Powers Wiki - User contributions [en]

Adding user accounts

2019-08-02T20:38:28Z

Eriekeberg: /* Setting up basic credentials */

When new group members join, they'll need access to our file and program server on both Windows and Linux, and a few odds and ends. Here's how to get that done the right way.

'''FIRST:''' Have the user decide on a username and password that they will re-enter continuously during this process. They will be denoted as ''new_username'' and ''new_password'' throughout this set of instructions.

= Linux =
== Setting up basic credentials ==
* Log in '''as root''' to the cluster head node, either ''via'' SSH or at the machine.
* Add the user account:

useradd -g powers -m -s /bin/bash ''new_username''

* Add a password to the new account:

passwd ''new_username''

* Add a Samba password to the new account:

smbpasswd -c /etc/samba/smb.conf -a ''new_username''

* Add an Apache password to the new account:

htpasswd /etc/apache2/htpasswd ''new_username''

* Allow the user to log in ''via'' secure shell:

sed -e 's,^$AllowUsers$,\1 ''new_username'',' -i /etc/ssh/sshd_config

* Add a couple lines to the bash config:

echo 'source /opt/bashrc' >> /home/''new_username''/.bashrc
echo 'source /opt/bashrc' >> /home/''new_username''/.bash_profile

* Now create a secure shell asymmetric key pair for the user:

su -l ''new_username''
ssh-keygen -t rsa -b 4096
exit

(Use the default file in which to save the key)

== Archiving the credentials ==
* Log in '''as root''' to the cluster head node, either ''via'' SSH or at the machine.
* Physically plug the sysadmin flash drive into the cluster head node.
* Mount the sysadmin flash drive:

mount /dev/sdc1 /mnt/flash

* Navigate into the flash drive:

cd /mnt/flash/admin-tools/linux/workstations

* Add the user into the sub-scripts:

echo ''new_username'' >> bashrc/users.lst
echo ''new_username'' >> passwd/users.lst

* Copy the passwd/shadow information:

grep ^''new_username'' /etc/passwd >> passwd/etc_passwd
grep ^''new_username'' /etc/shadow >> passwd/etc_shadow

* Copy the secure shell key pair:

mkdir ssh-rsa/clients/''new_username''_bionmr
cp /home/''new_username''/.ssh/id_rsa* ssh-rsa/clients/''new_username''_bionmr/

* Unmount the sysadmin flash drive:

cd
umount /mnt/flash

= Windows =
== Creating the account ==
* Log in to the user's workstation on an existing account, and use the Control Panel to create a new '''Administrator account'''.
* Add a password to the newly created account. Make sure the user can remember their password.
* Log out and back into the new account.

== Setting up the network drive ==
* Open Windows Explorer (''not'' Internet Explorer) and click on '''Computer'''
* Click on '''Map Network Drive'''
* Type ''\\bionmr\DATA'' into the '''Folder:''' entry
* Click on '''Finish'''

== Setting up the PuTTY key ==
Using PuTTY to log into the secure linux shell from a Windows workstation requires a PuTTY-format private key (''*.PPK'') to be made. If the key has been made already and saved to the sysadmin flash drive, then you can skip the generation step. If not, proceed in order.

=== Creating the PuTTY key for the first time ===
* Insert the sysadmin flash drive into the user's computer, in Windows
* '''DO NOT CLEAN OR REPAIR OR FIX OR FORMAT THE FLASH DRIVE'''
* Open then PuTTYgen program and click on '''Conversions''', then '''Import key'''
* Open the following file from the flash drive:

admin-tools/linux/workstations/ssh-rsa/clients/''new_username''_bionmr/id_rsa

* Type the user's password to unlock the key file
* Click on '''Save private key''' and save to the following file:

admin-tools/linux/workstations/ssh-rsa/clients/''new_username''_bionmr/id_rsa.ppk

* All done here!

=== Installing the PuTTY key ===
* Insert the sysadmin flash drive into the user's computer, in Windows
* '''DO NOT CLEAN OR REPAIR OR FIX OR FORMAT THE FLASH DRIVE'''
* Copy the following file from the flash drive:

admin-tools/linux/workstations/ssh-rsa/clients/''new_username''_bionmr/id_rsa.ppk

* ... and save it to:

C:\Users\''new_username''\

* Open PuTTY and type''new_username''@bionmr.unl.edu in the '''Host Name''' entry
* Type ''new_username''@bionmr.unl.edu inthe '''Saved Sessions''' entry
* In the left pane, expand '''SSH''' and click on '''Auth'''
* Click '''Browse...''' and open the PuTTY private key you just copied from the flash drive
* In the left pane, click on '''Session'''
* Click on '''Save''' to save the session information
* All done here!

=Wiki=
== Adding New Users ==
*New Users can be added using the administrator account "wiki administrator". The SysAdmin has the password.
*There will an "add new user" button at the top of the page.

[[Category:Sysadmin]]

Installing workstations

2019-08-01T15:39:51Z

Eriekeberg:

Workstations in the group are 64-bit (a.k.a. ''x86_64'' or ''amd64'') machines set up to run both Windows 7 and one of the many various flavors of Linux. When you came into the group, odds are a preconfigured workstation was placed in front of you, ready to rock. But how was it configured, you ask? Read on...

'''FIRST''', I recommend that you read this like a book, a manual of steps that you will follow in linear order. Failure to do so will make things difficult, if not impossible.

'''Second''', please understand that this process never goes the same way on any two workstations. I can't prepare you for every tiny little problem you may run into, but only set the most important, critical steps before you as a skeletal framework. Good luck, starfighter.

-Eli

= Beginning =
It should be fairly obvious that you'll need an assembled PC to work with. Not so obvious is the software you'll need:

* Windows 10 x64
* Opensuse Tumbleweed x86_64 (or another distro if you are feeling dangerous)

Other than operating system discs/ISOs, you'll need the following Windows software:

* Microsoft Office 32-bit (can be downloaded by users after setup through their husker email)
* CorelDRAW Graphics Suite X4
* EndNote X8 (These have machine-specific license keys! Ask the sysadmin if you need access to one.)

Finally, you'll need the administrator flash drive. You know the drive of which I speak. Keep it secret. Keep it safe. It is precious and holds the key to vast untold riches. And possibly, graduation.

= Windows =
This section details installing the Windows 7 OS and software.

== OS ==
Place the Windows 7 DVD into the drive and reboot the system. This will require the BIOS to be configured to boot optical discs before the hard drive. Once the prompt comes up, choose 'Install now'. Accept the license agreement and choose 'Custom' on the next screen.

You should now arrive at a screen that shows the [[:Wikipedia:Disk_partitioning|current partition state]] of the drive. First, click on 'Drive options (advanced)'. If partitions exist, delete them by selecting the partition in the list and then clicking 'Delete'. Now, click 'New' and enter a partition size (in MB) that equals about half the total drive space. It doesn't have to be exact; the partitioner will round to the nearest sector anyways. The installer will give you some garbage about creating extra special partitions for Windows system files, and that's fine. Once the Windows partition was made, proceed.

All the other options (time zone, language, etc.) will be self-explanatory. For automatic updates, choose 'Use recommended settings'. The installer will at some point ask for a user account and password; make this your cluster username and password, or the cluster username and password of whoever will use the system most.

== Updates ==
Once you've logged into your account, don't think that Windows is installed. It will need at least two hours of babysitting while it installs the largest pile of updates you've ever witnessed. You will repeat the following process until no more updates exist:

# Click on the Windows icon (for old-timers, that's the 'Start' button)
# Click on 'Control Panel'
# Click on 'System and Security'
# Click on 'Check for Updates' under the 'Windows Update' heading
# Click on 'Check for Updates' in the left-hand pane
# Install all available updates
# Restart the computer after updates install
# Go back to Step 1.

Patience, grasshopper.

== Configuration ==
You will have to configure a few things in Windows.

=== Power management ===
In ''Control Panel => System and Security => Power Options'', select '''High performance''' from the list. You may have to click 'Show additional plans' to see this option.

=== Remote desktop access ===
In ''Control Panel => System and Security => System'', select ''Remote settings'' in the left-hand pane. Under 'Remote Desktop', select ''Allow connections only from computers running Remote Desktop with Network Level Authentication (more secure)''.

== Software ==
Typical members of this group need a plentiful plethora of packages installed onto their Windows systems in order to function as researchers. Here's what you'll need to install:

* Google Chrome
* Anti-virus
* Adobe Reader
* Microsoft Office
* EndNote X4
* CorelDRAW X4
* ChemDraw
* ACD/NMR 12
* Java
* NMRViewJ
* PuTTY
* Brother LaserJet drivers
* Brother Color Laser drivers

=== Chrome ===
Open Internet Explorer. Click the Stop button about a billion times until IE actually stops loading the page. Navigate to [http://www.google.com Google]. Take Google up on its recommendation to download Chrome. The rest is cake.

