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Category:Protocols

2021-01-21T21:26:59Z

Isintuna:

''General Maintenance''
*[[Changing the high pressure dewar]]
*[[Filling a Magnet with Nitrogen]]
*[[Autoclaving Laboratory Glassware and Media]]
*[[Chemical Disinfection of Glassware]]
*[[Requesting Balance Calibration]]
*[[Requesting Pipette Calibration]]
*[[Using the UV-Vis]]
*[[Using and Maintaining pH Meter]]
*[[-80 Freezer Storage and Maintenance]]
*[[Freeze Dryer Maintenance]]
*[[Lab Notebook Guidelines]]
*[[Sample Barcoding]]

''Protein Preparation''
*[[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]]

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]]

2D NMR Processing in Linux and Windows

2021-01-21T21:24:31Z

Isintuna: Created page with "'''Processing in Linux:''' After all data is transferred from Gambrinus into desired folder on Z Drive - open your desired sample folder. For all commands, do not type "". Ev..."

'''Processing in Linux:'''

After all data is transferred from Gambrinus into desired folder on Z Drive - open your desired sample folder. For all commands, do not type "". Everything within "" is command.

1. Building Fid
*a. Right click and select "Open terminal here" and type “bruker” in terminal
*b. Make sure that you are….
**i. 2D, mode = states, acquisition mode: x=DQD y=Echo-Antiecho
*c. Click "Read Parameters"
*d. Update script (do this after you have read the parameters and nothing is highlighted in yellow)
*e. Save script
2. In terminal
*a. Type “./fid.com” this runs the script
*b. Type “./hsqcproc.com”
*c. Type “nmrDraw” -- this opens NMR draw
*d. Go File --> select file --> hsqc_1.ft2 --> read & draw (the blue = positive, the red = negative or noise)
*e. Then go draw --> estimate noise --> continue --> draw
*f. Use the factor +/- feature to play with noise to get a good level and find the TMSP peak in the upper right corner.
*g. When you locate the TMSP peak, then go mouse --> 2D Location --> z --> right click (this zooms in) --> L --> shift C or file --> calibrate axis --> new ppm value = 0.00 --> apply --> save --> continue x2 --> follow same steps for the y-axis --> f to zoom out
3. Phase it: H gives hydrogen axis, V gives carbon axis. You can access each by pressing H or V key on keyboard.
*a. Play with PO and P1 for both until looks phased. (This is when the yellow quadratic shapes are even on both sides). Make sure this is true for two or so peaks for carbon and hydrogen. Make sure to write down the PO and P1 for each.
4. In Terminal
*a. Type “vi hspqcproc.com”
*b. Type “i” to edit and edit values. Replace PO and P1 values to the manual ones calculated.
*c. Press the escape key and type “:wq!” and enter
*d. Type “./hsqcproc.com”
*e. Type nmrDraw and select file (instructions above) and check to make sure phasing is still accurate. If not, repeat step 3 and 4.
5. Copy "fid.com" and "hsqcproc.com" files into all sample folders and phases all samples.
6. Once all fid files are phased (should be one per sample – best to rename HSQC_1.ft to number related to sample) you need to convert to .nv file
*a. Create a processed folder and put all phased HSQC_.ft files in folder. MAKE SURE ALL FILE NAMES HAVE THE SAME # OF CHARACTERS OR NEXT STEP WILL NOT WORK PROPERLY.
*b. Copy and paste a “./addNMR3.com” file to folder. This can be found in other processed folders. Right click and select "open terminal here"
*c. In the terminal type “./addNMR3.com”
6. Once all files are converted to .nv files, copy and paste results.nv info nvoutput file and reboot in windows.

'''Processing Spectra in Windows:'''

1. First open NMRViewJ
*a. Datasets --> open and draw --> open the processed folder you want --> select reults.nv file --> open
*b. Play around with the contour buttons (blue and red arrow at top) to make sure contour is just before noise level
*c. Right click --> attributes --> peak pick --> pick --> delete all peaks in water line and those not on the diagonal. Keep the TMSP peak labeled for reference Use the red and black cross hairs to do this.
*d. Right click --> attributes --> list --> select results --> close
*e. In toolbar, Peak --> show peak table --> peak --> edit --> compress and degap --> okay
*f. In toobar, Analysis --> rate analysis --> in prefix matrix type “Final_” --> check autofit --> click load time file --> open processed folder you want --> select nvoutput folder you working in --> select rate.txt --> open --> measure all (should have as many T columns as number of spectra) --> save table --> title “peak intensities” --> close (If you recieve error message after clicking "measure all" try opening all "Final_.nv" spectra and try again.)
*g. Peak --> file --> write list --> open nvoutput file your working with --> title “peak list” --> close
2. Open an Excel workbook page
*a. Open processed folder your working in, open nvoutput and drag both peak intensities and peak list into excel workbook. Each will generate its own document in excel. Save as "peak list" and "peak intensities" excel workbook document.

