Category:Protocols: Difference between revisions

Latest revision as of 04:31, 11 September 2021

Subcategories

This category has the following 22 subcategories, out of 22 total.

A

AutoDock‎ (2 P)

F

FAST-NMR‎ (6 P)

G

Gel‎ (2 P)
General Maintenance‎ (14 P)

L

Lab Safety‎ (14 P)

M

Metabolomics‎ (1 C, 4 P)
Molecular Docking‎ (1 P)
MVAPACK‎ (4 P)

N

Needs Updating‎ (25 P)
NMR Usage‎ (1 C, 10 P)

P

Protein Work‎ (3 C, 2 P)
Proteomics‎ (empty)

S

Sample Preparation‎ (9 P)

T

Troubleshooting‎ (2 P)

U

Update Wiki‎ (3 P)

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-==Load the data==
+<!--''General Maintenance''
-The data can be prepared in csv or text file to load the data in to R
+*[[Changing the high pressure dewar]]
-===Type: read.csv("your file name.csv")===
+*[[Filling a Magnet with Nitrogen]]
-e.g  data <- read.csv (“list.csv”)
+*[[Autoclaving Laboratory Glassware and Media]]
-==To name the rows of the heat map==
+*[[Chemical Disinfection of Glassware]]
-===Type: Row.names(data) <- data$Name===
+*[[Requesting Balance Calibration]]
-==To exclude the first column from the heat map==
+*[[Requesting Pipette Calibration]]
-===Type:Data <- data [,2: n]===
+*[[Using the UV-Vis]]
-  where n is the number of columns to be included in the heat map
+*[[Using and Maintaining pH Meter]]
-==To change the loaded data in to data matrix==
+*[[-80 Freezer Storage and Maintenance]]
-===Type: Data_matrix <- data.matrix (data)===
+*[[Freeze Dryer Maintenance]]
-==To use gnuplot library==
+*[[Lab Notebook Guidelines]]
-  Note: Gnuplot package must be installed in R.
+*[[Sample Barcoding]]
-===Type:library("gplots")===
-==To make heat map==
+''Protein Preparation''
-===Type: heatmap.2 (Data_matrix, dendrogram="row", col= redgreen (75), scale="none", key = TRUE, keysize = 1.0, margins = c(4,30),  density.info="none", trace="none")===
+*[[Buffer Exchange and Solution Concentration]]
+*[[Finding a Protein Target on the NESG website]]
+*[[Choosing a Plasmid]]
+*[[Plasmid Purification and Transformation Protocol]]
+*[[Creating Stock Cultures of Bacteria]]
+*[[Luria-Bertani Media]]
+*[[M9 Minimal Media]]
+*[[Protein Overexpression and Extraction]]
+*[[SDS-PAGE Protocol]]
+*[[Running a Cobalt Affinity Column]]
+*[[Dialysis]]
+*[[Centrifugal Protein Concentration and Buffer Exchange]]
+*[[Using the Stirred Cell Concentrator]]
+''Data Collection''
+*[[Gap Sampling]]
+*[[Water Suppression with presaturation pulses (zgpr/zgcppr]]
+*[[Non-uniform Sampling]]
+*[[Collecting a 15N Edited HSQC]]
+*[[Collecting CEST Data]]
+''Data Processing and Analysis''
+*[[Analysis of 1D Line-Broadening Screen]]
+*[[FastModelFree]]
+*[[2D NMR Analysis (CCPNMR)]]
+*[[1H NMR Analysis (SIMCA)]]
+*[[1H NMR Analysis (ACDLab)]]
+*[[Processing CEST Data]]
+*[[Titration Data Analysis in nmrPipe]]
+*[[Non-Uniform Sampling]]
+*[[Chara]]
+*[[2D NMR Processing in Linux and Windows]]
+*[[2D Metabolomics NMRPipe Processing]]
+*[[1D NMR Processing in Linux and Windows Example Script]]
+*[[NMR Batch Correction Example Script]]
+*[[PCA Classify Example Script]]
+*[[Sample Collection and Processing for Protein Backbone Assignments]]
+*[[Example Scripts for NMRPipe Processing]]
+''Miscellaneous''
+*[[Agarose Gel]]
+*[[700 MHz NMR checklist]]
+*[[500 MHz NMR checklist]]
+*[[1D Macro]]
+*[[Setting Up a Virtual Screen with AutoDock]]
+*[[Simple Protein Crosslinking]]
+*[[1D NMR Titrations]]
+*[[Setting Up & Running MD Simulations]]
+*[[Analyzing MD Simulations]]
+*[[iRed Analysis of MD Simulations]]
+Cell Culturing
+*[[Cell Culturing Dr. Franco Lab]]
+''Metabolomics''
+*[[Metabolite Extraction]]
+*[[MetPa for metabolomics]]
+*[[Making Heatmaps]]
+*[[One way ANOVA in R]]
+*[[P-Value adjustment for multiple comparisons]]
+*[[PCA-Utils]]
+*[[NMR Tube Deep Cleaning]]
+*[[Noise Removal for PCA]]
+*[[Weighted Linear Least Squares]]
+*[[Serum Preparation for 1D NMR]]
+*[[Whole Blood Preparation for 1D NMR]]
+*[[Urine Preparation for 1D NMR]]
+*[[Cell Culture Preparation for 1D NMR]]
+*[[LC-MS metabolomics guide-CIBC collaborations]]
+''Demos''
+*[[Peroxide Clock]]
+*[[Traffic Light Reaction]]
+*[[Orange Juice Clock]]
+*[[Gummy Bear Freeze]]
+*[[Lava Lamps]]
+*[[Women in Science: Checklist]]
+*[[Maxey Day: Checklist]]
+-->