=== Anti-virus ===
Open Chrome and navigate to [http://is.unl.edu is.unl.edu]. Under 'Quick Picks', click on 'Anti-virus'. Click on 'DOWNLOAD HERE'. Click on 'WINDOWS 64bit Version'. The rest is cake.

=== Adobe Reader ===
Open Chrome and navigate to [http://get.adobe.com/reader get.adobe.com/reader]. The rest is cake.

=== Microsoft Office ===
Insert the Office DVD and select 'Run autorun.exe' when the popup comes up. The rest is cake.

=== EndNote X4 ===
Make sure any Microsoft Office programs are ''closed''. Insert the EndNote X4 CD and select 'Run autorun.exe' when the popup comes up. The rest is cake. Now, restart Windows and log back in. Then, open Microsoft Word. Click on 'EndNote X4' in the top bar. Then click on 'Go to EndNote'. If you get the message, ''Invalid Class String'', then go [http://help.thomson.com/default.asp?portalid=tsc&refid=TS_ENCWYWFAQ13 here] to find the solution.

=== CorelDRAW X4 ===
Insert the CorelDRAW DVD and follow the steps. The rest is cake.

=== Chemdraw ===
Point your web browser to sitelicense.cambridgesoft.com. When the page loads, go to the link for University of Nebraska, Lincoln and enter your huskers email address. You should then be able to download the software. The activation key should be sent to your email almost immediately.

=== ACD/NMR 12 ===
ACD Labs offers a free version of their 1D and 2D NMR processor software for academics. Open Chrome and navigate to [http://www.acdlabs.com/resources/freeware/nmr_proc/index.php this address], then click 'Download'. You'll need to set up a user account to download the software. Once you've got the installer downloaded, just run it and follow the steps. Yep, the rest is cake.

Alternatively, you should be able to run '''nmrproc_academia12.exe''' from '''Z:\bworley\admin\software''' without having to download anything or make any accounts.

=== Java ===
Open Chrome and navigate to [http://www.java.com/en/download/index.jsp this address]. Click on 'Free Java Download' and follow the steps. Cake.

=== NMRViewJ ===
This software is now non-free, but we have the last/latest available free version on the cluster. Run '''nvjinstall8_0_3.exe''' in '''Z:\bworley\admin\software\nmrviewj''' and follow the steps. Cake.

=== PuTTY ===
Best for last! Open Chrome and navigate to [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html this address]. Click on '''putty-0.62-installer.exe''' to download the installer. Run the installer; all the default options are fine.

Once PuTTY is installed, you'll need to insert the administrator flash drive. In the flash drive, go to '''ssh-rsa\clients\myusername''', where ''myusername'' is the cluster username that you're setting the computer up for. In that directory, there is an '''id_rsa.ppk''' file. Copy that file somewhere that only the current user has read access to, such as '''C:\Users\myusername'''. Now, open PuTTY and type ''myusername@bionmr-c1.unl.edu'' into both the 'Host Name' and 'Saved Sessions' text boxes. In the left-hand pane, click the plus sign next to 'SSH' and click on 'Auth'. Click 'Browse' and open the '''id_rsa.ppk''' file in the location you copied it to. Finally, click back to 'Session' in the left-hand pane and click 'Save' under 'Saved Sessions'.

You're ready to rock. Return the administrator flash drive to its sacred resting place.

=== Brother printer drivers ===
The Brother printer driver CDs are available in the lab office. Use those CDs to install drivers (only drivers, no software suites) for the two Brother printers outside the office. The IP addresses of the printers will be requested by the installer software; you can get those addresses by printing off the ''printer status'' information from each printer via their front panel buttons.
NOTE: If you try to discover the printers over the network and none are found, try temporarily disabling your firewalls. After the printer is installed, you should be able to bring the firewall back up without affecting the printer.

= Linux =
This section details installing and configuring the Linux OS.

== OS ==
Insert the Debian DVD and reboot the computer. When the Debian boot prompt comes up, press the Tab key, type '''desktop=xfce''', and hit enter. Most of the options will be self-explanatory until you get to the partitioning. You will select ''Use custom layout'' and click next.

The partitioning of linux systems in the group is done as follows:

* 128 MB of ext2 mounted on /boot (made at the beginning of the free space)
* All remaining space allocated as ext4 and mounted on '''/'''
* 2048 MB of swap (made at the end of the free space)

Make the partitions in the above order. After making the boot partition, subtract 2048 MB from the remaining free space to get the size of the '''/''' partition. Then use the rest of the free space (about 2048 MB, but it will rarely be exact) as swap.

You should now have a partitioning scheme that spans the entire disk that looks something like this:

* '''sda1:''' Windows system files (few hundred MB)
* '''sda2:''' Windows partition (few hundred GB, about half the drive)
* '''sda3:''' Linux boot partition (128 MB)
* '''sda4:''' Extended partition
* '''sda5:''' Linux root partition (few hundred GB, about half the drive)
* '''sda6:''' Linux swap partition (roughly 2048 MB)

Everything else will be much more self-explanatory, and the defaults are A-OK for almost all the other options.

== Configuration ==
You will have to configure the system a bit more to get it talking with the cluster and running properly. Once the system boots up, use '''Ctrl'''+'''Alt'''+'''F1''' to navigate to the terminal and log in as root. Once you're logged in, insert and mount the system administrator flash drive, like so:

mkdir /mnt/flash
mount /dev/sdb1 /mnt/flash

Where the above example assumes that ''/dev/sdb1'' is the flash drive device node. Once mounted, run the following commands:

cd /mnt/flash/admin-scripts/linux/workstations
./run

The script will ask if you're ready to proceed. As long as everything above went OK, it's safe to say 'yes' here. Hopefully, the script will complete without errors and your linux workstation will be properly configured. Unmount the flash drive:

cd
umount /mnt/flash
reboot

[[category:Sysadmin]]

Cluster Maintenance

2019-07-23T17:39:10Z

Eriekeberg:

= Hardware =
The cluster was built from parts ordered from [http://www.newegg.com Newegg]. The important components of the system are as follows:

* '''PSU:''' ''(1x)'' Corsair RM850 850W 92% Efficiency Active-PFC
* '''Mobo:''' ''(1x)'' Gigabyte GA-EP45-UD3P (rev 1.1)
* '''CPU:''' ''(1x)'' Intel Core 2 Quad Q8300 2.5GHz
* '''RAM:''' ''(4x)'' Corsair XMS2 DDR2 800 (PC2 6400) 2GB
* '''Gfx:''' ''(1x)'' NVIDIA GeForce 9500 GT PCI-E 2.0 x8
* '''RAID:''' ''(1x)'' 3ware 9650SE-4LMPL PCI-E 2.0 x1
* '''RAID:''' ''(4x)'' WD 1TB 7200RPM SATA-II HDD

= Operating System =
The cluster currently runs Debian 8.0 ''amd64''. The recommended method of installing the base operating system is to download the ''Small CD'' ISO from [http://www.debian.org/distrib/netinst Debian] and burn it to a CD/DVD.

The (MBR) partitioning of the main 1TB disk should be:

{|
| Num. || Size || Filesystem || Mount point
|-
| 1 || 256 MB || ext2 || /boot
|-
| 2 || 317 GB || ext4 || /
|-
| 3 || 2.5 GB || swap || swap
|}

The 2.7TB RAID5 array should ''already be partitioned'' (GPT). '''At all costs, maintain the integrity of the data already contained on the RAID5 array.''' Keep frequent backups of the array to at least one external source.

Other important settings to choose during the installation are summarized below:
FIXME

= Software =
The software on the cluster consists of packages installed through the Debian repositories and third-party software installed into '''/opt'''. It is highly recommended that the software in this section be installed in the order it is listed here, if possible.

== Debian Packages ==
Install Debian packages before third-party software, if at all possible. Many of these commands will require mounting the administrator flash drive, in which case this documentation assumes it will be mounted to '''/mnt/flash'''.

=== Initial configuration ===
We don't want all the ports on our precious cluster to be out there flapping in the breeze. Install some files that loosely restrict which daemons can provide services to which addresses:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.allow /etc/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts.deny /etc/

Install a file that defines WAN and LAN IP-hostname mappings:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/hosts /etc/

Add support for hosting both 32-bit and 64-bit packages on this 64-bit system:

dpkg --add-architecture i386
apt-get update

Now install the the following packages using ''apt-get'':

* libc6-i686
* libx11-6:i386
* libxext6:i386

=== The groundwork ===
Some miscellaneous software packages need to be installed as boilerplate. Install the following packages using ''apt-get''...

