebook/Tools
<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 ==================== */
- menu * {
margin: 0; padding: 0; }
- 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; }
- menu ul {
float: left; list-style: none; }
- menu ul li {
background-color:transparent;
position:relative;
float:left; list-style: none; padding: 10px 20px 0 0;
font-weight: bold; width: auto;
}
- menu a {
color: #FFFFFF; display: inline; text-decoration: none; }
- menu a:visited {
color:#FFFFFF; text-decoration: none }
- menu a:hover {
color: #00a5ea; }
- 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;
}
- menu ul li:hover ul {
display: inline;
background-position: bottom;
}
- 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">
- SubWrapper {width: 645px;}
- news {width: 317px;}
- super_main_wrapper {position:static;}
- navigation {left: 15px;}
- 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=" " 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.
- 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.
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
- 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
- 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
- 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 |