The remaining steps only work in the Excel workbook documents.

*b. In peak list, select all --> data --> text to columns --> select delimited and hit next --> select tab and space and hit next --> press and next and finish
*c. Insert a column B and C in peak intensities, copy and paste 1H.W and 13C.W from peak list respectively.
*d. Save all work!

'''Metabolite Assigning'''

1. In a web browser, type http://prime.psc.riken.jp/. Click on "SpinAssign"

2. Copy and paste 1H.W and 13C.W into query peaks box. Make sure 1H.W is the left hand column.
*a. 1H tolerance = 0.08, 13C tolerance = 0.25, Solvent = H20/KPi. Make sure spectrum type is ([1H,13C]-2D)
*b. Click “dospinassign” --> at the bottom of the page, click get the "result at tab delimited" --> step in box --> control A (selects all) --> control C (copies all) --> paste in peak intensities workbook in additional sheet
*c. About ¾ down the page of the PRIMe: SpinAssign webpage, follow the same steps from b from above. This will give same info in another format for checks and balances when assigning metabolites.

'''Tips for assigning metabolites:'''

1. Find peaks that have unique metabolites (peak with one metabolite assigned to them)

2. Verify that those peaks exist
*a. For E. Coli --> check the E. Coli Metabolome datebase (http://ecmdb.ca/)
3. Go through and categorize Nucleic Acids, Fatty Acids, Amino Acids, etc and continue labeling from the categories.

Category:Protocols

2021-01-21T21:20:48Z

Isintuna:

''General Maintenance''
*[[Changing the high pressure dewar]]
*[[Filling a Magnet with Nitrogen]]
*[[Autoclaving Laboratory Glassware and Media]]
*[[Chemical Disinfection of Glassware]]
*[[Requesting Balance Calibration]]
*[[Requesting Pipette Calibration]]
*[[Using the UV-Vis]]
*[[Using and Maintaining pH Meter]]
*[[-80 Freezer Storage and Maintenance]]
*[[Freeze Dryer Maintenance]]
*[[Lab Notebook Guidelines]]
*[[Sample Barcoding]]

''Protein Preparation''
*[[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]]
*[[NMRFAM-SPARKY: Automated Peak Assignment]]
*[[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]]

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]]

Non-Uniform Sampling

2021-01-21T21:19:20Z

Isintuna: Created page with "This page details how to get started collecting decent-quality nonuniformly sampled (NUS) NMR datasets. = Schedule creation = For two-dimensional (2D) NMR datasets, determini..."

This page details how to get started collecting decent-quality nonuniformly sampled (NUS) NMR datasets.

= Schedule creation =
For two-dimensional (2D) NMR datasets, deterministic Sine-Burst sampling (''a.k.a.'' SB) is recommended, as it has a lower average IST reconstruction error than pseudorandom Poisson-Gap sampling (''a.k.a'' PG).

== Deterministic Sine-Gap ==
There's an easy web interface for ''dgs'', [http://bionmr.unl.edu/dgs.php located here]. Also, the ''dpg'' program is available in the path on our cluster, so you can run it from Linux/PuTTY without issues, like so:

dpg 50 512

Since printing the numbers to the screen is fairly useless, you can write a schedule like so:

dpg 50 512 > sched-10-512

In the ''dpg'' command, the first value is the number of points to sample in the schedule, and the second value is the total number of complex points in the uniform (reconstructed) dataset.

== Pseudorandom Poisson-Gap ==
The Wagner group hosts an online PG schedule generator [http://gwagner.med.harvard.edu/intranet/hmsIST/gensched_new.html here].