First, install some required shells:

* tcsh
* bash-completion

Lay down a decent text editor:

* vim

Add a few extra utilities:

* zip
* nmap
* links
* rsync
* screen
* gnuplot
* imagemagick

Now install some more language support:

* pkg-config
* build-essential
* libtool
* texlive
* texi2html
* ruby
* gfortran
* perl

=== Python ===
A few Python packages are standard fare for programmers in the group. Install the following packages using ''apt-get'':

* python3
* python2.7
* python3.2
* python-numpy
* python-sklearn
* python-matplotlib

=== R ===
The R language is useful to some people, I guess.

* r-base
* r-recommended

=== Sudo ===
Install the ''sudo'' package using ''apt-get''. Then add the following line to the '''/etc/sudoers''' file:

%bionmr ALL=(ALL:ALL) ALL

=== OpenSSH ===
The OpenSSH daemon allows users to log into the cluster from anywhere in the world using their RSA private key. First, install the following packages using ''apt-get'':

* openssh-client
* openssh-server

Then install the '''/etc/ssh/sshd_config''' file from the administrator flash drive and restart the SSH daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/ssh/sshd_config /etc/ssh/
service ssh restart

=== NFS ===
The NFS server allows users to access their files on campus from Debian Linux workstations. First, install the following packages using ''apt-get'':

* nfs-kernel-server
* portmap

Then install the '''/etc/exports''' file from the administrator flash drive and restart the NFS daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/exports /etc/
service nfs-kernel-server restart

=== Samba ===
The Samba server allows users to access their files on campus from Windows workstations. First, install the following packages using ''apt-get'':

* cifs-utils
* samba

Then install the Samba configuration and password files and restart the Samba daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/samba/smb.conf /etc/samba/
install -v -m 600 -o root -g root /mnt/flash/admin-tools/linux/cluster/var/lib/samba/passdb.tdb /var/lib/samba/
service samba restart

=== MTA ===
The exim4 package allows the server to send emails out to users about various things emails need to be sent for, and such. Mail transfer agent. You get the idea. Install the following package using ''apt-get'':

* exim4

Next, reconfigure the package using the following commands:

dpkg-reconfigure exim4
chmod +x /usr/sbin/exim4
rm -f /var/log/exim4/paniclog
touch /var/log/exim4/paniclog
service start exim4

You'll want to use the default values for every option during the configuration. Once that's done, you can test that the MTA is working by running the following command:

=== MySQL ===
FIXME

* mysql-client
* mysql-server

=== Apache ===
The Apache server hosts the group website, plain and simple. Install the following packages using ''apt-get'':

* apache2
* apache2-doc

Then install the password file and an updated site configuration file and restart the Apache daemon:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/htpasswd /etc/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/apache2/sites-available/default /etc/apache2/sites-available
service apache2 restart

=== PHP ===
The PHP interpreter is required to host the website using the UNL university style templates. Install the following packages using ''apt-get'':

* php5
* php5-mysql
* php5-sqlite
* libapache-mod-php5

Then download and install Pyrus (PEAR2) using the following commands:

wget http://pear2.php.net/pyrus.phar
install -v -m 644 -o root -g root pyrus.phar /usr/bin/
rm pyrus.phar

Open a new file in ''vi'' called '''/usr/bin/pyrus''' and add the following text:

#!/bin/bash
/usr/bin/php -dphar.readonly=0 /usr/bin/pyrus.phar $*

Save the file and make it executable:

chmod 755 /usr/bin/pyrus

Now run ''pyrus'' for the first time. Tell it ''yes'' to initialize the configuration. Tell it to install packages to '''/usr/share/pear''' by default, when it asks. Now install the UNL template package:

pyrus channel-discover pear.unl.edu
pyrus install -o pear.unl.edu/UNL_Templates-beta

Finally, install updated configuration files for PHP, restart the Apache server and remove the placeholder html page:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/apache2/php.ini /etc/php5/apache2/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/php5/cli/php.ini /etc/php5/cli/
service apache2 restart
rm /var/www/index.html

=== DHCP ===
The cluster LAN is managed by a DHCP server on the second Ethernet port. Install the following package using ''apt-get'':

* isc-dhcp-server
* bridge-utils
* dnsmasq

Install the configuration files for the DHCP server:

install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/dhcp/dhcpd.conf /etc/dhcp/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/default/isc-dhcp-server /etc/default/
install -v -m 644 -o root -g root /mnt/flash/admin-tools/linux/cluster/etc/network/interfaces /etc/network/

Bring up the second Ethernet interface and restart the DHCP server:

ifup eth1
service isc-dhcp-server restart

Run the following commands:

brctl addbr br0
brctl addif br0 eth0 eth1
ifup br0

=== Octave ===
The Octave programming environment provides users with mathematical routines that simplify data handling. Install the following packages using ''apt-get'':

* octave
* liboctave-dev
* octave-audio
* octave-control
* octave-data-smoothing
* octave-fixed
* octave-fpl
* octave-general
* octave-geometry
* octave-image
* octave-io
* octave-linear-algebra
* octave-odepkg
* octave-optim
* octave-optiminterp
* octave-pkg-dev
* octave-plot
* octave-quaternion
* octave-signal
* octave-specfun
* octave-statistics
* octave-strings

== Third-party Software ==
FIXME

[[Category:Sysadmin]]

Category:Protocols

2019-07-23T17:37:18Z

Eriekeberg:

''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/Maintaining pH Meter]]

''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]]
*[[NMR Processing in Linux and Windows]]

''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]]

Cell Culturing
*[[Cell Culturing Dr. Franco Lab]]

''Metabolomics''
*[[MetPa for metabolomics]]
*[[Making Heatmaps]]
*[[Metabolite Extraction]]
*[[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]]
*[[Urine Preparation for 1D NMR]]

''Safety and Inspections''
*[[Lab Responsibilities]]
*[[Inspection Checklist]]
*[[Safety Contacts, Resources]]

''Demos''
*[[Peroxide Clock]]
*[[Traffic Light Reaction]]
*[[Orange Juice Clock]]
*[[Gummy Bear Freeze]]
*[[Batteries]]
*[[Rocket Launcher]]
*[[Women in Science: Checklist]]
*[[Maxey Day: Checklist]]

Category:Protocols

2019-07-23T17:35:43Z

Eriekeberg:

''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/Maintaining pH Meter]]

''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]]
*[[NMR Processing in Linux and Windows]]

''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]]

Cell Culturing
*[[Cell Culturing Dr. Franco Lab]]

''Metabolomics''
*[[MetPa for metabolomics]]
*[[Making Heatmaps]]
*[[Metabolite Extraction]]
*[[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]]
*[[Urine Preparation for 1D NMR]]

''Safety and Inspections''
*[[Lab Responsibilities]]
*[[Inspection Checklist]]
*[[Safety Contacts, Resources]]

''Demos''
*[[Peroxide Clock]]
*[[Traffic Light Reaction]]
*[[Orange Juice Clock]]
*[[Gummy Bear Freeze]]
*[[Batteries]]
*[[Rocket Launcher]]
*[[Women in Science: Checklist]]
*[[Maxey Day: Checklist]]

Category:Protocols

2019-07-23T17:35:17Z

Eriekeberg:

''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/Maintaining pH Meter]]

''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]]
*[[NMR Processing in Linux and Windows]]

''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]]

Cell Culturing
*[[Cell Culturing Dr. Franco Lab]]

''Metabolomics''
*[[MetPa for metabolomics]]
*[[Making Heatmaps]]
*[[Metabolite Extraction]]
*[[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]]
*[[Urine Preparation for 1D NMR]]

''Safety and Inspections''
*[[Lab Responsibilities]]
*[[Inspection Checklist]]
*[[Safety Contacts, Resources]]

''Demos''
*[[Peroxide Clock]]
*[[Traffic Light Reaction]]
*[[Orange Juice Clock]]
*[[Gummy Bear Freeze]]
*[[Batteries]]
*[[Rocket Launcher]]
*[[Women in Science: Checklist]]
*[[Maxey Day: Checklist]]

Category:Protocols

2019-07-23T17:23:57Z

Eriekeberg:

Test

2017-03-15T00:03:09Z

Eriekeberg:

Just a test page.

