1. The lab’s computers are all custom builds, designed for a particular role. The different roles determine the best way to use each machine. The roles are:

a) single-user machines in B1-282, one for each grad student and postdoc
b) shared machine in B1-282, for undergrads, single license software, and the lab database
c) shared machine in B1-285, for undergrads, single license software, and using the high-power microscope and NanoZ
d) shared experimental equipment machines: for recording in PAS 1272 and 1278

One of these will be exclusively yours to use during your tenure in the lab. You are free to install software and change settings to suit your needs as long as any changes (1) do not interfere with the machine’s ability to support research, and (2) fall within the uWaterloo guidelines.

Single user machines have a boot drive (C:\) for the operating system and frequently used software. This is a fast SSD drive with limited space, so be mindful of what you install here. Absolutely do not use this drive for any documents or data.

Save your work and data files on the data drive (D:\), because this is automatically backed up using RAID (i.e. there are actually two ‘mirrored’ hard disks which behave as one virtual disk). Run RaidXpert’s check utility periodically to ensure the health of the RAID array.

Unlike the single user machines, when using the shared machine you will need to consider how your actions affect other users. A few guidelines:

• If need to save your work, create a folder with your name on the Data drive. Do not leave work or data files on the desktop. If you find anything that’s not supposed to be there on the desktop or anywhere else, put it in the lost-and-found folder on the desktop.
• Do not install any software, or change any software and system settings, without discussing with MvdM first. Do not delete any files, but place them in lost-and-found instead.
• If you log in to web services, make sure you log out when you are done.
• A quirk of this machine: the RAID array that hosts the lab database can be powered on or off using the green buttons on the drive cage. If it is turned on when the machine (re)boots, it will try to boot from the RAID array and fail. It needs to be turned off to boot successfully.

The above considerations for shared machines apply. In addition:

• If you acquire data for your project, use correct renaming and backup procedure when you finish your acquisition session. This is absolutely essential: data is expensive, and you individually and the lab as a whole cannot afford to lose any of it, EVER. Do not leave data in the acquisition folder.
• If you encounter a potential data file or folder that is not yours and seems lost, make an effort to find out whose data it might be.
• NEVER delete anything that looks like it might be data, unless you are absolutely certain that it has been backed up correctly. If you want to clean up, don't delete it but place in a folder named “lost-and-found”

2. All machines, even the single-use ones, use the mvdmlab account. This is because of MATLAB licensing.

3. Machines are distributed across physically different locations. To facilitate communication and data sharing, we maintain a list with machine names, MAC and IP addresses, and the network port they are plugged in to. Remember to update this if anything changes.

To move data between machines, we use freeSSHd, Dropbox, and WinVNC.

The lab database (on mvdmlab-apollo) can be accessed using a SSH client such as WinSCP (129.97.62.97; \\mvdmlab-apollo sometimes also works). There is a specific RAID array (F:\) for the database, which can be accessed through a symbolic link placed in C:\. The 2nd lab database (on mvdmlab-nas) can be accessed using a SSH client such as WinSCP (129.97.62.84; in case the first one is full).

Sometimes the freeSSHd server fails; it will need to be restarted manually on mvdmlab-apollo from the Start menu or with a reboot.

I highly recommend installing WinVNC on your machine; if it is not yet installed, go ahead and purchase it ($30 I believe for the Personal Edition); complete a reimbursement form to get this back from the lab.

The lab also has a Dropbox account (mvdmlab@gmail.com, see below) for the sharing of protocols, weight sheets, et cetera; if there is a problem with the SSH server this can be used for emergency data backup. Log in to this account on dropbox.com and share the Protocols folder with your own Dropbox account.

4. Web services accounts

• gmail: mvdmlab@gmail.com
• dropbox: mvdmlab@gmail.com
• skype: vandermeerlab (for contacting suppliers and other lab-related business)

5. The main lab printer is in B1-282, it’s a HP 2025dn color laser with duplex (two-sides) printing. Win7 drivers are here; make sure you enable duplex printing by default. Its IP is currently 172.17.10.7 (a special subnet that can only be accessed from campus).

Please be considerate when using the printer. Keeping an electronic library of PDFs using an iPad, Dropbox and iAnnotate is a worthwhile investment that will make it much easier to find papers and your comments in the future, and will save a LOT of paper! Don't print in color unless you need to, and print papers using multiple pages per sheet.

The recording computers both have local printers attached for obtaining protocols and weight sheets.

6. If you see Windows updates to install on any machine, go ahead and install them. If a computer needs rebooting because of updates and you can do so safely, go ahead.

7. Use of University computers (which includes all lab computers) is governed by the Guidelines on Use of Waterloo Computing and Network Resources. These are generally common sense, and not overly long so have a look.

→ e-mail MvdM with the subject “computing” and body: “I have read and agree to the Guidelines on the use of Waterloo Computing and Network Resources.”

Once you collect experimental data of any kind (behavior, electrophysiology, electrode imaging) it is critical that you ensure its safety. There are three steps to this process: renaming, backup, and safe removal.

Renaming:

Each electrophysiology recording session gets its own folder. When acquisition is complete, rename this folder using the following format:

RXXX-YYYY-MM-DD where XXX is the rat’s number, followed by the date in year, month, day order.

If for some reason you collect multiple data sets from the same animal on a given day (if at all possible you want to avoid this) you can use the RXXX-YYYY-MM-DD_modifier format.

This consistent format will make later (meta)analysis a lot easier.

Backup:

First, make sure that any files used to collect the data (e.g. Neuralynx .cfg file, MATLAB control script, et cetera) are copied into the data folder. If applicable, delete files you don’t need and compress the video files.

When your data folder has been renamed, copy it to the Incoming folder on the database using WinSCP. If you have your own machine, also copy it there (you will need it for analysis later).

The renaming and backup steps are an integral part of the data collection process! No experimental session is complete without these steps; do not leave these until later.

Safe removal:

Safe removal rule: only delete data from the recording machine if copies exist in TWO different locations!

It is often useful to leave a few days of data on the experimental machines; this is OK as long as plenty of space remains for new data acquisition. As you copy data to the database, check to see if any data can be safely removed (i.e. obeying the rule above).

Lab code repository:

https://github.com/mvdm/vandermeerlab

Software:

Most digital productivity in the lab is accomplished by these software packages:

• Data processing, analysis: MATLAB (with MClust)
• 3D parts design: SolidWorks
• Document generation: LaTeX (with your favorite editor: e.g. LyX, emacs, SublimeText)
• Reference management: Mendeley and/or JabRef
• Graphics (figures, posters): Adobe Creative Suite (Photoshop, Illustrator, InDesign)

Setting up MATLAB

SolidWorks:

LaTeX:

Mendeley and JabRef:

Adobe:

uWaterloo resources:

Computer Help & Information Place (CHIP)