= Data collection =
Once you've generated a schedule, you'll need to set up an experiment in Topspin that uses that new schedule file. On the spectrometer PC, copy the schedule file into the directory that contains variable counter lists:

cp -iv /path/to/my/schedule/file /opt/topspin3.2.6/exp/stan/nmr/lists/vc/

Now, open Topspin and create a new experiment. Set '''FnTYPE''' to ''non-uniform sampling'', set '''TD(F1)''' to the number of total complex data points that you used to build your schedule, and set '''NUSLIST''' to the filename of your schedule that you just placed in the '''vc''' directory. (''e.g.'' it would be '''file''' for the above example copy statement)

'''CAUTION!''' NEVER click ''Calculate'' or ''Show table'' once you've set the '''NUSLIST''' parameter. Doing so will blow away your carefully crafted Poisson-Gap schedule file, turning it into a useless uniform-random schedule file.

= Data processing =
This section describes the reconstruction and processing of NUS data using hmsIST and nmrPipe. If you want to use different software packages, you'll have to look elsewhere for documentation.

== Format conversion ==
Converting from the Bruker binary format into the nmrPipe format works exactly as before, with the exception that the number of complex points in any nonuniformly sampled dimension must reflect the number of ''sampled'' points, not the number of ''total'' points. The following script should serve as an example:

#!/bin/bash
# fid.sh: generated as usual from `bruker’

bruk2pipe -in 1/ser \
-bad 0.0 -aswap -DMX -decim 2200 -dspfvs 20 \
-grpdly 67.986083984375 \
-xN 8192 -yN 100 \
-xT 4096 -yT 50 \
-xMODE DQD -yMODE Echo-AntiEcho \
-xSW 9090.909 -ySW 29239.766 \
-xOBS 700.213 -yOBS 176.081 \
-xCAR 4.700 -yCAR 75.000 \
-xLAB 1H -yLAB 13C \
-ndim 2 -aq2D States \
-out 1/hsqc.fid -verb -ov

The above dataset was collected by sampling 50 complex data points from a Nyquist grid having 512 complex points. (''i.e.'' the '''TD''' field in Topspin for 13C was set to 1024)

== Direct-dimension processing ==
Processing the uniformly sampled direct dimension proceeds just like you'd expect, so the '''proc1.sh''' script is basically the top half of the '''proc.sh''' script used to process uniformly sampled data.

#!/bin/bash
# proc1.sh: basically the first half of proc.sh

nmrPipe -in 1/hsqc.fid | \
nmrPipe -fn SOL | \
nmrPipe -fn SP -off 0.45 -end 0.98 -pow 2 | \
nmrPipe -fn ZF -auto | \
nmrPipe -fn FT | \
nmrPipe -fn PS -p0 -43.0 -p1 0.0 -di \
-verb -ov -out 1/hsqc.nus

The output file, ''1/hsqc.nus'' will be processed in the direct dimension only. It's important to open up the ''1/hsqc.nus'' file in nmrDraw to check that the first slice is phased properly before proceeding to the next step.

== Reconstruction ==
Once the direct dimension is processed, the nonuniformly sampled indirect dimension may be reconstructed. The following script shows how to take the ''hsqc.nus'' file generated in the previous step and reconstruct the complete dataset into ''hsqc.ft1'':

#!/bin/bash
# procR.sh: reconstruction of the full Nyquist grid

nmrPipe -in 1/hsqc.nus | \
nmrPipe -fn TP | \
hmsIST \
-ref 0 \
-vlist 1/nuslist \
-xN 512 \
-itr 500 \
-user 1 \
-verb 0 > \
1/hsqc.ft1

The most important options you'll need to edit will be the '''xN''' (number of complex total points) and '''itr''' (number of reconstruction iterations) flags. Just about everything else can always remain the same.

== Indirect-dimension processing ==
Once reconstruction is complete, you can process the indirect dimension in nmrPipe as you normally would. The following script, which should look eerily like the bottom half of the uniform ''proc.sh'', does exactly that:

#!/bin/bash
# proc2.sh: basically the second half of proc.sh

nmrPipe -in 1/hsqc.ft1 | \
nmrPipe -fn SP -off 0.45 -end 0.98 -pow 2 -size 512 -c 0.5 | \
nmrPipe -fn FT | \
nmrPipe -fn PS -p0 -90.0 -p1 0.0 -di | \
nmrPipe -fn TP \
-verb -ov -out 1/hsqc.ft2

P-Value adjustment for multiple comparisons

2021-01-21T21:18:18Z

Isintuna: Created page with "Having a set of p-valued and adjust them for multiple comparisons * Read the file in R: metab <- read.csv("sample.csv", header=F) <br> * Change the data to matrix and then..."