-Eli

Running SDS-PAGE

2017-03-08T17:20:19Z

Eriekeberg:

[[Category:Protocols]]
[[Category:Protein expression]]

[[File:SDS_PAGE.pdf]]
==Running SDS-PAGE==

#Make ready the samples to run
#Make ready the sample running buffer
#Make ready the gel
#Have the SDS-PAGE apparatus
#Place the the gel in the SDS-PAGE stand
#Place the stand with the gel in the SDS-PAGE apparatus bath
#fill the space between the gels with running buffer
#Take off the combs of the gel (take it out gently)
#Load the sample to each well
#Do not use the wells at the left and right end of the gel
#fill the SDS-PAGE apparatus bath with running buffer to the bottom of the gel
#Place the cover of the SDS-PAGE
## '''N.B''' Make sure the correct plug is connected to the correct electrode (red goes to red and black goes to black)
#Plug the cables to the SDS-PAGE apparatus power source
#Turn of the SDS-PAGE power source
#Set to constant voltage
#Use 200 V
#Press the Run button to start the electrophoresis
## The voltage increases to 200 V from 0 V
##For 4% staking gel and 12.5 % separating gel the current reaches 50-60 mA and the power 10 -12 W
##The current the the power decreases in time but not reach zero (if it reaches zero see the troubleshoot)
##For the state type of gel it takes 35 - 40 min

===Troubleshoot===
#The power drops to zero
* really old buffer
* the space in between the gels is not filled with buffer to the top

File:SDS PAGE.pdf

2017-03-08T17:17:18Z

Eriekeberg: SDS Gel Preparation Protocol from Provost and Wallert. Original Webpage Now Defunct; File Hosted Here until original link can be found.

SDS Gel Preparation Protocol from Provost and Wallert.
Original Webpage Now Defunct; File Hosted Here until original link can be found.

99p

2016-08-16T16:21:27Z

Eriekeberg: Created page with "There a lot of problems that arise whenever you start relying on computers for your work. Here are 99 random problems you'll probably never run into. When you do though, you'..."

There a lot of problems that arise whenever you start relying on computers for your work.

Here are 99 random problems you'll probably never run into. When you do though, you'll be glad you have this list.
Solutions to various problems will be kept here until a more permanent resting place is found.

nmrDraw Troubleshooting:
Having problems with a "segmentation fault" error? Especially if you're on one of the newer workstations?
Try checking your memory limits.
Type "ulimit -a" for information. The number of open files should be set to 1024. You can do this by typing "ulimit -n 1024".
If it is higher, you'll almost always get a segmentation fault. This was first discovered on macs, but it also holds true for linux based systems.
EDIT: "ulimit -n 1024" only works for the currently open terminal window. It will reset as soon as you open a new terminal.
If you want to set this limit permanently, you can add the function to your .bashrc file in your home directory. This will set the limit in every new terminal window you open.

Source: https://beta.groups.yahoo.com/neo/groups/nmrpipe/conversations/messages/2603

Troubleshooting

2016-08-03T16:53:01Z

Eriekeberg:

There a number of problems that you might encounter on your workstation. This page is an attempt to catalog the most commonly encountered problems, and fixes as they are found.

This list is by no means exhaustive, and may not contain a solution for every problem.

Windows
-Mouse and Keyboard Not Working?
--This can happen pretty frequently, especially if you start building new workstations. Most of us use wireless USB keyboards, and newer motherboards have options in their BIOS to enable/disable drivers for USB 3.0 ports. If these options exist, you'll generally want XHCI Hand-off enabled, and EHCI hand-off DISABLED. This is particularly relevant if the keyboard and mouse work in the BIOS and GRUB but not in Windows.
Link: http://superuser.com/questions/770198/should-i-enabled-or-disable-xhci-hand-off-in-bios-setup-when-running-windows-7

Linux

Updates not working Correctly? Check your sources list. Some of us are running Debian 7 (wheezy) and some are on Debian 8 (Jessie). If you notice that updates are not working, or dependencies can't be resolved because of broken packages, it could very likely be your sources list. An excellent discussion can be found on the debian website.
Link: https://wiki.debian.org/SourcesList

Troubleshooting

2016-08-03T16:50:49Z

Eriekeberg: Created page with "There a number of problems that you might encounter on your workstation. This page is an attempt to catalog the most commonly encountered problems, and fixes as they are found..."

Installing workstations

2016-06-16T20:23:03Z

Eriekeberg: /* Software */

Workstations in the group are 64-bit (a.k.a. ''x86_64'' or ''amd64'') machines set up to run both Windows 7 and Debian Linux. When you came into the group, odds are a preconfigured workstation was placed in front of you, ready to rock. But how was it configured, you ask? Read on...

'''FIRST''', I recommend that you read this like a book, a manual of steps that you will follow in linear order. Failure to do so will make things difficult, if not impossible.

'''Second''', please understand that this process never goes the same way on any two workstations. I can't prepare you for every tiny little problem you may run into, but only set the most important, critical steps before you as a skeletal framework. Good luck, starfighter.

= Beginning =
It should be fairly obvious that you'll need an assembled PC to work with. Not so obvious is the software you'll need:

* Windows 7 x64
* Debian 7 x86_64

Other than operating system discs, you'll need the following Windows software discs:

* Microsoft Office 2010 32-bit
* CorelDRAW Graphics Suite X4
* EndNote X4 Media - Windows (These have machine-specific license keys!)

Finally, you'll need the administrator flash drive. You know the drive of which I speak. Keep it secret. Keep it safe.

= Windows =
This section details installing the Windows 7 OS and software.

== OS ==
Place the Windows 7 DVD into the drive and reboot the system. This will require the BIOS to be configured to boot optical discs before the hard drive. Once the prompt comes up, choose 'Install now'. Accept the license agreement and choose 'Custom' on the next screen.

You should now arrive at a screen that shows the [[:Wikipedia:Disk_partitioning|current partition state]] of the drive. First, click on 'Drive options (advanced)'. If partitions exist, delete them by selecting the partition in the list and then clicking 'Delete'. Now, click 'New' and enter a partition size (in MB) that equals about half the total drive space. It doesn't have to be exact; the partitioner will round to the nearest sector anyways. The installer will give you some garbage about creating extra special partitions for Windows system files, and that's fine. Once the Windows partition was made, proceed.

All the other options (time zone, language, etc.) will be self-explanatory. For automatic updates, choose 'Use recommended settings'. The installer will at some point ask for a user account and password; make this your cluster username and password, or the cluster username and password of whoever will use the system most.

== Updates ==
Once you've logged into your account, don't think that Windows is installed. It will need at least two hours of babysitting while it installs the largest pile of updates you've ever witnessed. You will repeat the following process until no more updates exist:

# Click on the Windows icon (for old-timers, that's the 'Start' button)
# Click on 'Control Panel'
# Click on 'System and Security'
# Click on 'Check for Updates' under the 'Windows Update' heading
# Click on 'Check for Updates' in the left-hand pane
# Install all available updates
# Restart the computer after updates install
# Go back to Step 1.

Patience, grasshopper.

== Configuration ==
You will have to configure a few things in Windows.

=== Power management ===
In ''Control Panel => System and Security => Power Options'', select '''High performance''' from the list. You may have to click 'Show additional plans' to see this option.

=== Remote desktop access ===
In ''Control Panel => System and Security => System'', select ''Remote settings'' in the left-hand pane. Under 'Remote Desktop', select ''Allow connections only from computers running Remote Desktop with Network Level Authentication (more secure)''.

== Software ==
Typical members of this group need a plentiful plethora of packages installed onto their Windows systems in order to function as researchers. Here's what you'll need to install:

* Google Chrome
* Anti-virus
* Adobe Reader
* Microsoft Office
* EndNote X4
* CorelDRAW X4
* ChemDraw
* ACD/NMR 12
* Java
* NMRViewJ
* PuTTY
* HP LaserJet drivers
* Dell Color Laser drivers

=== Chrome ===
Open Internet Explorer. Click the Stop button about a billion times until IE actually stops loading the page. Navigate to [http://www.google.com Google]. Take Google up on its recommendation to download Chrome. The rest is cake.

=== Anti-virus ===
Open Chrome and navigate to [http://is.unl.edu is.unl.edu]. Under 'Quick Picks', click on 'Anti-virus'. Click on 'DOWNLOAD HERE'. Click on 'WINDOWS 64bit Version'. The rest is cake.

=== Adobe Reader ===
Open Chrome and navigate to [http://get.adobe.com/reader get.adobe.com/reader]. The rest is cake.

=== Microsoft Office ===
Insert the Office DVD and select 'Run autorun.exe' when the popup comes up. The rest is cake.

