Monday, October 16, 2017

NIH subcontract


Document needed.

1.       Statement of Work
2.       Budget
3.       Budget justification
4.       Biosketch
5.       Facilities/equipment document
6.       Letter of Support from Key Personnel
7.       Institutional Letter of Support

yeast single cell protein levels

collection of yeast cells and localization pattern
http://cyclops.ccbr.utoronto.ca/


bout CYCLoPs
  • The data stored in CYCLoPs correspond to studies described in Judice L.Y. Koh, Yolanda Chong, Brenda Andrews, Jason Moffat. CYCLoPs - A database of protein fluxes in Yeast Cell (Manuscript in preparation).
  • 18 screens were conducted in the study, comprising of 2 chemical treatments and 1 genetic mutation, they include:
    ScreenConditionTime courseWild-typeScreenConditionTime courseWild-type
    WT1wild-type--WT2wild-type--
    WT3wild-type--RAP60rapamycin treatment60 minWT3
    RAP140rapamycin treatment140 minWT3RAP220rapamycin treatment220 minWT3
    RAP300rapamycin treatment300 minWT3RAP380rapamycin treatment380 minWT3
    RAP460rapamycin treatment460 minWT3RAP540rapamycin treatment540 minWT3
    RAP620rapamycin treatment620 minWT3RAP700rapamycin treatment700 minWT3
    HU80hydroxyurea treatment80 minWT3HU120hydroxyurea treatment120 minWT3
    HU160hydroxyurea treatment160 minWT3rpd3del_1rpd3 knockout-WT3
    rpd3del_2rpd3 knockout-WT3rpd3del_3rpd3 knockout-WT3
    AF100alpha factor treatment100 minWT1AF140alpha factor treatment140 minWT1
    AF180alpha factor treatment180 minWT1


MYSQL is used.

fluorescent labels



http://www.clontech.com/US/Products/Fluorescent_Proteins_and_Reporters/Fluorescent_Proteins/Fusions/Red

http://www.clontech.com/US/Products/Fluorescent_Proteins_and_Reporters/Fluorescent_Proteins/Fucci_Cell_Cycle_Vectors?sitex=10020:22372:US&PEBCL1=PecQzqNVe9wzSLzBdE2uoNDO4A&PEBCL1_pses=ZGA8D8F214383771F0C0DB76A3075304A12F9A86A5827CFE3228A1B0DF9BA9D13CA93EB3593F96367AD0B93113BDB1E664E8DA5C56C31220DE


Tuesday, October 3, 2017

Dell workstation


I don't know what your budget is, but we just purchased and configured a couple very nice Dell Precision 7810 Desktops. They each had 64GB RAM, 512GB SSD, and a 8 core Xeon chip, as well as a slightly upgraded NVIDIA GPU. These machines ran about $3500 each, a little on the high end, but quite nice. There were also a couple 24 inch monitors that we purchased with each desktop that ran about $350-$450 each; I don't remember the exact price. Basically, each desktop came with two monitors and we spend just under $4000 for each setup.

If that is too much, we could get the same machine with less exorbitant specs or simply purchase a couple Dell XPS desktops. I know that these are pretty decent but I'm not sure about the price right now. They'll be quite a bit cheaper. We have a pretty good relationship with Dell so we typically purchase from them.

So, I guess the first question is: what is your budget? That would be a good starting point for this conversation. Maybe, next time you're at the SimCenter, we can talk about it?


Thursday, September 28, 2017

ARCHS4: All RNA and ChIP-Seq Sample and Signature Search

ARCHS4: All RNA and ChIP-Seq Sample and Signature Search


http://amp.pharm.mssm.edu/archs4/

pmr1 DR has exponential viability curve

Dr. Guo show that pmr1 DR has exponential survival curve, while YPD still have good Gompertz shape.




From H Guo:
"A quick test for pmr1-DR does show smaller AIC (3154.3) for the "exp" model than both "gompertz" (3155.0) and "weibull" (3155.9); meaning that the exponential model is more probable than Gompertz by 2 times, and than Weibull by 5 times."