scientific format of floating point numbers in R

cellmap.org provide p-values in scientific format like 1.1e-01.  R can read.table() this column as 'num'.

data for network changes during aging

Protein biogenesis machinery is a driver of replicative aging in yeast https://elifesciences.org/articles/08527 . This paper gives a 'directed graph' that can be used for controllability analysis. 

CYCLOP: rapamycin data

arduino

https://www.arduino.cc/

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 http://cyclops.ccbr.utoronto.ca/

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:

  Screen	Condition	Time course	Wild-type		Screen	Condition	Time course	Wild-type
  WT1	wild-type	-	-		WT2	wild-type	-	-
  WT3	wild-type	-	-		RAP60	rapamycin treatment	60 min	WT3
  RAP140	rapamycin treatment	140 min	WT3		RAP220	rapamycin treatment	220 min	WT3
  RAP300	rapamycin treatment	300 min	WT3		RAP380	rapamycin treatment	380 min	WT3
  RAP460	rapamycin treatment	460 min	WT3		RAP540	rapamycin treatment	540 min	WT3
  RAP620	rapamycin treatment	620 min	WT3		RAP700	rapamycin treatment	700 min	WT3
  HU80	hydroxyurea treatment	80 min	WT3		HU120	hydroxyurea treatment	120 min	WT3
  HU160	hydroxyurea treatment	160 min	WT3		rpd3del_1	rpd3 knockout	-	WT3
  rpd3del_2	rpd3 knockout	-	WT3		rpd3del_3	rpd3 knockout	-	WT3
  AF100	alpha factor treatment	100 min	WT1		AF140	alpha factor treatment	140 min	WT1
  AF180	alpha factor treatment	180 min	WT1

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

*** cpsc2100 software design and development, python

https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-00-introduction-to-computer-science-and-programming-fall-2008/assignments/

https://courses.edx.org/courses/course-v1:MITx+6.00.1x+2T2017_2/course/

https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-00-introduction-to-computer-science-and-programming-fall-2008/readings/

Using python for research
https://courses.edx.org/courses/course-v1:HarvardX+PH526x+1T2018/course/

python objects
https://courses.edx.org/courses/course-v1:HarvardX+PH526x+1T2018/courseware/6862667a32ef4801a65b558ca1b9361e/1dc918f84e7846fb90b2b05a9f4aa57f/3?activate_block_id=block-v1%3AHarvardX%2BPH526x%2B1T2018%2Btype%40vertical%2Bblock%40ad748d8eb5a14a0daf48a2be2f75473e

https://youtu.be/_RcVC9nSsGc

computer science for biology major books

https://www.amazon.com/Developing-Bioinformatics-Computer-Skills-Introduction/dp/1565926641/ref=sr_1_sc_2?ie=UTF8&qid=1507904075&sr=8-2-spell&keywords=bioinformtics+skills


https://www.amazon.com/Bioinformatics-Data-Skills-Reproducible-Research/dp/1449367372/ref=sr_1_1?ie=UTF8&qid=1507904147&sr=8-1&keywords=bioinformatics+skills

large matrix, big data

https://blog.dominodatalab.com/pca-on-very-large-neuroimaging-datasets-using-pyspark/

Singular matrix, invertible matrix

https://en.wikipedia.org/wiki/Invertible_matrix

Moxi flow, next generation flow cytometer

Moxi flow ~ $9000
moxiflow kits
https://www.orflo.com/product_p/mxf002.htm
flow cytometer cassettee, 2 test per cassette, $160 for 25 cassettee and 50 test. This means about $3.2 per test.  For 100-day assay of 50 strains, it means $160*100 = $16K.

Moxi flow Go 2, $21K from VWR
https://us.vwr.com/store/supplier/id/0000012763/ORFLO+TECHNOLOGIES

next generation flow cytometer
https://www.ncbi.nlm.nih.gov/pubmed/28104919

https://www.nature.com/articles/nbt.1919.pdf

UT ESM requisition training materials

PROCUREMENT SERVICES

https://procurement.tennessee.edu/training/esm-requisition-training/

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?

verbal wheel for bloom's taxonomy

Verbal that are considered "measurable" outcomes.

Object-Oriented Design and Patterns, 2nd Edition

http://bcs.wiley.com/he-bcs/Books?action=index&itemId=0471744875&bcsId=2562