=== EndNote X4 ===
Make sure any Microsoft Office programs are ''closed''. Insert the EndNote X4 CD and select 'Run autorun.exe' when the popup comes up. The rest is cake. Now, restart Windows and log back in. Then, open Microsoft Word. Click on 'EndNote X4' in the top bar. Then click on 'Go to EndNote'. If you get the message, ''Invalid Class String'', then go [http://help.thomson.com/default.asp?portalid=tsc&refid=TS_ENCWYWFAQ13 here] to find the solution.

=== CorelDRAW X4 ===
Insert the CorelDRAW DVD and follow the steps. The rest is cake.

=== Chemdraw ===
Point your web browser to sitelicense.cambridgesoft.com. When the page loads, go to the link for University of Nebraska, Lincoln and enter your huskers email address. You should then be able to download the software. The activation key should be sent to your email almost immediately.

=== ACD/NMR 12 ===
ACD Labs offers a free version of their 1D and 2D NMR processor software for academics. Open Chrome and navigate to [http://www.acdlabs.com/resources/freeware/nmr_proc/index.php this address], then click 'Download'. You'll need to set up a user account to download the software. Once you've got the installer downloaded, just run it and follow the steps. Yep, the rest is cake.

Alternatively, you should be able to run '''nmrproc_academia12.exe''' from '''Z:\bworley\admin\software''' without having to download anything or make any accounts.

=== Java ===
Open Chrome and navigate to [http://www.java.com/en/download/index.jsp this address]. Click on 'Free Java Download' and follow the steps. Cake.

=== NMRViewJ ===
This software is now non-free, but we have the last/latest available free version on the cluster. Run '''nvjinstall8_0_3.exe''' in '''Z:\bworley\admin\software\nmrviewj''' and follow the steps. Cake.

=== PuTTY ===
Best for last! Open Chrome and navigate to [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html this address]. Click on '''putty-0.62-installer.exe''' to download the installer. Run the installer; all the default options are fine.

Once PuTTY is installed, you'll need to insert the administrator flash drive. In the flash drive, go to '''ssh-rsa\clients\myusername''', where ''myusername'' is the cluster username that you're setting the computer up for. In that directory, there is an '''id_rsa.ppk''' file. Copy that file somewhere that only the current user has read access to, such as '''C:\Users\myusername'''. Now, open PuTTY and type ''myusername@bionmr-c1.unl.edu'' into both the 'Host Name' and 'Saved Sessions' text boxes. In the left-hand pane, click the plus sign next to 'SSH' and click on 'Auth'. Click 'Browse' and open the '''id_rsa.ppk''' file in the location you copied it to. Finally, click back to 'Session' in the left-hand pane and click 'Save' under 'Saved Sessions'.

You're ready to rock. Return the administrator flash drive to its sacred resting place.

=== Brother printer drivers ===
The Brother printer driver CDs are available in the lab office. Use those CDs to install drivers (only drivers, no software suites) for the two Brother printers outside the office. The IP addresses of the printers will be requested by the installer software; you can get those addresses by printing off the ''printer status'' information from each printer via their front panel buttons.
NOTE: If you try to discover the printers over the network and none are found, try temporarily disabling your firewalls. After the printer is installed, you should be able to bring the firewall back up without affecting the printer.

= Linux =
This section details installing and configuring the Linux OS.

== OS ==
Insert the Debian DVD and reboot the computer. When the Debian boot prompt comes up, press the Tab key, type '''desktop=xfce''', and hit enter. Most of the options will be self-explanatory until you get to the partitioning. You will select ''Use custom layout'' and click next.

The partitioning of linux systems in the group is done as follows:

* 128 MB of ext2 mounted on /boot (made at the beginning of the free space)
* All remaining space allocated as ext4 and mounted on '''/'''
* 2048 MB of swap (made at the end of the free space)

Make the partitions in the above order. After making the boot partition, subtract 2048 MB from the remaining free space to get the size of the '''/''' partition. Then use the rest of the free space (about 2048 MB, but it will rarely be exact) as swap.

You should now have a partitioning scheme that spans the entire disk that looks something like this:

* '''sda1:''' Windows system files (few hundred MB)
* '''sda2:''' Windows partition (few hundred GB, about half the drive)
* '''sda3:''' Linux boot partition (128 MB)
* '''sda4:''' Extended partition
* '''sda5:''' Linux root partition (few hundred GB, about half the drive)
* '''sda6:''' Linux swap partition (roughly 2048 MB)

Everything else will be much more self-explanatory, and the defaults are A-OK for almost all the other options.

== Configuration ==
You will have to configure the system a bit more to get it talking with the cluster and running properly. Once the system boots up, use '''Ctrl'''+'''Alt'''+'''F1''' to navigate to the terminal and log in as root. Once you're logged in, insert and mount the system administrator flash drive, like so:

mkdir /mnt/flash
mount /dev/sdb1 /mnt/flash

Where the above example assumes that ''/dev/sdb1'' is the flash drive device node. Once mounted, run the following commands:

cd /mnt/flash/admin-scripts/linux/workstations
./run

The script will ask if you're ready to proceed. As long as everything above went OK, it's safe to say 'yes' here. Hopefully, the script will complete without errors and your linux workstation will be properly configured. Unmount the flash drive:

cd
umount /mnt/flash
reboot

[[category:Sysadmin]]

Computer station

2016-05-25T17:30:04Z

Eriekeberg: /* Preparation */

At the computer station, students will graph the data points they collected from the Spec20 station and draw three molecular structures. The handout to be given to students is available here: [[File:Maxey_-_Computer_Station_Handout.docx]].

== Preparation ==

''This should be ready the day before)''

* Six to eight laptops should be provided and they are all set in a classroom in the Maxey elementary school.
*Laptops can be checked out from the 501 building; they are general use student laptops. E-mail Wade Felker (Collaboration Technologies Associate with ITS; wfelker2@unl.edu), a week in advance to reserve as many laptops as you need.
* If the laptops don't give you admin access to install software: (Set up an account for Maxey demo for each laptop.)
* Install ChemBioDraw and KaleidaGraph software on each laptop. (We have licenses for both pieces of software; ask Eli.)
* Set up wireless printer/router for each laptop. (You can also set them up as a wired system if all else fails)

== Experiment A - KaleidaGraph ==

KaleidaGraph is used for processing the Spec20 Data. ''(Make sure the students finish the Spec20 experiment before they come to this station.)''

# Click the first white box in the toolbar and you can open an empty spreadsheet with three columns.
# Input the data of concentration and absorbance in column A and B. (Do not input the percentage symbol or the unknown sample absorbance.)
# Go to “Gallery" from the menu, click “linear” then “scattering”, then there is a window popping up. Choose the A column to be the X-axis, B column to be the y-axis and click “new plot” icon down below.
# After you have the plot, change the title to be "Absorbance vs. concentration"
# Go to “file” and click “print graphics”.
# After the students print out their graph, you may want to help them draw a trendline manually using a ruler. Then you can demonstrate determining the concentration of their unknown using this trendline.

== Experiment B - ChemDraw ==

*NOTE: You usually don't have time to get to this station. Use your best judgement, and go on if the students have extra time.

Three molecules will be drawn by using ChemBioDraw: Acetic acid is the main component of vinegar. Acetylsalicylic acid is the active reagent of aspirin. Glucose is the major energy source in our body.

On the left side of the working window, a toolbar contains all the tools that are handy for drawing those molecules, such as single bonds, double bonds, benzene, texting and eraser.

# Find an empty place and draw the first bond by dragging the icon of a bond from the toolbar to that place and loose your mouse.
# Move the mouse to the end of that bond where you want to start another bond or a word (for example, "H" is for proton or hydrogen. "C" is for carbon and "O" is for oxygen).
# After drawing the molecule, use the “lasso” from the toolbar to select the whole molecule, and then go to the menu and select “convert structure to name”. Find out if you do the right thing by comparing the name that the computer tells you with the name you are supposed to draw.

[[Category:Maxey Demos]]

Computer station

2016-05-23T15:55:03Z

Eriekeberg: /* Experiment A - KaleidaGraph */

At the computer station, students will graph the data points they collected from the Spec20 station and draw three molecular structures. The handout to be given to students is available here: [[File:Maxey_-_Computer_Station_Handout.docx]].

== Preparation ==

''This should be ready the day before)''

* Six to eight laptops should be provided and they are all set in a classroom in the Maxey elementary school.
*Laptops can be checked out from the 501 building; they are general use student laptops. E-mail Wade Felker (wfelker2@unl.edu), a week in advance to reserve as many laptops as you need.
* If the laptops don't give you admin access to install software: (Set up an account for Maxey demo for each laptop.)
* Install ChemBioDraw and KaleidaGraph software on each laptop. (We have licenses for both pieces of software; ask Eli.)
* Set up wireless printer/router for each laptop. (You can also set them up as a wired system if all else fails)

== Experiment A - KaleidaGraph ==

KaleidaGraph is used for processing the Spec20 Data. ''(Make sure the students finish the Spec20 experiment before they come to this station.)''

