Biomod/2011/TeamJapan/Tokyo/Notebook/Tools

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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
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