Having a set of p-valued and adjust them for multiple comparisons
* Read the file in R:
metab <- read.csv("sample.csv", header=F) <br>
* Change the data to matrix and then to vector (N.B the p.adjust function only works with vector)
metab <- data.matrix(metab)
metab <- as.vector(metab)

*Adjust the p-value: load the p-value and decide the method

padj <- p.adjust(metab, method= "fdr")

'''N.B:''' The adjustment methods include the Bonferroni correction ("bonferroni") in which the p-values are multiplied by the number of comparisons. Less conservative correction are also included by Holm (1979) ("holm"), Hochberg (1988) ("hochberg"), Hommel (1988) ("hommel"), Benjamini & Hochberg (1995) ("BH" or its alias "fdr"), and Benjamini & Yekutieli (2001) ("BY"), respectively. A pass-through option ("none") is also included. The set of methods are contained in the p.adjust.methods vector for the benefit of methods that need to have the method as an option and pass it on to p.adjust.

For detailed information read:
https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html

NMR Tube Deep Cleaning

2021-01-21T21:13:59Z

Isintuna: Created page with "1. Empty all contents from dirty NMR tubes into appropriate residue container. Remove the labels on the NMR tube by rinsing with ethanol. 2. Fill the container outside the pr..."

1. Empty all contents from dirty NMR tubes into appropriate residue container. Remove the labels on the NMR tube by rinsing with ethanol.

2. Fill the container outside the protect bottles with liquid nitrogen and cool it down.

3. Load the tubes into the tube cleaning apparatus (tube washer) with proper solvents as noted below.

4. The operation of the tube washer:

a)With the left valve closed, slowly and briefly opening the T-valve to the vacuum position evacuates the air from the Labconco®
vacuum bottle and places it under a slight vacuum without removing the solvent.
b)Turn the T-valve to the vent position opens the vacuum bottle to atmosphere breaking the vacuum and forcing solvent into the NMR tube.
c)Switch the T-valve back to the vacuum position places the NMR tubes back under vacuum and remove the solvent from the NMR tube.
d)Repeat the process two or three times effectively washes the NMR tubes with solvent.
e)Switch the T-valve to the vent position and opening the left valve rapidly removes the solvent from the NMR tube cleaner into the
filter flask. The process can be repeated with other solvents.

5. Rinse NMR tubes with nano pure water by filling with water then empty all contents from dirty NMR tubes into appropriate residue container.

6. Rinse NMR tubes with ethanol by filling with ethanol then empty all contents from dirty NMR tubes into appropriate residue container.

7. Rinse NMR tubes with acetone by filling with acetone then empty all contents from dirty NMR tubes into appropriate residue container. The amount of organic solvents should be well-controlled.

8. Fill tubes with nano pure water.

9. Place NMR tubes in a concentrated nitric acid bath and soak 24hrs.

10. Empty contents of NMR tubes into the acid bath.

11. Rinse the NMR tubes under the tap water to remove most of the acid.

12. Load the tubes back to the tube washer.

13. Rinse NMR tubes in baking soda solution to neutralize acid.

14. Rinse NMR tube thoroughly with nano pure water until the solvent waste is neutral.

15. Dry NMR tubes: lay tubes horizontally in the oven.

16. Once dry inspect tubes for any crack, divots or other defect. The tubes with crack on the opening should be collected for further modification and reuse. Other problematic tubes have to be disposed.

[[File:Tubewasher1.jpg]][[File:Tubewasher2.jpg]]

A demonstration video can be found at here [http://bionmr.unl.edu/files/misc/tubewasher-instructions.wmv]

Category:Protocols

2021-01-21T21:12:03Z

Isintuna:

''General Maintenance''
*[[Changing the high pressure dewar]]
*[[Filling a Magnet with Nitrogen]]
*[[Autoclaving Laboratory Glassware and Media]]
*[[Chemical Disinfection of Glassware]]
*[[Requesting Balance Calibration]]
*[[Requesting Pipette Calibration]]
*[[Using the UV-Vis]]
*[[Using and Maintaining pH Meter]]
*[[-80 Freezer Storage and Maintenance]]
*[[Freeze Dryer Maintenance]]
*[[Lab Notebook Guidelines]]
*[[Sample Barcoding]]

''Protein Preparation''
*[[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]]
*[[NMRFAM-SPARKY Guide]]
*[[NMRFAM-SPARKY: Automated Peak Assignment]]
*[[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]]

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]]