# Click the first white box in the toolbar and you can open an empty spreadsheet with three columns.
# Input the data of concentration and absorbance in column A and B. (Do not input the percentage symbol or the unknown sample absorbance.)
# Go to “Gallery" from the menu, click “linear” then “scattering”, then there is a window popping up. Choose the A column to be the X-axis, B column to be the y-axis and click “new plot” icon down below.
# After you have the plot, change the title to be "Absorbance vs. concentration"
# Go to “file” and click “print graphics”.
# After the students print out their graph, you may want to help them draw a trendline manually using a ruler. Then you can demonstrate determining the concentration of their unknown using this trendline.

== Experiment B - ChemDraw ==

*NOTE: You usually don't have time to get to this station. Use your best judgement, and go on if the students have extra time.

Three molecules will be drawn by using ChemBioDraw: Acetic acid is the main component of vinegar. Acetylsalicylic acid is the active reagent of aspirin. Glucose is the major energy source in our body.

On the left side of the working window, a toolbar contains all the tools that are handy for drawing those molecules, such as single bonds, double bonds, benzene, texting and eraser.

# Find an empty place and draw the first bond by dragging the icon of a bond from the toolbar to that place and loose your mouse.
# Move the mouse to the end of that bond where you want to start another bond or a word (for example, "H" is for proton or hydrogen. "C" is for carbon and "O" is for oxygen).
# After drawing the molecule, use the “lasso” from the toolbar to select the whole molecule, and then go to the menu and select “convert structure to name”. Find out if you do the right thing by comparing the name that the computer tells you with the name you are supposed to draw.

[[Category:Maxey Demos]]

Computer station

2016-05-23T15:53:59Z

Eriekeberg: /* Experiment B - ChemDraw */

At the computer station, students will graph the data points they collected from the Spec20 station and draw three molecular structures. The handout to be given to students is available here: [[File:Maxey_-_Computer_Station_Handout.docx]].

== Preparation ==

''This should be ready the day before)''

* Six to eight laptops should be provided and they are all set in a classroom in the Maxey elementary school.
*Laptops can be checked out from the 501 building; they are general use student laptops. E-mail Wade Felker (wfelker2@unl.edu), a week in advance to reserve as many laptops as you need.
* If the laptops don't give you admin access to install software: (Set up an account for Maxey demo for each laptop.)
* Install ChemBioDraw and KaleidaGraph software on each laptop. (We have licenses for both pieces of software; ask Eli.)
* Set up wireless printer/router for each laptop. (You can also set them up as a wired system if all else fails)

== Experiment A - KaleidaGraph ==

KaleidaGraph is used for processing the Spec20 Data. ''(Make sure the students finish the Spec20 experiment before they come to this station.)''

# Click the first white box in the toolbar and you can open an empty spreadsheet with three columns.
# Input the data of concentration and absorbance in column A and B. (Do not input the percentage symbol or the unknown sample absorbance.)
# Go to “Gallery" from the menu, click “linear” then “scattering”, then there is a window popping up. Choose the A column to be the X-axis, B column to be the y-axis and click “new plot” icon down below.
# After you have the plot, change the title to be "Absorbance vs. concentration"
# Go to “file” and click “print graphics”.

== Experiment B - ChemDraw ==

*NOTE: You usually don't have time to get to this station. Use your best judgement, and go on if the students have extra time.

Three molecules will be drawn by using ChemBioDraw: Acetic acid is the main component of vinegar. Acetylsalicylic acid is the active reagent of aspirin. Glucose is the major energy source in our body.

On the left side of the working window, a toolbar contains all the tools that are handy for drawing those molecules, such as single bonds, double bonds, benzene, texting and eraser.

# Find an empty place and draw the first bond by dragging the icon of a bond from the toolbar to that place and loose your mouse.
# Move the mouse to the end of that bond where you want to start another bond or a word (for example, "H" is for proton or hydrogen. "C" is for carbon and "O" is for oxygen).
# After drawing the molecule, use the “lasso” from the toolbar to select the whole molecule, and then go to the menu and select “convert structure to name”. Find out if you do the right thing by comparing the name that the computer tells you with the name you are supposed to draw.

[[Category:Maxey Demos]]

Computer station

2016-05-23T15:52:38Z

Eriekeberg: /* Preparation */

At the computer station, students will graph the data points they collected from the Spec20 station and draw three molecular structures. The handout to be given to students is available here: [[File:Maxey_-_Computer_Station_Handout.docx]].

== Preparation ==

''This should be ready the day before)''

* Six to eight laptops should be provided and they are all set in a classroom in the Maxey elementary school.
*Laptops can be checked out from the 501 building; they are general use student laptops. E-mail Wade Felker (wfelker2@unl.edu), a week in advance to reserve as many laptops as you need.
* If the laptops don't give you admin access to install software: (Set up an account for Maxey demo for each laptop.)
* Install ChemBioDraw and KaleidaGraph software on each laptop. (We have licenses for both pieces of software; ask Eli.)
* Set up wireless printer/router for each laptop. (You can also set them up as a wired system if all else fails)

== Experiment A - KaleidaGraph ==

KaleidaGraph is used for processing the Spec20 Data. ''(Make sure the students finish the Spec20 experiment before they come to this station.)''

# Click the first white box in the toolbar and you can open an empty spreadsheet with three columns.
# Input the data of concentration and absorbance in column A and B. (Do not input the percentage symbol or the unknown sample absorbance.)
# Go to “Gallery" from the menu, click “linear” then “scattering”, then there is a window popping up. Choose the A column to be the X-axis, B column to be the y-axis and click “new plot” icon down below.
# After you have the plot, change the title to be "Absorbance vs. concentration"
# Go to “file” and click “print graphics”.

== Experiment B - ChemDraw ==

Three molecules will be drawn by using ChemBioDraw: Acetic acid is the main component of vinegar. Acetylsalicylic acid is the active reagent of aspirin. Glucose is the major energy source in our body.

On the left side of the working window, a toolbar contains all the tools that are handy for drawing those molecules, such as single bonds, double bonds, benzene, texting and eraser.

# Find an empty place and draw the first bond by dragging the icon of a bond from the toolbar to that place and loose your mouse.
# Move the mouse to the end of that bond where you want to start another bond or a word (for example, "H" is for proton or hydrogen. "C" is for carbon and "O" is for oxygen).
# After drawing the molecule, use the “lasso” from the toolbar to select the whole molecule, and then go to the menu and select “convert structure to name”. Find out if you do the right thing by comparing the name that the computer tells you with the name you are supposed to draw.

[[Category:Maxey Demos]]

Access Gambrinus

2016-04-13T15:36:15Z

Eriekeberg: Created page with "In order to access Gambrinus from your computer, open the file explorer. Then, right click on Computer in the left-hand sidebar. Click on add a network location, and keep hitt..."

In order to access Gambrinus from your computer, open the file explorer.
Then, right click on Computer in the left-hand sidebar. Click on add a network location, and keep hitting next until you reach a textbox.

Type in your access credentials, which are "ftp://rpowers@gambrinus.unl.edu/".

See the network administrator if you have any problems.

Remote Access

2016-02-12T20:49:31Z

Eriekeberg:

There are a number of options available to access computing resources for the group.

On-Campus:
Cluster Access
-Your personal workstation is given a name such as "Bionmr-##". Occasionally, you will need more computing power than is available on your workstation.
You can access the cluster (denoted "Bionmr" without any numbers) using the SSH utility on linux or an SSH client for Windows (such as PUTTY).
Ask the system administrator for details.

Off-Campus:
NOTE: The university is working to make connections to on-campus resources more secure. If you are unable to connect, you may need to download and install the University VPN client [http://its.unl.edu/vpn]
Try connecting to the vpn client first, and then reattempt your connection.

Access to the cluster is only available through SSH or SSH clients.

If you want to be able to connect to your personal workstation remotely, you can do so with any client you want to use. Ask for recommendations.
BEWARE: Many remote desktop clients are shut off upon reboot. If your computer restarts to apply updates, you won't be able to connect until you open the client again on the host machine.

[[Category:Sysadmin]]

Remote Access

2016-02-12T20:48:40Z

Eriekeberg: Created page with "There are a number of options available to access computing resources for the group. On-Campus: Cluster Access -Your personal workstation is given a name such as "Bionmr-##"...."

Mvapack stats

2015-08-21T20:17:13Z

Eriekeberg: Created page with "To obtain stats on the number of registered users and downloads by these users of MVAPACK, perform the following: On the cluster, go to /home/bworley/research/mvapack/misc/do..."

To obtain stats on the number of registered users and downloads by these users of MVAPACK, perform the following:

On the cluster, go to /home/bworley/research/mvapack/misc/downloads.

Within this folder, execute the pull.sh script. (./pull.sh)

This will display the following text:
Users to date: xxx
Downloads to date: xxx

NOTE: Some users are registered multiple times, and some users have multiple downloads.

[[Category:Sysadmin]]

Installing workstations

2015-08-17T21:54:55Z

Eriekeberg: /* Brother printer drivers */

Workstations in the group are 64-bit (a.k.a. ''x86_64'' or ''amd64'') machines set up to run both Windows 7 and Debian Linux. When you came into the group, odds are a preconfigured workstation was placed in front of you, ready to rock. But how was it configured, you ask? Read on...

'''FIRST''', I recommend that you read this like a book, a manual of steps that you will follow in linear order. Failure to do so will make things difficult, if not impossible.

'''Second''', please understand that this process never goes the same way on any two workstations. I can't prepare you for every tiny little problem you may run into, but only set the most important, critical steps before you as a skeletal framework. Good luck, starfighter.

= Beginning =
It should be fairly obvious that you'll need an assembled PC to work with. Not so obvious is the software you'll need:

* Windows 7 x64
* Debian 7 x86_64

Other than operating system discs, you'll need the following Windows software discs:

* Microsoft Office 2010 32-bit
* CorelDRAW Graphics Suite X4
* EndNote X4 Media - Windows (These have machine-specific license keys!)

Finally, you'll need the administrator flash drive. You know the drive of which I speak. Keep it secret. Keep it safe.

= Windows =
This section details installing the Windows 7 OS and software.

== OS ==
Place the Windows 7 DVD into the drive and reboot the system. This will require the BIOS to be configured to boot optical discs before the hard drive. Once the prompt comes up, choose 'Install now'. Accept the license agreement and choose 'Custom' on the next screen.

You should now arrive at a screen that shows the [[:Wikipedia:Disk_partitioning|current partition state]] of the drive. First, click on 'Drive options (advanced)'. If partitions exist, delete them by selecting the partition in the list and then clicking 'Delete'. Now, click 'New' and enter a partition size (in MB) that equals about half the total drive space. It doesn't have to be exact; the partitioner will round to the nearest sector anyways. The installer will give you some garbage about creating extra special partitions for Windows system files, and that's fine. Once the Windows partition was made, proceed.

All the other options (time zone, language, etc.) will be self-explanatory. For automatic updates, choose 'Use recommended settings'. The installer will at some point ask for a user account and password; make this your cluster username and password, or the cluster username and password of whoever will use the system most.

== Updates ==
Once you've logged into your account, don't think that Windows is installed. It will need at least two hours of babysitting while it installs the largest pile of updates you've ever witnessed. You will repeat the following process until no more updates exist:

# Click on the Windows icon (for old-timers, that's the 'Start' button)
# Click on 'Control Panel'
# Click on 'System and Security'
# Click on 'Check for Updates' under the 'Windows Update' heading
# Click on 'Check for Updates' in the left-hand pane
# Install all available updates
# Restart the computer after updates install
# Go back to Step 1.

Patience, grasshopper.

== Configuration ==
You will have to configure a few things in Windows.

=== Power management ===
In ''Control Panel => System and Security => Power Options'', select '''High performance''' from the list. You may have to click 'Show additional plans' to see this option.

=== Remote desktop access ===
In ''Control Panel => System and Security => System'', select ''Remote settings'' in the left-hand pane. Under 'Remote Desktop', select ''Allow connections only from computers running Remote Desktop with Network Level Authentication (more secure)''.

== Software ==
Typical members of this group need a plentiful plethora of packages installed onto their Windows systems in order to function as researchers. Here's what you'll need to install:

* Google Chrome
* Anti-virus
* Adobe Reader
* Microsoft Office
* EndNote X4
* CorelDRAW X4
* ACD/NMR 12
* Java
* NMRViewJ
* PuTTY
* HP LaserJet drivers
* Dell Color Laser drivers

=== Chrome ===
Open Internet Explorer. Click the Stop button about a billion times until IE actually stops loading the page. Navigate to [http://www.google.com Google]. Take Google up on its recommendation to download Chrome. The rest is cake.

=== Anti-virus ===
Open Chrome and navigate to [http://is.unl.edu is.unl.edu]. Under 'Quick Picks', click on 'Anti-virus'. Click on 'DOWNLOAD HERE'. Click on 'WINDOWS 64bit Version'. The rest is cake.

=== Adobe Reader ===
Open Chrome and navigate to [http://get.adobe.com/reader get.adobe.com/reader]. The rest is cake.

=== Microsoft Office ===
Insert the Office DVD and select 'Run autorun.exe' when the popup comes up. The rest is cake.

=== EndNote X4 ===
Make sure any Microsoft Office programs are ''closed''. Insert the EndNote X4 CD and select 'Run autorun.exe' when the popup comes up. The rest is cake. Now, restart Windows and log back in. Then, open Microsoft Word. Click on 'EndNote X4' in the top bar. Then click on 'Go to EndNote'. If you get the message, ''Invalid Class String'', then go [http://help.thomson.com/default.asp?portalid=tsc&refid=TS_ENCWYWFAQ13 here] to find the solution.

=== CorelDRAW X4 ===
Insert the CorelDRAW DVD and follow the steps. The rest is cake.

=== ACD/NMR 12 ===
ACD Labs offers a free version of their 1D and 2D NMR processor software for academics. Open Chrome and navigate to [http://www.acdlabs.com/resources/freeware/nmr_proc/index.php this address], then click 'Download'. You'll need to set up a user account to download the software. Once you've got the installer downloaded, just run it and follow the steps. Yep, the rest is cake.

Alternatively, you should be able to run '''nmrproc_academia12.exe''' from '''Z:\bworley\admin\software''' without having to download anything or make any accounts.

=== Java ===
Open Chrome and navigate to [http://www.java.com/en/download/index.jsp this address]. Click on 'Free Java Download' and follow the steps. Cake.

=== NMRViewJ ===
This software is now non-free, but we have the last/latest available free version on the cluster. Run '''nvjinstall8_0_3.exe''' in '''Z:\bworley\admin\software\nmrviewj''' and follow the steps. Cake.

=== PuTTY ===
Best for last! Open Chrome and navigate to [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html this address]. Click on '''putty-0.62-installer.exe''' to download the installer. Run the installer; all the default options are fine.

Once PuTTY is installed, you'll need to insert the administrator flash drive. In the flash drive, go to '''ssh-rsa\clients\myusername''', where ''myusername'' is the cluster username that you're setting the computer up for. In that directory, there is an '''id_rsa.ppk''' file. Copy that file somewhere that only the current user has read access to, such as '''C:\Users\myusername'''. Now, open PuTTY and type ''myusername@bionmr-c1.unl.edu'' into both the 'Host Name' and 'Saved Sessions' text boxes. In the left-hand pane, click the plus sign next to 'SSH' and click on 'Auth'. Click 'Browse' and open the '''id_rsa.ppk''' file in the location you copied it to. Finally, click back to 'Session' in the left-hand pane and click 'Save' under 'Saved Sessions'.

You're ready to rock. Return the administrator flash drive to its sacred resting place.

=== Brother printer drivers ===
The Brother printer driver CDs are available in the lab office. Use those CDs to install drivers (only drivers, no software suites) for the two Brother printers outside the office. The IP addresses of the printers will be requested by the installer software; you can get those addresses by printing off the ''printer status'' information from each printer via their front panel buttons.
NOTE: If you try to discover the printers over the network and none are found, try temporarily disabling your firewalls. After the printer is installed, you should be able to bring the firewall back up without affecting the printer.

= Linux =
This section details installing and configuring the Linux OS.

== OS ==
Insert the Debian DVD and reboot the computer. When the Debian boot prompt comes up, press the Tab key, type '''desktop=xfce''', and hit enter. Most of the options will be self-explanatory until you get to the partitioning. You will select ''Use custom layout'' and click next.

The partitioning of linux systems in the group is done as follows:

* 128 MB of ext2 mounted on /boot (made at the beginning of the free space)
* All remaining space allocated as ext4 and mounted on '''/'''
* 2048 MB of swap (made at the end of the free space)

Make the partitions in the above order. After making the boot partition, subtract 2048 MB from the remaining free space to get the size of the '''/''' partition. Then use the rest of the free space (about 2048 MB, but it will rarely be exact) as swap.

You should now have a partitioning scheme that spans the entire disk that looks something like this:

* '''sda1:''' Windows system files (few hundred MB)
* '''sda2:''' Windows partition (few hundred GB, about half the drive)
* '''sda3:''' Linux boot partition (128 MB)
* '''sda4:''' Extended partition
* '''sda5:''' Linux root partition (few hundred GB, about half the drive)
* '''sda6:''' Linux swap partition (roughly 2048 MB)

Everything else will be much more self-explanatory, and the defaults are A-OK for almost all the other options.

== Configuration ==
You will have to configure the system a bit more to get it talking with the cluster and running properly. Once the system boots up, use '''Ctrl'''+'''Alt'''+'''F1''' to navigate to the terminal and log in as root. Once you're logged in, insert and mount the system administrator flash drive, like so:

mkdir /mnt/flash
mount /dev/sdb1 /mnt/flash

Where the above example assumes that ''/dev/sdb1'' is the flash drive device node. Once mounted, run the following commands:

cd /mnt/flash/admin-scripts/linux/workstations
./run

The script will ask if you're ready to proceed. As long as everything above went OK, it's safe to say 'yes' here. Hopefully, the script will complete without errors and your linux workstation will be properly configured. Unmount the flash drive:

cd
umount /mnt/flash
reboot

[[category:Sysadmin]]

Adding user accounts

2015-08-11T20:51:07Z

Eriekeberg:

When new group members join, they'll need access to our file and program server on both Windows and Linux, and a few odds and ends. Here's how to get that done the right way.

'''FIRST:''' Have the user decide on a username and password that they will re-enter continuously during this process. They will be denoted as ''new_username'' and ''new_password'' throughout this set of instructions.

= Linux =
== Setting up basic credentials ==
* Log in '''as root''' to the cluster head node, either ''via'' SSH or at the machine.
* Add the user account:

useradd -g bionmr -m -s /bin/bash ''new_username''

* Add a password to the new account:

passwd ''new_username''

* Add a Samba password to the new account:

smbpasswd -c /etc/samba/smb.conf -a ''new_username''

* Add an Apache password to the new account:

htpasswd /etc/apache2/htpasswd ''new_username''

* Allow the user to log in ''via'' secure shell:

sed -e 's,^$AllowUsers$,\1 ''new_username'',' -i /etc/ssh/sshd_config

* Add a couple lines to the bash config:

echo 'source /opt/bashrc' >> /home/''new_username''/.bashrc
echo 'source /opt/bashrc' >> /home/''new_username''/.bash_profile

* Now create a secure shell asymmetric key pair for the user:

su -l ''new_username''
ssh-keygen -t rsa -b 4096
exit

(Use the default file in which to save the key)

== Archiving the credentials ==
* Log in '''as root''' to the cluster head node, either ''via'' SSH or at the machine.
* Physically plug the sysadmin flash drive into the cluster head node.
* Mount the sysadmin flash drive:

mount /dev/sdc1 /mnt/flash

* Navigate into the flash drive:

cd /mnt/flash/admin-tools/linux/workstations

* Add the user into the sub-scripts:

echo ''new_username'' >> bashrc/users.lst
echo ''new_username'' >> passwd/users.lst

* Copy the passwd/shadow information:

grep ^''new_username'' /etc/passwd >> passwd/etc_passwd
grep ^''new_username'' /etc/shadow >> passwd/etc_shadow

* Copy the secure shell key pair:

mkdir ssh-rsa/clients/''new_username''_bionmr
cp /home/''new_username''/.ssh/id_rsa* ssh-rsa/clients/''new_username''_bionmr/

* Unmount the sysadmin flash drive:

cd
umount /mnt/flash

= Windows =
== Creating the account ==
* Log in to the user's workstation on an existing account, and use the Control Panel to create a new '''Administrator account'''.
* Add a password to the newly created account. Make sure the user can remember their password.
* Log out and back into the new account.

== Setting up the network drive ==
* Open Windows Explorer (''not'' Internet Explorer) and click on '''Computer'''
* Click on '''Map Network Drive'''
* Type ''\\bionmr\DATA'' into the '''Folder:''' entry
* Click on '''Finish'''

== Setting up the PuTTY key ==
Using PuTTY to log into the secure linux shell from a Windows workstation requires a PuTTY-format private key (''*.PPK'') to be made. If the key has been made already and saved to the sysadmin flash drive, then you can skip the generation step. If not, proceed in order.

=== Creating the PuTTY key for the first time ===
* Insert the sysadmin flash drive into the user's computer, in Windows
* '''DO NOT CLEAN OR REPAIR OR FIX OR FORMAT THE FLASH DRIVE'''
* Open then PuTTYgen program and click on '''Conversions''', then '''Import key'''
* Open the following file from the flash drive:

admin-tools/linux/workstations/ssh-rsa/clients/''new_username''_bionmr/id_rsa

* Type the user's password to unlock the key file
* Click on '''Save private key''' and save to the following file:

admin-tools/linux/workstations/ssh-rsa/clients/''new_username''_bionmr/id_rsa.ppk

* All done here!

=== Installing the PuTTY key ===
* Insert the sysadmin flash drive into the user's computer, in Windows
* '''DO NOT CLEAN OR REPAIR OR FIX OR FORMAT THE FLASH DRIVE'''
* Copy the following file from the flash drive:

admin-tools/linux/workstations/ssh-rsa/clients/''new_username''_bionmr/id_rsa.ppk

* ... and save it to:

C:\Users\''new_username''\

* Open PuTTY and type''new_username''@bionmr.unl.edu in the '''Host Name''' entry
* Type ''new_username''@bionmr.unl.edu inthe '''Saved Sessions''' entry
* In the left pane, expand '''SSH''' and click on '''Auth'''
* Click '''Browse...''' and open the PuTTY private key you just copied from the flash drive
* In the left pane, click on '''Session'''
* Click on '''Save''' to save the session information
* All done here!

=Wiki=
== Adding New Users ==
*New Users can be added using the administrator account "wiki administrator". The SysAdmin has the password.
*There will an "add new user" button at the top of the page.

[[Category:Sysadmin]]

Media preparation

2015-07-15T14:23:07Z

Eriekeberg: Formatting Only

[[Category:Protocols]]
[[Category:Protein expression]]
===1. General Protocols For Minimal Media Protein Expression===

Preparing M9 minimal media begins with preparing a 5x stock solution of M9 salts. Generally, M9 salts contain a nitrogen source in the form of NH4Cl. Since we want to add a labeled nitrogen source, our 5x salts are prepared minus NH4Cl. Standard 5 X M9 Minimal Media salts minus nitrogen source for 1L 5xM9 salts:

64 g Na2HPO4-7H2O

15 g KH2PO4

2.5 g NaCl

H2O to final 1L volume and autoclave
To prepare 500 mL M9 minimal media:

100mL of 5xM9 salts:

1 mL 1 M MgSO4

50 uL 1 M CaCl2

5 mL 100x Basal Medium Eagle Vitamin Solution (Gibco)

2.5 mL filter sterilized NH4Cl (0.2 g/mL) or 0.5 g dry 10 mL 20% d-glucose or 2 g dry

Glass distilled & autoclaved H2O to final volume of 500 mL pH solution to 7.3 and filter sterilize (0.2 um filter).

Introduce media to a pre-autoclaved, wide-bottom (baffled) 2 L flask and add ampicillin to a final concentration of 70-100 ug/mL (or any antibiotics used to select the strains).

Grow 5mL overnight culture in same media to inoculate 500mL M9.
Shake culture at 37 oC until an OD600 of 0.7
± 0.2 then induce protein expression with the addition of IPTG (0.01-0.1 mM final concentration).

===2. General Protocols For LB Media===

For 1 L media preparation

10 g Bacto-tryptone

5 g yeast extract

10 g NaCl

Sterilized by autoclave

Add any antibiotics used to select the strains properly after the medium temperature is blew 37 oC.

===3. General Protocols For High-Cell-Density Media===

For 1 L media preparation

50 mM Na2HPO4.7H2O

25 mM KH2PO4 (pH 8.0-8.2)

10 mM NaCl

5 mM MgSO4

0.2 mM CaCl2

0.1% NH4Cl or 15NH4Cl

1.0% Glucose or 13C-Glucose

To prepare the media, glucose and metal solution are filtered to sterilize. The salt solution is autoclaved and the cooled solution is added by metal solution and glucose.